Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 23:15:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mvy_24058/04_2023/7mvy_24058.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mvy_24058/04_2023/7mvy_24058.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mvy_24058/04_2023/7mvy_24058.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mvy_24058/04_2023/7mvy_24058.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mvy_24058/04_2023/7mvy_24058.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mvy_24058/04_2023/7mvy_24058.pdb" } resolution = 2.39 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 56 5.16 5 C 8464 2.51 5 N 2276 2.21 5 O 2422 1.98 5 H 13337 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 1247": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1308": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1417": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1432": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 291": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 26555 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 25701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1641, 25701 Classifications: {'peptide': 1641} Link IDs: {'PCIS': 1, 'PTRANS': 69, 'TRANS': 1570} Chain breaks: 14 Chain: "B" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 854 Classifications: {'peptide': 53} Link IDs: {'TRANS': 52} Time building chain proxies: 11.14, per 1000 atoms: 0.42 Number of scatterers: 26555 At special positions: 0 Unit cell: (79.704, 109.836, 186.624, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 O 2422 8.00 N 2276 7.00 C 8464 6.00 H 13337 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 21.03 Conformation dependent library (CDL) restraints added in 2.3 seconds 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3236 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 1 sheets defined 76.1% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 12 through 19 Processing helix chain 'A' and resid 25 through 36 Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 43 through 52 Processing helix chain 'A' and resid 52 through 61 Processing helix chain 'A' and resid 61 through 66 removed outlier: 3.855A pdb=" N VAL A 65 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE A 66 " --> pdb=" O PRO A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 66' Processing helix chain 'A' and resid 71 through 80 Processing helix chain 'A' and resid 89 through 103 Processing helix chain 'A' and resid 106 through 120 Processing helix chain 'A' and resid 120 through 127 Processing helix chain 'A' and resid 131 through 142 Processing helix chain 'A' and resid 163 through 172 Processing helix chain 'A' and resid 173 through 205 Processing helix chain 'A' and resid 211 through 226 Processing helix chain 'A' and resid 237 through 242 Processing helix chain 'A' and resid 242 through 260 removed outlier: 4.131A pdb=" N THR A 246 " --> pdb=" O THR A 242 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR A 247 " --> pdb=" O MET A 243 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU A 252 " --> pdb=" O MET A 248 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP A 253 " --> pdb=" O ASN A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 299 Processing helix chain 'A' and resid 306 through 321 removed outlier: 3.765A pdb=" N GLU A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 332 through 352 Proline residue: A 338 - end of helix Processing helix chain 'A' and resid 352 through 363 Processing helix chain 'A' and resid 371 through 374 Processing helix chain 'A' and resid 375 through 393 removed outlier: 3.530A pdb=" N GLY A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 419 removed outlier: 4.792A pdb=" N VAL A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 471 removed outlier: 4.011A pdb=" N PHE A 467 " --> pdb=" O PRO A 463 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN A 471 " --> pdb=" O PHE A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 489 Processing helix chain 'A' and resid 491 through 504 Processing helix chain 'A' and resid 513 through 531 removed outlier: 4.061A pdb=" N LEU A 522 " --> pdb=" O ALA A 518 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL A 523 " --> pdb=" O ARG A 519 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N PHE A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 550 Processing helix chain 'A' and resid 564 through 577 removed outlier: 3.606A pdb=" N ASN A 568 " --> pdb=" O ALA A 564 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL A 570 " --> pdb=" O SER A 566 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N