Starting phenix.real_space_refine on Wed Dec 13 17:59:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mvv_24057/12_2023/7mvv_24057.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mvv_24057/12_2023/7mvv_24057.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mvv_24057/12_2023/7mvv_24057.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mvv_24057/12_2023/7mvv_24057.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mvv_24057/12_2023/7mvv_24057.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mvv_24057/12_2023/7mvv_24057.pdb" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= -0.002 sd= 0.049 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 67 5.16 5 C 8233 2.51 5 N 2175 2.21 5 O 2382 1.98 5 H 12907 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 99": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 188": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 304": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 305": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 329": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 452": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 503": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 985": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1259": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1300": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1506": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1634": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 25764 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 24672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1542, 24672 Classifications: {'peptide': 1542} Link IDs: {'PTRANS': 58, 'TRANS': 1483} Chain breaks: 16 Chain: "B" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 911 Classifications: {'peptide': 56} Link IDs: {'TRANS': 55} Chain: "D" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain: "C" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 155 Classifications: {'peptide': 9} Link IDs: {'PTRANS': 2, 'TRANS': 6} Time building chain proxies: 10.37, per 1000 atoms: 0.40 Number of scatterers: 25764 At special positions: 0 Unit cell: (86.6688, 117.926, 194.65, 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 67 16.00 O 2382 8.00 N 2175 7.00 C 8233 6.00 H 12907 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: 20.30 Conformation dependent library (CDL) restraints added in 2.5 seconds 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3090 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 2 sheets defined 76.9% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.23 Creating SS restraints... Processing helix chain 'A' and resid 5 through 22 Processing helix chain 'A' and resid 27 through 38 removed outlier: 3.767A pdb=" N THR A 33 " --> pdb=" O GLN A 29 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A 34 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU A 36 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A 37 " --> pdb=" O THR A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 44 removed outlier: 3.953A pdb=" N ALA A 44 " --> pdb=" O ASP A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 removed outlier: 3.560A pdb=" N ARG A 56 " --> pdb=" O ASP A 52 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A 60 " --> pdb=" O ARG A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 91 removed outlier: 3.845A pdb=" N ASN A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP A 82 " --> pdb=" O ASP A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 108 Processing helix chain 'A' and resid 109 through 114 Processing helix chain 'A' and resid 116 through 144 removed outlier: 3.535A pdb=" N GLY A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL A 122 " --> pdb=" O TRP A 118 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG A 129 " --> pdb=" O PHE A 125 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N MET A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 164 removed outlier: 3.540A pdb=" N PHE A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY A 157 " --> pdb=" O GLN A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 212 removed outlier: 3.777A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 251 Processing helix chain 'A' and resid 256 through 269 removed outlier: 3.639A pdb=" N PHE A 260 " --> pdb=" O THR A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 292 removed outlier: 3.641A pdb=" N ILE A 278 " --> pdb=" O ASP A 274 " (cutoff:3.500A) Proline