This integration test tests repacking a symmetric pose with strong electron density constraints. The ccp4 file was generated with this command phenix.model_vs_data map="2mFo-DFc" and output below. Note the final highest resolution is 1.9A. Frank Dimaio suggests using grid spacing ~45% of the resolution. So the grid spacing should be .85A but for integration test, use the larger grid spacing of 3A to make it faster. This integration test uses 1xu1FH_D.pdb from the make_symmdef_file integration test to conserve space. As a consistency check, the generated symmetry definition file, '../../tests/make_symmdef_file/1xu1FH_D.symm' should match 'inputs/1xu1FH_D.symm' /////// phenix.model_vs_data output //////////// pdb /home/momeara/scr/data/pdb/xu/pdb1xu1.ent sf /home/momeara/scr/data/structure_factors/xu/r1xu1sf.ent begin: /home/momeara/scr/data/pdb/xu/pdb1xu1.ent miller array size: 44519 miller array size: 44519 Unit cell: (59.339, 91.839, 102.268, 90, 90, 90) Space group: P 21 21 21 (No. 19) number of symmetry operations: 4 Number of models: 1 Model #1: Number of residues in alternative conformations: 0 Residue content: element : 1 water : 130 amino_acid : 524 Atoms: content: 4280 Ni count: 1 occupancy sum: 1.00 C count: 2619 occupancy sum: 2616.00 S count: 33 occupancy sum: 33.00 O count: 873 occupancy sum: 873.00 N count: 754 occupancy sum: 751.00 ADP (min,max,mean): all (4280 atoms): 12.3 88.4 30.2 side chains (2053 atoms): 12.5 88.4 33.7 main chains (2096 atoms): 12.3 71.4 26.5 macromolecule (4149 atoms): 12.3 88.4 30.1 ligands (1 atoms): 18.8 18.8 18.8 solvent (130 atoms): 18.6 51.9 33.5 mean bonded (Bi-Bj) : 3.25 occupancies (min,max,mean) : 0.00 1.00 1.00 number_of_anisotropic : 4150 number_of_non_positive_definite : 0 Stereochemistry statistics (mean, max, count) - overall: bonds : 0.0087 0.1008 4254 angles : 1.3139 9.6412 5730 dihedrals : 16.4309 88.0722 1559 chirality : 0.0893 0.3084 628 planarity : 0.0044 0.0233 737 non-bonded (min) : 2.2193 Stereochemistry statistics (mean, max, count) - macromolecule: bonds : 0.0087 0.1008 4254 angles : 1.3139 9.6412 5730 dihedrals : 16.4309 88.0722 1559 chirality : 0.0893 0.3084 628 planarity : 0.0044 0.0233 737 non-bonded (min) : 2.3433 Stereochemistry statistics (mean, max, count) - ligands: bonds : 0.0000 0.0000 0 angles : 0.0000 0.0000 0 dihedrals : 0.0000 0.0000 0 chirality : 0.0000 0.0000 0 planarity : 0.0000 0.0000 0 non-bonded (min) : 0.0000 Stereochemistry statistics - solvent: non-bonded (min) : 2.4925 Molprobity statistics: Ramachandran plot, number of: outliers : 0 (0.00 %) allowed : 10 (1.95 %) favored : 502 (98.05 %) Rotamer outliers : 10 (2.18 %) Cbeta deviations >0.25A : 0 All-atom clashscore : 4.75 (steric overlaps >0.4A per 1000 atoms) Data: data_label : r1xu1sf,_refln.F_meas_au,_refln.F_meas_sigma_au high_resolution : 1.90 low_resolution : 35.69 completeness_in_range : 1.00 completeness(d_min-inf) : 1.00 completeness(6A-inf) : 0.91 wilson_b : 24.2 number_of_reflections : 44515 number_of_reflections(non-anomalous) : 44515 test_set_size : 0.0999 test_flag_value : 0 number_of_Fobs_outliers : 4 twinned : False anomalous_flag : False Model_vs_Data: r_work(re-computed) : 0.1803 r_free(re-computed) : 0.2102 bulk_solvent_(k_sol,b_sol) : 0.40 60.00 overall_anisotropic_scale_(b_cart) : 1.20 -1.24 0.04 -0.00 0.00 0.00 solvent_content_estimated_via_mask : 43.9 % mFo-DFc map: positive and negative peak numbers: > 3 sigma: 507 > 6 sigma: 7 > 9 sigma: 1 < -3 sigma: 264 < -6 sigma: 5 < -9 sigma: 0 Information extracted from PDB file header: program_name : REFMAC year : 4 r_work : 0.167 r_free : 0.203 high_resolution : 1.9 low_resolution : 30.0 sigma_cutoff : 0.0 matthews_coeff : 2.1 solvent_cont : 40.0 % TLS : True (number of groups: 6) After applying resolution and sigma cutoffs: n_refl_cutoff : 44514 r_work_cutoff : 0.1803 r_free_cutoff : 0.2102 Statistics in resolution bins: SIGMAA vs Resolution: resolution(A) sigmaa 35.811 0.941 8.173 0.941 5.698 0.944 4.544 0.957 3.855 0.958 3.391 0.945 3.057 0.946 2.805 0.941 2.609 0.940 2.453 0.942 2.328 0.943 2.225 0.947 2.142 0.938 2.074 0.954 2.020 0.954 1.976 0.951 1.943 0.951 1.918 0.945 1.903 0.945 1.895 0.947 Bin Resolution Range Compl. Nwork Rwork Scale 1 35.6974 - 8.1589 0.72 465 0.2277 0.9965 546.198 2 8.1589 - 6.4886 0.92 548 0.2185 0.9684 492.555 3 6.4886 - 5.6721 0.87 517 0.2263 0.9307 498.759 4 5.6721 - 5.1552 0.89 515 0.2008 0.9648 562.053 5 5.1552 - 4.7866 0.91 528 0.1709 0.9888 676.739 6 4.7866 - 4.5050 0.88 517 0.1657 1.0169 682.474 7 4.5050 - 4.2798 0.90 501 0.1461 1.0277 705.744 8 4.2798 - 4.0937 0.89 517 0.1667 1.0406 653.365 9 4.0937 - 3.9363 0.87 479 0.1683 1.0010 588.191 10 3.9363 - 3.8007 0.87 513 0.1754 1.0240 582.195 11 3.8007 - 3.6820 0.98 552 0.1825 1.0216 526.675 12 3.6820 - 3.5768 0.85 479 0.1628 1.0171 512.757 13 3.5768 - 3.4827 0.84 469 0.1691 1.0123 503.798 14 3.4827 - 3.3978 1.00 567 0.1691 1.0210 449.483 15 3.3978 - 3.3206 0.84 474 0.1735 1.0099 435.406 16 3.3206 - 3.2500 1.00 575 0.1881 1.0056 393.467 17 3.2500 - 3.1850 0.79 432 0.1769 1.0270 382.777 18 3.1850 - 3.1250 1.00 542 0.1817 0.9908 370.553 19 3.1250 - 3.0692 0.75 443 0.1820 0.9813 340.370 20 3.0692 - 3.0172 1.00 559 0.1857 0.9967 321.643 21 3.0172 - 2.9686 0.79 435 0.1825 0.9912 313.964 22 2.9686 - 2.9229 1.00 578 0.2116 0.9860 282.766 23 2.9229 - 2.8799 0.74 391 0.1859 0.9835 271.032 24 2.8799 - 2.8394 1.00 564 0.2154 0.9827 264.009 25 2.8394 - 2.8010 0.84 483 0.2068 0.9817 248.052 26 2.8010 - 2.7647 0.92 517 0.2036 