Starting phenix.real_space_refine on Tue Mar 19 23:30:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mvv_24057/03_2024/7mvv_24057.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mvv_24057/03_2024/7mvv_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_24057/03_2024/7mvv_24057.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mvv_24057/03_2024/7mvv_24057.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mvv_24057/03_2024/7mvv_24057.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mvv_24057/03_2024/7mvv_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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 11.34, per 1000 atoms: 0.44 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: 20.73 Conformation dependent library (CDL) restraints added in 2.7 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: 1.68 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: 10.15 Time building geometry restraints manager: 21.62 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 - 11.89: 11422 11.89 - 23.79: 490 23.79 - 35.68: 104 35.68 - 47.57: 63 47.57 - 59.46: 59 Dihedral angle restraints: 12138 sinusoidal: 6616 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 12135 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: 0.860 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: 0.400 Extract box with map and model: 5.280 Check model and map are aligned: 0.420 Set scattering table: 0.270 Process input model: 81.680 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.990 ------------------------------------------------------------------------------- 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 : 2.255 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: A 57 GLU cc_start: 0.7742 (tm-30) cc_final: 0.6803 (mm-30) REVERT: A 471 ILE cc_start: 0.8263 (mt) cc_final: 0.7703 (mt) REVERT: A 1404 PHE cc_start: 0.8916 (t80) cc_final: 0.8690 (t80) outliers start: 1 outliers final: 0 residues processed: 187 average time/residue: 0.7294 time to fit residues: 182.8781 Evaluate side-chains 112 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.764 ------------------------------------------------------------------------------- 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: 2.9990 chunk 120 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 92 optimal weight: 0.0770 chunk 144 optimal weight: 8.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN A1063 GLN A1402 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13100 Z= 0.205 Angle : 0.521 6.164 17731 Z= 0.269 Chirality : 0.035 0.143 2038 Planarity : 0.004 0.059 2260 Dihedral : 2.570 15.360 1720 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.64 % Allowed : 5.86 % 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: 1.18 (0.22), residues: 1569 helix: 1.70 (0.15), residues: 1163 sheet: None (None), residues: 0 loop : -2.02 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 118 HIS 0.003 0.001 HIS A1668 PHE 0.026 0.001 PHE A 467 TYR 0.011 0.001 TYR A1089 ARG 0.011 0.001 ARG A1184 *********************** 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 120 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 111 time to evaluate : 2.280 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: A 57 GLU cc_start: 0.7582 (tm-30) cc_final: 0.6732 (mm-30) REVERT: A 1086 MET cc_start: 0.8807 (mmp) cc_final: 0.8583 (mmp) REVERT: A 1718 ARG cc_start: 0.8718 (mmt-90) cc_final: 0.8400 (mmm-85) REVERT: B 247 ASP cc_start: 0.7396 (t0) cc_final: 0.6976 (t0) outliers start: 9 outliers final: 5 residues processed: 116 average time/residue: 0.7393 time to fit residues: 116.9160 Evaluate side-chains 103 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 98 time to evaluate : 2.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 298 PHE 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: 1.9990 chunk 120 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 144 optimal weight: 0.4980 chunk 156 optimal weight: 7.9990 chunk 128 optimal weight: 4.9990 chunk 143 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 677 ASN ** A1668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13100 Z= 0.261 Angle : 0.532 6.366 17731 Z= 0.284 Chirality : 0.035 0.143 2038 Planarity : 0.004 0.036 2260 Dihedral : 3.092 18.984 1720 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.64 % Allowed : 5.64 % Favored : 93.71 % 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: 1.63 (0.22), residues: 1569 helix: 1.95 (0.15), residues: 1161 sheet: None (None), residues: 0 loop : -1.58 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 331 HIS 0.011 0.001 HIS A1674 PHE 0.036 0.002 PHE A1338 TYR 0.014 0.002 TYR A 901 ARG 0.015 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: 9 poor density : 92 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: A 57 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7399 (tm-30) REVERT: A 1338 PHE cc_start: 0.7738 (m-80) cc_final: 0.6993 (t80) outliers start: 9 outliers final: 6 residues processed: 99 average time/residue: 0.6809 time to fit residues: 91.8437 Evaluate side-chains 88 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain A residue 1185 ILE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 295 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 16 optimal weight: 0.0170 chunk 69 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 145 optimal weight: 8.9990 chunk 153 optimal weight: 10.0000 chunk 137 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 overall best weight: 1.5824 ------------------------------------------------------------------------------- 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: 0.8106 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13100 Z= 0.185 Angle : 0.475 6.336 17731 Z= 0.246 Chirality : 0.033 0.150 2038 Planarity : 0.003 0.033 2260 Dihedral : 2.992 16.576 1720 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.71 % Allowed : 5.86 % Favored : 93.43 % 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: 2.14 (0.22), residues: 1569 helix: 2.36 (0.15), residues: 1164 sheet: None (None), residues: 0 loop : -1.52 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 674 HIS 0.006 0.001 HIS A1674 PHE 0.014 0.001 PHE A1404 TYR 0.014 0.001 TYR A1089 ARG 0.005 0.000 ARG A1644 *********************** 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 95 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 2.322 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: A 57 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7390 (tm-30) REVERT: A 1338 PHE cc_start: 0.7650 (m-80) cc_final: 0.7028 (t80) REVERT: B 269 GLU cc_start: 0.9226 (tm-30) cc_final: 0.8973 (pp20) outliers start: 10 outliers final: 6 residues processed: 92 average time/residue: 0.7090 time to fit residues: 90.8691 Evaluate side-chains 84 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 2.