residue: A 282 - end of helix Processing helix chain 'A' and resid 299 through 311 removed outlier: 3.720A pdb=" N ARG A 305 " --> pdb=" O GLN A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 337 removed outlier: 3.688A pdb=" N GLY A 325 " --> pdb=" O LEU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 371 Processing helix chain 'A' and resid 371 through 384 removed outlier: 3.538A pdb=" N LYS A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 394 removed outlier: 3.968A pdb=" N LEU A 394 " --> pdb=" O PRO A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 437 Processing helix chain 'A' and resid 437 through 455 removed outlier: 3.580A pdb=" N LEU A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 475 Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 483 through 488 removed outlier: 4.308A pdb=" N ASP A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 500 Processing helix chain 'A' and resid 505 through 519 Processing helix chain 'A' and resid 522 through 534 Processing helix chain 'A' and resid 551 through 568 Processing helix chain 'A' and resid 592 through 613 Processing helix chain 'A' and resid 614 through 621 removed outlier: 3.537A pdb=" N ILE A 621 " --> pdb=" O ARG A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 637 Processing helix chain 'A' and resid 641 through 656 removed outlier: 3.836A pdb=" N ARG A 645 " --> pdb=" O PRO A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 677 removed outlier: 3.708A pdb=" N ASN A 677 " --> pdb=" O ALA A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 712 removed outlier: 3.792A pdb=" N GLU A 706 " --> pdb=" O GLN A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 730 Processing helix chain 'A' and resid 758 through 772 removed outlier: 3.808A pdb=" N VAL A 762 " --> pdb=" O ILE A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 798 Processing helix chain 'A' and resid 802 through 812 Processing helix chain 'A' and resid 820 through 831 Processing helix chain 'A' and resid 832 through 841 removed outlier: 3.580A pdb=" N PHE A 841 " --> pdb=" O MET A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 854 removed outlier: 3.580A pdb=" N ILE A 846 " --> pdb=" O ASN A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 863 removed outlier: 3.949A pdb=" N LEU A 860 " --> pdb=" O ASP A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 894 removed outlier: 5.115A pdb=" N GLU A 888 " --> pdb=" O LEU A 884 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N THR A 889 " --> pdb=" O GLU A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 905 Processing helix chain 'A' and resid 919 through 925 removed outlier: 4.220A pdb=" N GLY A 923 " --> pdb=" O ALA A 919 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE A 924 " --> pdb=" O PHE A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 937 removed outlier: 4.112A pdb=" N VAL A 932 " --> pdb=" O LEU A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 940 No H-bonds generated for 'chain 'A' and resid 938 through 940' Processing helix chain 'A' and resid 942 through 959 Processing helix chain 'A' and resid 960 through 967 Processing helix chain 'A' and resid 978 through 983 Processing helix chain 'A' and resid 987 through 1002 removed outlier: 3.510A pdb=" N ALA A1002 " --> pdb=" O ALA A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1031 Processing helix chain 'A' and resid 1037 through 1044 removed outlier: 3.703A pdb=" N GLN A1041 " --> pdb=" O THR A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1076 Processing helix chain 'A' and resid 1088 through 1107 removed outlier: 3.532A pdb=" N SER A1107 " --> pdb=" O LEU A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1110 No H-bonds generated for 'chain 'A' and resid 1108 through 1110' Processing helix chain 'A' and resid 1111 through 1120 Processing helix chain 'A' and resid 1122 through 1131 Processing helix chain 'A' and resid 1148 through 1153 removed outlier: 4.190A pdb=" N LEU A1152 " --> pdb=" O CYS A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1154 through 1183 removed outlier: 3.738A pdb=" N ALA A1158 " --> pdb=" O ASP A1154 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1198 removed outlier: 4.077A pdb=" N LYS A1189 " --> pdb=" O ILE A1185 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG A1190 " --> pdb=" O PRO A1186 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLN A1191 " --> pdb=" O SER A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1212 through 1217 