0.9782 235.404 27 2.7647 - 2.7301 1.00 548 0.2050 0.9663 229.476 28 2.7301 - 2.6972 0.72 390 0.1940 0.9805 233.086 29 2.6972 - 2.6659 1.00 573 0.2075 0.9693 224.233 30 2.6659 - 2.6359 0.99 548 0.1852 0.9670 218.167 31 2.6359 - 2.6073 0.72 411 0.1845 0.9683 222.158 32 2.6073 - 2.5799 1.00 549 0.1893 0.9599 203.006 33 2.5799 - 2.5535 0.94 534 0.1908 0.9568 202.213 34 2.5535 - 2.5283 0.76 430 0.1954 0.9629 201.080 35 2.5283 - 2.5040 1.00 542 0.1978 0.9727 191.269 36 2.5040 - 2.4806 0.97 529 0.1927 0.9549 186.399 37 2.4806 - 2.4580 0.69 384 0.1930 0.9589 182.424 38 2.4580 - 2.4363 1.00 570 0.1904 0.9700 178.681 39 2.4363 - 2.4153 1.00 523 0.1623 1.0101 190.959 40 2.4153 - 2.3950 0.65 383 0.1598 0.9729 182.452 41 2.3950 - 2.3754 1.00 529 0.1758 0.9877 181.926 42 2.3754 - 2.3564 1.00 574 0.1902 0.9921 176.247 43 2.3564 - 2.3380 0.78 418 0.1837 0.9977 175.455 44 2.3380 - 2.3201 0.86 487 0.1773 1.0039 175.217 45 2.3201 - 2.3028 1.00 546 0.1745 1.0064 167.929 46 2.3028 - 2.2860 1.00 549 0.1710 1.0125 167.244 47 2.2860 - 2.2697 0.65 349 0.1742 1.0011 159.205 48 2.2697 - 2.2538 1.00 592 0.1636 1.0208 171.048 49 2.2538 - 2.2384 1.00 540 0.1722 1.0294 164.322 50 2.2384 - 2.2234 0.99 545 0.1819 1.0308 158.630 51 2.2234 - 2.2087 0.60 328 0.1605 1.0151 160.867 52 2.2087 - 2.1945 1.00 544 0.1821 0.9967 143.500 53 2.1945 - 2.1806 1.00 559 0.1618 1.0148 155.727 54 2.1806 - 2.1671 0.99 560 0.1644 1.0273 149.309 55 2.1671 - 2.1538 0.59 327 0.1606 1.0109 157.832 56 2.1538 - 2.1410 1.00 530 0.1724 0.9952 140.134 57 2.1410 - 2.1284 1.00 580 0.1718 1.0387 142.970 58 2.1284 - 2.1161 1.00 519 0.1820 1.0275 133.995 59 2.1161 - 2.1040 0.62 361 0.1498 1.0208 142.911 60 2.1040 - 2.0923 0.94 518 0.1641 1.0026 127.932 61 2.0923 - 2.0808 1.00 535 0.1517 1.0163 132.766 62 2.0808 - 2.0696 1.00 557 0.1606 1.0615 136.788 63 2.0696 - 2.0585 0.91 488 0.1565 1.0288 139.390 64 2.0585 - 2.0478 0.62 345 0.1683 1.0079 124.714 65 2.0478 - 2.0372 1.00 556 0.1563 1.0192 123.833 66 2.0372 - 2.0269 1.00 533 0.1526 1.0235 125.338 67 2.0269 - 2.0167 1.00 576 0.1594 1.0153 123.371 68 2.0167 - 2.0068 0.96 533 0.1590 1.0201 120.441 69 2.0068 - 1.9971 0.90 461 0.1653 1.0107 116.735 70 1.9971 - 1.9875 0.90 506 0.1560 1.0107 116.930 71 1.9875 - 1.9781 0.90 510 0.1495 0.9930 115.429 72 1.9781 - 1.9689 0.88 467 0.1587 1.0007 107.108 73 1.9689 - 1.9599 0.91 522 0.1605 0.9992 103.532 74 1.9599 - 1.9510 0.91 493 0.1600 1.0016 98.184 75 1.9510 - 1.9423 0.90 513 0.1692 0.9913 96.951 76 1.9423 - 1.9338 0.89 468 0.1728 0.9686 96.263 77 1.9338 - 1.9254 0.91 504 0.1705 0.9933 97.129 78 1.9254 - 1.9171 0.91 477 0.1645 0.9803 95.672 79 1.9171 - 1.9090 0.90 502 0.1703 0.9552 89.589 80 1.9090 - 1.9010 0.87 491 0.1910 0.9226 83.575 done: /home/momeara/scr/data/pdb/xu/pdb1xu1.ent