TYR A 571 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N MET A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LEU A 575 " --> pdb=" O TYR A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 583 Processing helix chain 'A' and resid 584 through 591 Processing helix chain 'A' and resid 595 through 610 removed outlier: 4.073A pdb=" N PHE A 599 " --> pdb=" O GLU A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 617 removed outlier: 3.796A pdb=" N ALA A 617 " --> pdb=" O LYS A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 626 Processing helix chain 'A' and resid 635 through 641 removed outlier: 4.158A pdb=" N ARG A 640 " --> pdb=" O ALA A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 719 Processing helix chain 'A' and resid 731 through 755 removed outlier: 3.602A pdb=" N THR A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 755 " --> pdb=" O LEU A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 771 Processing helix chain 'A' and resid 779 through 792 Processing helix chain 'A' and resid 800 through 821 removed outlier: 4.076A pdb=" N ALA A 819 " --> pdb=" O HIS A 815 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL A 820 " --> pdb=" O ALA A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 830 removed outlier: 3.588A pdb=" N VAL A 825 " --> pdb=" O CYS A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 848 removed outlier: 3.656A pdb=" N ARG A 846 " --> pdb=" O ARG A 843 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A 847 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR A 848 " --> pdb=" O SER A 845 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 843 through 848' Processing helix chain 'A' and resid 854 through 877 removed outlier: 4.686A pdb=" N LEU A 860 " --> pdb=" O GLU A 856 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU A 861 " --> pdb=" O ARG A 857 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER A 863 " --> pdb=" O ASP A 859 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS A 866 " --> pdb=" O SER A 862 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N CYS A 877 " --> pdb=" O ASP A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 926 Processing helix chain 'A' and resid 933 through 957 removed outlier: 4.213A pdb=" N ARG A 937 " --> pdb=" O SER A 933 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 955 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS A 956 " --> pdb=" O VAL A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 964 removed outlier: 3.641A pdb=" N THR A 963 " --> pdb=" O SER A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 979 Processing helix chain 'A' and resid 989 through 1001 Processing helix chain 'A' and resid 1008 through 1035 Processing helix chain 'A' and resid 1042 through 1055 removed outlier: 4.283A pdb=" N HIS A1046 " --> pdb=" O PRO A1042 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN A1049 " --> pdb=" O THR A1045 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A1053 " --> pdb=" O GLN A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1060 Processing helix chain 'A' and resid 1061 through 1063 No H-bonds generated for 'chain 'A' and resid 1061 through 1063' Processing helix chain 'A' and resid 1064 through 1081 Processing helix chain 'A' and resid 1091 through 1097 removed outlier: 3.881A pdb=" N TYR A1095 " --> pdb=" O SER A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1109 Processing helix chain 'A' and resid 1118 through 1134 Processing helix chain 'A' and resid 1137 through 1145 Processing helix chain 'A' and resid 1169 through 1179 removed outlier: 3.816A pdb=" N ALA A1173 " --> pdb=" O SER A1169 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU A1176 " --> pdb=" O ALA A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1203 removed outlier: 3.835A pdb=" N ALA A1191 " --> pdb=" O GLN A1187 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR A1202 " --> pdb=" O SER A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1214 removed outlier: 3.888A pdb=" N ALA A1209 " --> pdb=" O TRP A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1214 through 1228 removed outlier: 3.804A pdb=" N ASP A1218 " --> pdb=" O LYS A1214 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU A1220 " --> pdb=" O VAL A1216 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG A1221 " --> pdb=" O VAL A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1240 through 1266 removed outlier: 3.962A pdb=" N PHE A1244 " --> pdb=" O ALA A1240 " (cutoff:3.500A) Processing helix chain 'A' and resid 1269 through 1277 Processing helix chain 'A' and resid 1280 through 1287 Processing