Processing helix chain 'A' and resid 1258 through 1276 removed outlier: 3.693A pdb=" N ILE A1264 " --> pdb=" O LYS A1260 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN A1276 " --> pdb=" O TYR A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1327 removed outlier: 3.512A pdb=" N VAL A1286 " --> pdb=" O PHE A1282 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU A1295 " --> pdb=" O LYS A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1335 through 1353 Proline residue: A1348 - end of helix Processing helix chain 'A' and resid 1359 through 1374 removed outlier: 4.003A pdb=" N GLU A1363 " --> pdb=" O ASP A1359 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL A1367 " --> pdb=" O GLU A1363 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA A1368 " --> pdb=" O LEU A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1389 through 1414 removed outlier: 3.584A pdb=" N LEU A1406 " --> pdb=" O GLN A1402 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N CYS A1407 " --> pdb=" O LEU A1403 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN A1413 " --> pdb=" O SER A1409 " (cutoff:3.500A) Processing helix chain 'A' and resid 1417 through 1434 removed outlier: 3.621A pdb=" N TYR A1424 " --> pdb=" O LEU A1420 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR A1425 " --> pdb=" O ARG A1421 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A1426 " --> pdb=" O SER A1422 " (cutoff:3.500A) Processing helix chain 'A' and resid 1455 through 1472 removed outlier: 3.527A pdb=" N ALA A1467 " --> pdb=" O ARG A1463 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A1468 " --> pdb=" O THR A1464 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR A1471 " --> pdb=" O ALA A1467 " (cutoff:3.500A) Processing helix chain 'A' and resid 1472 through 1483 removed outlier: 3.556A pdb=" N LEU A1476 " --> pdb=" O GLY A1472 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL A1478 " --> pdb=" O ARG A1474 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A1483 " --> pdb=" O ILE A1479 " (cutoff:3.500A) Processing helix chain 'A' and resid 1488 through 1508 removed outlier: 3.755A pdb=" N THR A1492 " --> pdb=" O THR A1488 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN A1499 " --> pdb=" O MET A1495 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A1500 " --> pdb=" O ILE A1496 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A1507 " --> pdb=" O HIS A1503 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER A1508 " --> pdb=" O THR A1504 " (cutoff:3.500A) Processing helix chain 'A' and resid 1520 through 1529 removed outlier: 3.625A pdb=" N ASP A1524 " --> pdb=" O CYS A1520 " (cutoff:3.500A) Processing helix chain 'A' and resid 1530 through 1539 removed outlier: 3.626A pdb=" N LEU A1539 " --> pdb=" O LEU A1535 " (cutoff:3.500A) Processing helix chain 'A' and resid 1541 through 1546 removed outlier: 3.828A pdb=" N GLU A1545 " --> pdb=" O GLU A1541 " (cutoff:3.500A) Processing helix chain 'A' and resid 1570 through 1587 Processing helix chain 'A' and resid 1589 through 1598 removed outlier: 3.901A pdb=" N ALA A1593 " --> pdb=" O THR A1589 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LYS A1594 " --> pdb=" O ARG A1590 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR A1595 " --> pdb=" O GLN A1591 " (cutoff:3.500A) Processing helix chain 'A' and resid 1600 through 1608 removed outlier: 3.652A pdb=" N ALA A1604 " --> pdb=" O ASN A1600 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU A1606 " --> pdb=" O PHE A1602 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN A1607 " --> pdb=" O ARG A1603 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER A1608 " --> pdb=" O ALA A1604 " (cutoff:3.500A) Processing helix chain 'A' and resid 1630 through 1654 removed outlier: 3.534A pdb=" N THR A1651 " --> pdb=" O GLY A1647 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG A1653 " --> pdb=" O ALA A1649 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY A1654 " --> pdb=" O VAL A1650 " (cutoff:3.500A) Processing helix chain 'A' and resid 1657 through 1668 removed outlier: 3.768A pdb=" N LYS A1663 " --> pdb=" O VAL A1659 " (cutoff:3.500A) Processing helix chain 'A' and resid 1670 through 1680 removed outlier: 3.555A pdb=" N VAL A1675 " --> pdb=" O LEU A1671 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN A1679 " --> pdb=" O VAL A1675 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA A1680 " --> pdb=" O LEU A1676 " (cutoff:3.500A) Processing helix chain 'A' and resid 1710 through 1734 Processing helix chain 'A' and resid 1734 through 1739 removed outlier: 3.913A pdb=" N TYR A1738 " --> pdb=" O GLY A1734 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 284 removed outlier: 3.657A pdb=" N LEU B 252 " --> pdb=" O VAL B 248 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER B 253 " --> pdb=" O ASP B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 299 removed outlier: 4.036A pdb=" N TYR B 295 " --> pdb=" O ARG B 291 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 1199 through 1200 818 hydrogen bonds defined for protein. 2436 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: 10.01 Time building geometry restraints manager: 20.84 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: 12875 1.03 - 1.23: 35 1.23 - 1.42: 5401 1.42 - 1.62: 7594 1.62 - 1.81: 102 Bond restraints: 26007 Sorted by residual: bond pdb=" N ALA A 721 " pdb=" CA ALA A 721 " ideal model delta sigma weight residual 1.458 1.392 0.067 1.26e-02 6.30e+03 2.81e+01 bond pdb=" CA ALA A 721 " pdb=" C ALA A 721 " ideal model delta sigma weight residual 1.524 1.458 0.065 1.32e-02 5.74e+03 2.46e+01 bond pdb=" C ILE A 723 " pdb=" O ILE A 723 " ideal model delta sigma weight residual 1.237 1.182 0.055 1.12e-02 7.97e+03 2.41e+01 bond pdb=" CA ALA A 721 " pdb=" CB ALA A 721 " ideal model delta sigma weight residual 1.529 1.463 0.066 1.62e-02 3.81e+03 1.67e+01 bond pdb=" C PHE A 722 " pdb=" O PHE A 722 " ideal model delta sigma weight residual 1.236 1.189 0.047 1.26e-02 6.30e+03 1.41e+01 ... (remaining 26002 not shown) Histogram of bond angle deviations from ideal: 100.77 - 107.41: 924 107.41 - 114.05: 30924 114.05 - 120.70: 9484 120.70 - 127.34: 5608 127.34 - 133.98: 140 Bond angle restraints: 47080 Sorted by residual: angle pdb=" CA ASN A 720 " pdb=" C ASN A 720 " pdb=" N ALA A 721 " ideal model delta sigma weight residual 117.63 111.47 6.16 1.25e+00 6.40e-01 2.43e+01 angle pdb=" O ASN A 720 " pdb=" C ASN A 720 " pdb=" N ALA A 721 " ideal model delta sigma weight residual 122.22 127.58 -5.36 1.17e+00 7.31e-01 2.10e+01 angle pdb=" C ILE A 723 " pdb=" N GLN A 724 " pdb=" CA GLN A 724 " ideal model delta sigma weight residual 120.28 125.69 -5.41 1.34e+00 5.57e-01 1.63e+01 angle pdb=" CA ILE A 723 " pdb=" C ILE A 723 " pdb=" N GLN A 724 " ideal model delta sigma weight residual 117.02 121.29 -4.27 1.11e+00 8.12e-01 1.48e+01 angle pdb=" CA ILE A 723 " pdb=" C ILE A 723 " pdb=" O ILE A 723 " ideal model delta sigma weight residual 121.05 117.89 3.16 1.11e+00 8.12e-01 8.12e+00 ... (remaining 47075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.76: 11133 10.76 - 21.53: 592 21.53 - 32.29: 111 32.29 - 43.05: 45 43.05 - 53.82: 6 Dihedral angle restraints: 11887 sinusoidal: 6365 harmonic: 5522 Sorted by residual: dihedral pdb=" CA ILE A1185 " pdb=" CB ILE A1185 " pdb=" CG1 ILE A1185 " pdb=" CD1 ILE A1185 " ideal model delta sinusoidal sigma weight residual 60.00 113.82 -53.82 3 1.50e+01 4.44e-03 9.24e+00 dihedral pdb=" C ILE A 723 " pdb=" N ILE A 723 " pdb=" CA ILE A 723 " pdb=" CB ILE A 723 " ideal model delta harmonic sigma weight residual -122.00 -129.27 7.27 0 2.50e+00 1.60e-01 8.47e+00 dihedral pdb=" CA ILE A1294 " pdb=" CB ILE A1294 " pdb=" CG1 ILE A1294 " pdb=" CD1 ILE A1294 " ideal model delta sinusoidal sigma weight residual 60.00 99.96 -39.96 3 1.50e+01 4.44e-03 7.10e+00 ... (remaining 11884 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1805 0.050 - 0.101: 209 0.101 - 0.151: 21 0.151 - 0.201: 0 0.201 - 0.251: 3 Chirality restraints: 2038 Sorted by residual: chirality pdb=" CA PHE A 722 " pdb=" N PHE A 722 " pdb=" C PHE A 722 " pdb=" CB PHE A 722 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA ILE A 723 " pdb=" N ILE A 723 " pdb=" C ILE A 723 " pdb=" CB ILE A 723 " both_signs ideal model delta sigma weight residual False 2.43 2.19 0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA ALA A 721 " pdb=" N ALA A 721 " pdb=" C ALA A 721 " pdb=" CB ALA A 721 " both_signs ideal model delta sigma weight residual False 2.48 2.28 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 2035 not shown) Planarity restraints: 3791 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 720 " 0.010 2.00e-02 2.50e+03 2.13e-02 4.55e+00 pdb=" C ASN A 720 " -0.037 2.00e-02 2.50e+03 pdb=" O ASN A 720 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA A 721 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 723 " 0.009 2.00e-02 2.50e+03 1.77e-02 3.13e+00 pdb=" N GLN A 724 " -0.030 2.00e-02 2.50e+03 