helix chain 'A' and resid 1294 through 1309 removed outlier: 3.674A pdb=" N HIS A1298 " --> pdb=" O ASN A1294 " (cutoff:3.500A) Processing helix chain 'A' and resid 1314 through 1318 removed outlier: 3.575A pdb=" N PHE A1317 " --> pdb=" O VAL A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1334 through 1342 removed outlier: 4.521A pdb=" N GLN A1340 " --> pdb=" O GLU A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1355 through 1391 removed outlier: 4.014A pdb=" N GLU A1359 " --> pdb=" O GLY A1355 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A1389 " --> pdb=" O LEU A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1396 through 1417 removed outlier: 3.504A pdb=" N PHE A1400 " --> pdb=" O GLU A1396 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN A1416 " --> pdb=" O LEU A1412 " (cutoff:3.500A) Processing helix chain 'A' and resid 1432 through 1447 removed outlier: 4.075A pdb=" N ALA A1436 " --> pdb=" O ARG A1432 " (cutoff:3.500A) Processing helix chain 'A' and resid 1452 through 1466 removed outlier: 3.770A pdb=" N LEU A1456 " --> pdb=" O ASP A1452 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ALA A1458 " --> pdb=" O THR A1454 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU A1459 " --> pdb=" O HIS A1455 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL A1460 " --> pdb=" O LEU A1456 " (cutoff:3.500A) Processing helix chain 'A' and resid 1475 through 1495 removed outlier: 3.639A pdb=" N PHE A1479 " --> pdb=" O ASP A1475 " (cutoff:3.500A) Processing helix chain 'A' and resid 1507 through 1517 removed outlier: 4.600A pdb=" N THR A1513 " --> pdb=" O GLN A1509 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ILE A1514 " --> pdb=" O GLN A1510 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A1515 " --> pdb=" O VAL A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1518 through 1531 Processing helix chain 'A' and resid 1544 through 1559 Processing helix chain 'A' and resid 1561 through 1565 Processing helix chain 'A' and resid 1567 through 1577 removed outlier: 4.278A pdb=" N ASN A1573 " --> pdb=" O VAL A1569 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ILE A1574 " --> pdb=" O GLN A1570 " (cutoff:3.500A) Processing helix chain 'A' and resid 1579 through 1589 removed outlier: 4.123A pdb=" N VAL A1583 " --> pdb=" O ASP A1579 " (cutoff:3.500A) Processing helix chain 'A' and resid 1619 through 1632 Processing helix chain 'A' and resid 1634 through 1643 Processing helix chain 'A' and resid 1643 through 1653 removed outlier: 4.292A pdb=" N LEU A1647 " --> pdb=" O CYS A1643 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY A1648 " --> pdb=" O ASP A1644 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N HIS A1649 " --> pdb=" O GLY A1645 " (cutoff:3.500A) Processing helix chain 'A' and resid 1655 through 1661 removed outlier: 3.803A pdb=" N ARG A1661 " --> pdb=" O GLY A1657 " (cutoff:3.500A) Processing helix chain 'A' and resid 1670 through 1683 Processing helix chain 'A' and resid 1683 through 1695 removed outlier: 3.546A pdb=" N ALA A1694 " --> pdb=" O ASN A1690 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A1695 " --> pdb=" O ILE A1691 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1710 Processing helix chain 'A' and resid 1710 through 1721 removed outlier: 4.387A pdb=" N LEU A1714 " --> pdb=" O PHE A1710 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE A1721 " --> pdb=" O SER A1717 " (cutoff:3.500A) Processing helix chain 'A' and resid 1746 through 1766 removed outlier: 3.540A pdb=" N GLU A1750 " --> pdb=" O LEU A1746 " (cutoff:3.500A) Processing helix chain 'A' and resid 1779 through 1789 Processing helix chain 'A' and resid 1794 through 1800 removed outlier: 3.989A pdb=" N ARG A1799 " --> pdb=" O LEU A1796 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A1800 " --> pdb=" O ARG A1797 " (cutoff:3.500A) Processing helix chain 'A' and resid 1834 through 1850 Processing helix chain 'B' and resid 248 through 254 Processing helix chain 'B' and resid 259 through 264 removed outlier: 3.993A pdb=" N MET B 263 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 299 removed outlier: 3.964A pdb=" N GLU B 269 " --> pdb=" O ALA B 265 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP B 276 " --> pdb=" O ALA B 272 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ALA B 277 " --> pdb=" O ARG B 273 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 630 through 632 removed outlier: 3.743A pdb=" N VAL A 632 " --> pdb=" O ALA A 698 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 698 " --> pdb=" O VAL A 632 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A 655 " --> pdb=" O GLU A 643 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU A 643 " --> pdb=" O ARG A 655 " (cutoff:3.500A) 839 hydrogen bonds defined for protein. 