pdb=" CA GLN A 724 " 0.008 2.00e-02 2.50e+03 pdb=" H GLN A 724 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 759 " -0.023 5.00e-02 4.00e+02 3.46e-02 1.92e+00 pdb=" N PRO A 760 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 760 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 760 " -0.019 5.00e-02 4.00e+02 ... (remaining 3788 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 1357 2.22 - 2.81: 55112 2.81 - 3.41: 67673 3.41 - 4.00: 83710 4.00 - 4.60: 133691 Nonbonded interactions: 341543 Sorted by model distance: nonbonded pdb=" O GLU A 161 " pdb=" H ILE A 167 " model vdw 1.621 1.850 nonbonded pdb=" O ASN A1122 " pdb=" HD1 HIS A1126 " model vdw 1.638 1.850 nonbonded pdb=" O SER A 421 " pdb=" HD1 HIS A 425 " model vdw 1.643 1.850 nonbonded pdb=" OE1 GLN A 460 " pdb=" H GLN A 460 " model vdw 1.648 1.850 nonbonded pdb=" OE1 GLU A1013 " pdb=" H GLU A1013 " model vdw 1.653 1.850 ... (remaining 341538 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=1.00 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.360 Extract box with map and model: 4.990 Check model and map are aligned: 0.370 Set scattering table: 0.210 Process input model: 77.760 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 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 0.067 13100 Z= 0.131 Angle : 0.355 6.164 17731 Z= 0.203 Chirality : 0.032 0.251 2038 Planarity : 0.002 0.035 2260 Dihedral : 6.426 53.817 4846 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.07 % Allowed : 2.00 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.66 (0.20), residues: 1569 helix: 0.28 (0.15), residues: 1122 sheet: None (None), residues: 0 loop : -2.18 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP A1296 HIS 0.001 0.000 HIS A1068 PHE 0.021 0.001 PHE A 722 TYR 0.012 0.000 TYR A1089 ARG 0.001 0.000 ARG A 478 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 186 time to evaluate : 2.059 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 outliers start: 1 outliers final: 0 residues processed: 187 average time/residue: 0.7559 time to fit residues: 190.3715 Evaluate side-chains 112 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 2.198 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 92 optimal weight: 0.4980 chunk 144 optimal weight: 8.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 302 GLN A1063 GLN A1402 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13100 Z= 0.181 Angle : 0.482 6.073 17731 Z= 0.250 Chirality : 0.034 0.140 2038 Planarity : 0.003 0.045 2260 Dihedral : 2.340 14.174 1720 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.57 % Allowed : 5.93 % Favored : 93.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.14 (0.22), residues: 1569 helix: 1.67 (0.16), residues: 1162 sheet: None (None), residues: 0 loop : -2.02 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 118 HIS 0.002 0.001 HIS A1068 PHE 0.022 0.001 PHE A 467 TYR 0.022 0.001 TYR A1172 ARG 0.009 0.000 ARG B 270 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 111 time to evaluate : 2.128 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 outliers start: 8 outliers final: 5 residues processed: 116 average time/residue: 0.7666 time to fit residues: 120.5656 Evaluate side-chains 107 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 102 time to evaluate : 1.891 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3138 time to fit residues: 5.1382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 156 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 116 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 457 ASN A 677 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 13100 Z= 0.282 Angle : 0.553 6.403 17731 Z= 0.296 Chirality : 0.035 0.144 2038 Planarity : 0.004 0.030 2260 Dihedral : 3.135 19.828 1720 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.36 % Allowed : 6.07 % Favored : 93.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.55 (0.22), residues: 1569 helix: 1.91 (0.15), residues: 1163 sheet: None (None), residues: 0 loop : -1.65 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 966 HIS 0.009 0.002 HIS A1674 PHE 0.021 0.002 PHE A 260 TYR 0.015 0.002 TYR A 901 ARG 0.007 0.001 ARG A1644 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 4.795 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 outliers start: 5 outliers final: 2 residues processed: 100 average time/residue: 0.7752 time to fit residues: 107.5405 Evaluate side-chains 87 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 85 time to evaluate : 2.025 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3721 time to fit residues: 3.9089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 153 optimal weight: 9.9990 chunk 137 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1344 GLN ** A1668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13100 Z= 0.204 Angle : 0.484 7.167 17731 Z= 0.252 Chirality : 0.033 0.138 2038 Planarity : 0.003 0.031 2260 Dihedral : 3.014 16.591 1720 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.36 % Allowed : 6.36 % Favored : 93.