2475 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.67 Time building geometry restraints manager: 21.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13313 1.03 - 1.23: 24 1.23 - 1.42: 5554 1.42 - 1.61: 7835 1.61 - 1.81: 88 Bond restraints: 26814 Sorted by residual: bond pdb=" N SER A 531 " pdb=" CA SER A 531 " ideal model delta sigma weight residual 1.456 1.492 -0.035 1.22e-02 6.72e+03 8.35e+00 bond pdb=" N ARG A 530 " pdb=" CA ARG A 530 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.33e-02 5.65e+03 8.35e+00 bond pdb=" N ARG A 530 " pdb=" H ARG A 530 " ideal model delta sigma weight residual 0.860 0.916 -0.056 2.00e-02 2.50e+03 7.83e+00 bond pdb=" N ALA A 532 " pdb=" H ALA A 532 " ideal model delta sigma weight residual 0.860 0.914 -0.054 2.00e-02 2.50e+03 7.41e+00 bond pdb=" N SER A 531 " pdb=" H SER A 531 " ideal model delta sigma weight residual 0.860 0.913 -0.053 2.00e-02 2.50e+03 7.08e+00 ... (remaining 26809 not shown) Histogram of bond angle deviations from ideal: 100.83 - 107.46: 1046 107.46 - 114.09: 31854 114.09 - 120.73: 9640 120.73 - 127.36: 5840 127.36 - 133.99: 153 Bond angle restraints: 48533 Sorted by residual: angle pdb=" N ALA A 532 " pdb=" CA ALA A 532 " pdb=" C ALA A 532 " ideal model delta sigma weight residual 112.45 108.10 4.35 1.39e+00 5.18e-01 9.81e+00 angle pdb=" N SER A 531 " pdb=" CA SER A 531 " pdb=" C SER A 531 " ideal model delta sigma weight residual 112.88 109.79 3.09 1.29e+00 6.01e-01 5.72e+00 angle pdb=" CA SER A 531 " pdb=" C SER A 531 " pdb=" O SER A 531 " ideal model delta sigma weight residual 119.59 117.03 2.56 1.18e+00 7.18e-01 4.72e+00 angle pdb=" N ILE A1001 " pdb=" CA ILE A1001 " pdb=" C ILE A1001 " ideal model delta sigma weight residual 111.88 109.79 2.09 1.06e+00 8.90e-01 3.87e+00 angle pdb=" N ARG A 530 " pdb=" CA ARG A 530 " pdb=" C ARG A 530 " ideal model delta sigma weight residual 112.89 110.60 2.29 1.24e+00 6.50e-01 3.40e+00 ... (remaining 48528 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 10568 17.91 - 35.81: 167 35.81 - 53.72: 27 53.72 - 71.63: 0 71.63 - 89.54: 1 Dihedral angle restraints: 10763 sinusoidal: 5006 harmonic: 5757 Sorted by residual: dihedral pdb=" N GLU A 67 " pdb=" CA GLU A 67 " pdb=" CB GLU A 67 " pdb=" CG GLU A 67 " ideal model delta sinusoidal sigma weight residual -180.00 -130.46 -49.54 3 1.50e+01 4.44e-03 8.79e+00 dihedral pdb=" CA LEU A1457 " pdb=" CB LEU A1457 " pdb=" CG LEU A1457 " pdb=" CD1 LEU A1457 " ideal model delta sinusoidal sigma weight residual 180.00 140.16 39.84 3 1.50e+01 4.44e-03 7.08e+00 dihedral pdb=" CA LEU A 844 " pdb=" CB LEU A 844 " pdb=" CG LEU A 844 " pdb=" CD1 LEU A 844 " ideal model delta sinusoidal sigma weight residual 180.00 140.18 39.82 3 1.50e+01 4.44e-03 7.07e+00 ... (remaining 10760 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1620 0.028 - 0.056: 342 0.056 - 0.085: 134 0.085 - 0.113: 47 0.113 - 0.141: 10 Chirality restraints: 2153 Sorted by residual: chirality pdb=" CA ILE A 682 " pdb=" N ILE A 682 " pdb=" C ILE A 682 " pdb=" CB ILE A 682 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CA ILE A 681 " pdb=" N ILE A 681 " pdb=" C ILE A 681 " pdb=" CB ILE A 681 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.73e-01 chirality pdb=" CA VAL A1561 " pdb=" N VAL A1561 " pdb=" C VAL A1561 " pdb=" CB VAL A1561 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.68e-01 ... (remaining 2150 not shown) Planarity restraints: 3946 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 529 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.11e+00 pdb=" C LYS A 529 " 0.035 2.00e-02 2.50e+03 pdb=" O LYS A 529 " -0.013 2.00e-02 2.50e+03 pdb=" N ARG A 530 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 532 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.70e+00 pdb=" N TYR A 533 " -0.033 2.00e-02 2.50e+03 pdb=" CA TYR A 533 " 0.008 2.00e-02 2.50e+03 pdb=" H TYR A 533 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A1700 " 0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO A1701 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A1701 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1701 " 0.027 5.00e-02 4.00e+02 ... (remaining 3943 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 1863 2.23 - 2.83: 61114 2.83 - 3.42: 69655 3.42 - 4.01: 90016 4.01 - 4.60: 143330 Nonbonded interactions: 365978 Sorted by model distance: nonbonded pdb=" OE1 GLU A1336 " pdb=" H GLU A1336 " model vdw 1.643 1.850 nonbonded pdb=" OE1 GLN A1509 " pdb=" H