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.06 (0.22), residues: 1569 helix: 2.31 (0.15), residues: 1165 sheet: None (None), residues: 0 loop : -1.59 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 331 HIS 0.007 0.001 HIS A1674 PHE 0.022 0.001 PHE A1338 TYR 0.014 0.001 TYR A1089 ARG 0.003 0.000 ARG A1184 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 85 time to evaluate : 2.229 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: 5 outliers final: 2 residues processed: 89 average time/residue: 0.6949 time to fit residues: 87.0682 Evaluate side-chains 79 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 1.767 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2883 time to fit residues: 3.4996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 114 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1674 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.5080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13100 Z= 0.234 Angle : 0.495 6.428 17731 Z= 0.262 Chirality : 0.033 0.139 2038 Planarity : 0.003 0.032 2260 Dihedral : 3.177 16.981 1720 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.57 % Allowed : 6.79 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.09 (0.22), residues: 1569 helix: 2.32 (0.15), residues: 1167 sheet: None (None), residues: 0 loop : -1.57 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1546 HIS 0.009 0.001 HIS A1674 PHE 0.021 0.001 PHE A1338 TYR 0.014 0.001 TYR A1089 ARG 0.009 0.000 ARG A 985 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 75 time to evaluate : 2.035 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: 8 outliers final: 4 residues processed: 80 average time/residue: 0.7236 time to fit residues: 82.0214 Evaluate side-chains 79 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 75 time to evaluate : 2.002 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3565 time to fit residues: 5.1363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 153 optimal weight: 8.9990 chunk 127 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 148 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.5195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13100 Z= 0.143 Angle : 0.447 6.349 17731 Z= 0.230 Chirality : 0.033 0.150 2038 Planarity : 0.003 0.030 2260 Dihedral : 3.028 17.234 1720 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.14 % Allowed : 6.86 % Favored : 93.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.57 (0.22), residues: 1569 helix: 2.69 (0.15), residues: 1167 sheet: None (None), residues: 0 loop : -1.45 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1296 HIS 0.004 0.001 HIS A 425 PHE 0.010 0.001 PHE A 745 TYR 0.015 0.001 TYR A1089 ARG 0.006 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 2.033 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 outliers start: 2 outliers final: 0 residues processed: 80 average time/residue: 0.6975 time to fit residues: 78.4807 Evaluate side-chains 73 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 2.047 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 94 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.5398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13100 Z= 0.184 Angle : 0.462 6.885 17731 Z= 0.240 Chirality : 0.033 0.133 2038 Planarity : 0.003 0.029 2260 Dihedral : 3.060 17.306 1720 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.14 % Allowed : 7.29 % Favored : 92.