GLN A1509 " model vdw 1.646 1.850 nonbonded pdb=" OE1 GLU A1669 " pdb=" H GLU A1669 " model vdw 1.650 1.850 nonbonded pdb=" O MET A1659 " pdb="HD21 ASN A1712 " model vdw 1.661 1.850 nonbonded pdb=" HE1 TRP A 638 " pdb=" O SER A 725 " model vdw 1.688 1.850 ... (remaining 365973 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.81 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.380 Extract box with map and model: 10.450 Check model and map are aligned: 0.390 Set scattering table: 0.220 Process input model: 80.990 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6331 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 13477 Z= 0.112 Angle : 0.392 5.046 18318 Z= 0.220 Chirality : 0.031 0.141 2153 Planarity : 0.002 0.048 2336 Dihedral : 6.612 89.537 4869 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.20), residues: 1662 helix: 0.40 (0.15), residues: 1154 sheet: -1.72 (1.93), residues: 9 loop : -2.05 (0.27), residues: 499 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 381 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 381 time to evaluate : 1.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 381 average time/residue: 2.3581 time to fit residues: 995.6551 Evaluate side-chains 208 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 207 time to evaluate : 2.088 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.3542 time to fit residues: 3.1679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 142 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 80 optimal weight: 0.2980 chunk 98 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN A1049 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 13477 Z= 0.240 Angle : 0.587 8.583 18318 Z= 0.299 Chirality : 0.035 0.152 2153 Planarity : 0.005 0.086 2336 Dihedral : 2.918 13.111 1826 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer Outliers : 2.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.21), residues: 1662 helix: 1.11 (0.15), residues: 1171 sheet: -0.19 (1.98), residues: 9 loop : -1.38 (0.28), residues: 482 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 257 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 216 time to evaluate : 2.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 14 residues processed: 243 average time/residue: 2.1763 time to fit residues: 594.6948 Evaluate side-chains 174 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 160 time to evaluate : 2.109 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 3 average time/residue: 0.8022 time to fit residues: 5.8845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 85 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 chunk 152 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1120 HIS A1268 GLN A1378 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.6824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.065 13477 Z= 0.360 Angle : 0.665 9.812 18318 Z= 0.344 Chirality : 0.039 0.181 2153 Planarity : 0.005 0.080 2336 Dihedral : 3.811 18.312 1826 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer Outliers : 3.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.21), residues: 1662 helix: 0.87 (0.15), residues: 1172 sheet: 0.25 (1.37), residues: 19 loop : -1.15 (0.29), residues: 471 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 233 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 183 time to evaluate : 2.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 13 residues processed: 219 average time/residue: 2.3144 time to fit residues: 566.4749 Evaluate side-chains 158 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 145 time to evaluate : 1.875 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 11 residues processed: 2 average time/residue: 1.1200 time to fit residues: 5.1943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 151 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 163 optimal weight: 0.0980 chunk 80 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 HIS A 412 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.7606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 13477 Z= 0.297 Angle : 0.602 9.687 18318 Z= 0.306 Chirality : 0.036 0.152 2153 Planarity : 0.005 0.066 2336 Dihedral : 3.735 21.045 1826 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer Outliers : 3.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.21), residues: 1662 helix: 1.23 (0.15), residues: 1164 sheet: -0.01 (1.28), residues: 19 loop : -1.18 (0.29), residues: 479 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 201 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 159 time to evaluate : 1.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 19 residues processed: 192 average time/residue: 2.1613 time to fit residues: 466.3723 Evaluate side-chains 159 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 140 time to evaluate : 2.046 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 16 residues processed: 4 average time/residue: 0.8459 time to fit residues: 6.9620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 136 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN A 412 HIS ** A1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.8069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 13477 Z= 0.303 Angle : 0.580 7.272 18318 Z= 0.301 Chirality : 0.036 0.149 2153 Planarity : 0.004 0.056 2336 Dihedral : 3.807 20.524 1826 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer Outliers : 3.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.21), residues: 1662 helix: 1.26 (0.15), residues: 1173 sheet: -0.29 (1.24), residues: 19 loop : -1.15 (0.29), residues: 470 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 197 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 150 time to evaluate : 1.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 21 residues processed: 184 average time/residue: 2.2836 time to fit residues: 469.6900 Evaluate side-chains 162 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 141 time to evaluate : 2.065 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 15 residues processed: 7 average time/residue: 0.7405 time to fit residues: 9.8705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 54 optimal weight: 0.6980 chunk 147 optimal weight: 0.0770 chunk 32 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 163 optimal weight: 10.0000 chunk 135 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 157 optimal weight: 0.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN A 412 HIS A 482 GLN A 538 GLN A1259 GLN A1447 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.8219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 13477 Z= 0.200 Angle : 0.547 6.759 18318 Z= 0.278 Chirality : 0.034 0.143 2153 Planarity : 0.004 0.060 2336 Dihedral : 3.618 20.458 1826 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 2.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.21), residues: 1662 helix: 1.53 (0.15), residues: 1178 sheet: -0.11 (1.26), residues: 19 loop : -1.10 (0.29), residues: 465 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 185 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 153 time to evaluate : 2.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 18 residues processed: 178 average time/residue: 2.2452 time to fit residues: 451.0748 Evaluate side-chains 151 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 133 time to evaluate : 2.089 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 16 residues processed: 3 average time/residue: 0.9959 time to fit residues: 6.4969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 18 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 162 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN A 412 HIS A 482 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.8546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 13477 Z= 0.276 Angle : 0.573 6.592 18318 Z= 0.295 Chirality : 0.035 0.147 2153 Planarity : 0.004 0.061 2336 Dihedral : 3.729 21.954 1826 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer Outliers : 3.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.21), residues: 1662 helix: 1.44 (0.15), residues: 1183 sheet: -0.30 (1.20), residues: 19 loop : -1.13 (0.29), residues: 460 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 187 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 145 time to evaluate : 2.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 24 residues processed: 177 average time/residue: 2.3163 time to fit residues: 459.8518 Evaluate side-chains 159 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 135 time to evaluate : 2.096 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 19 residues processed: 5 average time/residue: 0.7236 time to fit residues: 7.4512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 65 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 148 optimal weight: 9.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN A 412 HIS A 482 GLN A 538 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.8812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 13477 Z= 0.288 Angle : 0.585 7.266 18318 Z= 0.301 Chirality : 0.036 0.165 2153 Planarity : 0.004 0.064 2336 Dihedral : 3.825 23.264 1826 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer Outliers : 2.