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.59 (0.22), residues: 1569 helix: 2.70 (0.15), residues: 1167 sheet: None (None), residues: 0 loop : -1.44 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1296 HIS 0.004 0.001 HIS A 425 PHE 0.010 0.001 PHE A 745 TYR 0.014 0.001 TYR A1089 ARG 0.004 0.000 ARG A 985 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 73 time to evaluate : 2.020 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 outliers start: 2 outliers final: 2 residues processed: 75 average time/residue: 0.7089 time to fit residues: 74.1940 Evaluate side-chains 73 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 1.975 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3169 time to fit residues: 3.6823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 14 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 146 optimal weight: 0.7980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.5564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13100 Z= 0.161 Angle : 0.457 7.848 17731 Z= 0.236 Chirality : 0.033 0.159 2038 Planarity : 0.003 0.041 2260 Dihedral : 3.062 17.693 1720 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.72 (0.22), residues: 1569 helix: 2.82 (0.15), residues: 1167 sheet: None (None), residues: 0 loop : -1.46 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1296 HIS 0.004 0.001 HIS A 425 PHE 0.010 0.001 PHE A 745 TYR 0.014 0.001 TYR A1089 ARG 0.015 0.000 ARG A 754 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 2.247 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 outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.7022 time to fit residues: 73.5051 Evaluate side-chains 74 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 2.062 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 0.7980 chunk 142 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.5661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13100 Z= 0.154 Angle : 0.459 7.908 17731 Z= 0.237 Chirality : 0.033 0.138 2038 Planarity : 0.003 0.032 2260 Dihedral : 3.031 17.604 1720 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.14 % Allowed : 7.36 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.82 (0.22), residues: 1569 helix: 2.87 (0.15), residues: 1168 sheet: None (None), residues: 0 loop : -1.41 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1296 HIS 0.004 0.001 HIS A 425 PHE 0.014 0.001 PHE A1234 TYR 0.014 0.001 TYR A1089 ARG 0.006 0.000 ARG A 754 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 74 time to evaluate : 2.114 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 outliers start: 2 outliers final: 0 residues processed: 75 average time/residue: 0.6907 time to fit residues: 73.4425 Evaluate side-chains 72 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 2.156 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 158 optimal weight: 0.1980 chunk 145 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 134 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.5733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13100 Z= 0.140 Angle : 0.462 9.440 17731 Z= 0.235 Chirality : 0.033 0.145 2038 Planarity : 0.003 0.030 2260 Dihedral : 2.998 17.697 1720 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.07 % Allowed : 7.57 % Favored : 92.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.96 (0.22), residues: 1569 helix: 2.98 (0.15), residues: 1169 sheet: None (None), residues: 0 loop : -1.37 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1296 HIS 0.003 0.001 HIS A 425 PHE 0.010 0.001 PHE B 275 TYR 0.014 0.001 TYR A1089 ARG 0.007 0.000 ARG A 754 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 74 time to evaluate : 2.036 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 outliers start: 1 outliers final: 0 residues processed: 75 average time/residue: 0.6695 time to fit residues: 71.8571 Evaluate side-chains 71 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 2.092 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 0.0980 chunk 116 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 7 optimal weight: 6.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.075781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.057439 restraints weight = 200274.222| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 4.78 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.5822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13100 Z= 0.140 Angle : 0.457 9.517 17731 Z= 0.232 Chirality : 0.032 0.132 2038 Planarity : 0.003 0.030 2260 Dihedral : 2.966 17.360 1720 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.09 (0.22), residues: 1569 helix: 3.08 (0.15), residues: 1168 sheet: None (None), residues: 0 loop : -1.34 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1296 HIS 0.003 0.001 HIS A 425 PHE 0.010 0.001 PHE B 275 TYR 0.014 0.001 TYR A1089 ARG 0.010 0.000 ARG A 754 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4572.03 seconds wall clock time: 86 minutes 22.12 seconds (5182.12 seconds total)