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.21), residues: 1662 helix: 1.37 (0.15), residues: 1184 sheet: -0.29 (1.21), residues: 19 loop : -1.14 (0.29), residues: 459 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 177 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 143 time to evaluate : 2.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 21 residues processed: 171 average time/residue: 2.3253 time to fit residues: 444.9761 Evaluate side-chains 155 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 134 time to evaluate : 2.035 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 20 residues processed: 1 average time/residue: 0.2991 time to fit residues: 3.1958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 156 optimal weight: 8.9990 chunk 142 optimal weight: 3.9990 chunk 151 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 46 optimal weight: 0.1980 chunk 137 optimal weight: 0.9990 chunk 143 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 160 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN A 412 HIS A 482 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.8914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 13477 Z= 0.211 Angle : 0.563 6.679 18318 Z= 0.285 Chirality : 0.035 0.164 2153 Planarity : 0.004 0.071 2336 Dihedral : 3.717 21.921 1826 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer Outliers : 2.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.21), residues: 1662 helix: 1.58 (0.15), residues: 1183 sheet: -0.24 (1.23), residues: 19 loop : -1.00 (0.29), residues: 460 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 173 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 142 time to evaluate : 2.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 20 residues processed: 166 average time/residue: 2.2853 time to fit residues: 427.0871 Evaluate side-chains 153 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 133 time to evaluate : 2.053 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 19 residues processed: 2 average time/residue: 1.5034 time to fit residues: 6.2139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 97 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 13 optimal weight: 0.2980 chunk 103 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 chunk 142 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN A 412 HIS A 482 GLN A 538 GLN ** A1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1416 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.9041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 13477 Z= 0.241 Angle : 0.574 7.661 18318 Z= 0.292 Chirality : 0.035 0.177 2153 Planarity : 0.004 0.065 2336 Dihedral : 3.733 22.733 1826 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer Outliers : 2.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.21), residues: 1662 helix: 1.58 (0.15), residues: 1184 sheet: -0.29 (1.22), residues: 19 loop : -1.02 (0.29), residues: 459 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 163 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 135 time to evaluate : 2.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 22 residues processed: 160 average time/residue: 2.3779 time to fit residues: 425.8827 Evaluate side-chains 153 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 131 time to evaluate : 2.139 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 21 residues processed: 2 average time/residue: 0.4994 time to fit residues: 4.3111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 41 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 19 optimal weight: 0.0970 chunk 37 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 137 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN A 412 HIS A 482 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.149706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.117551 restraints weight = 65457.075| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.74 r_work: 0.3720 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.9136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 13477 Z= 0.242 Angle : 0.566 7.062 18318 Z= 0.289 Chirality : 0.035 0.177 2153 Planarity : 0.004 0.065 2336 Dihedral : 3.760 22.897 1826 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 1.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.21), residues: 1662 helix: 1.56 (0.15), residues: 1185 sheet: -0.29 (1.23), residues: 19 loop : -1.02 (0.29), residues: 458 =============================================================================== Job complete usr+sys time: 10217.78 seconds wall clock time: 179 minutes 24.42 seconds (10764.42 seconds total)