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain A residue 1638 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 268 LEU 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: 0.9980 chunk 63 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 0.0370 chunk 137 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.6064 ------------------------------------------------------------------------------- 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: 0.8127 moved from start: 0.4984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13100 Z= 0.196 Angle : 0.472 6.365 17731 Z= 0.247 Chirality : 0.033 0.144 2038 Planarity : 0.003 0.038 2260 Dihedral : 3.056 16.799 1720 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.71 % Allowed : 6.21 % Favored : 93.07 % 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: 2.34 (0.22), residues: 1569 helix: 2.50 (0.15), residues: 1166 sheet: None (None), residues: 0 loop : -1.44 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1546 HIS 0.007 0.001 HIS A1674 PHE 0.012 0.001 PHE A 745 TYR 0.014 0.001 TYR A1089 ARG 0.008 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 89 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 79 time to evaluate : 2.230 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: 10 outliers final: 4 residues processed: 88 average time/residue: 0.7023 time to fit residues: 87.6945 Evaluate side-chains 81 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 77 time to evaluate : 2.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 295 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 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: 0.9990 chunk 80 optimal weight: 0.7980 chunk 148 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.8106 moved from start: 0.5067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13100 Z= 0.128 Angle : 0.438 6.039 17731 Z= 0.222 Chirality : 0.033 0.153 2038 Planarity : 0.003 0.028 2260 Dihedral : 2.934 16.415 1720 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.43 % Allowed : 6.29 % 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: 2.75 (0.22), residues: 1569 helix: 2.80 (0.15), residues: 1166 sheet: None (None), residues: 0 loop : -1.31 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1296 HIS 0.004 0.001 HIS A1674 PHE 0.010 0.001 PHE A1404 TYR 0.014 0.001 TYR A1089 ARG 0.004 0.000 ARG A1644 *********************** 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 86 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 80 time to evaluate : 2.130 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: A 1338 PHE cc_start: 0.7545 (m-80) cc_final: 0.6917 (t80) outliers start: 6 outliers final: 4 residues processed: 85 average time/residue: 0.6916 time to fit residues: 82.0144 Evaluate side-chains 83 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 295 TYR 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: 3.9990 chunk 129 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 153 optimal weight: 8.9990 chunk 95 optimal weight: 0.0670 chunk 93 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- 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: 0.8099 moved from start: 0.5130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13100 Z= 0.123 Angle : 0.436 7.842 17731 Z= 0.220 Chirality : 0.032 0.134 2038 Planarity : 0.003 0.027 2260 Dihedral : 2.850 17.084 1720 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.50 % Allowed : 6.43 % Favored : 93.07 % 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: 2.99 (0.22), residues: 1569 helix: 2.98 (0.15), residues: 1168 sheet: None (None), residues: 0 loop : -1.24 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1296 HIS 0.004 0.001 HIS A1674 PHE 0.009 0.001 PHE A1404 TYR 0.014 0.001 TYR A1089 ARG 0.003 0.000 ARG A1644 *********************** 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 87 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 80 time to evaluate : 1.894 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: A 1 MET cc_start: 0.6369 (ppp) cc_final: 0.6083 (ppp) REVERT: A 515 MET cc_start: 0.8978 (ttp) cc_final: 0.8777 (ttp) REVERT: A 1338 PHE cc_start: 0.7634 (m-80) cc_final: 0.7022 (t80) outliers start: 7 outliers final: 4 residues processed: 87 average time/residue: 0.6744 time to fit residues: 82.1788 Evaluate side-chains 82 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 1.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 295 TYR 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: 0.8980 chunk 29 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 14 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 146 optimal weight: 0.1980 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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: 0.8100 moved from start: 0.5221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13100 Z= 0.123 Angle : 0.428 6.454 17731 Z= 0.216 Chirality : 0.032 0.157 2038 Planarity : 0.003 0.026 2260 Dihedral : 2.843 16.418 1720 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.43 % Allowed : 6.14 % Favored : 93.43 % 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: 3.12 (0.22), residues: 1569 helix: 3.07 (0.15), residues: 1168 sheet: None (None), residues: 0 loop : -1.20 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1296 HIS 0.004 0.000 HIS A1674 PHE 0.008 0.001 PHE A1404 TYR 0.013 0.001 TYR A1089 ARG 0.003 0.000 ARG A 985 *********************** 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 88 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 2.124 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: A 1338 PHE cc_start: 0.7609 (m-80) cc_final: 0.6997 (t80) REVERT: B 251 TYR cc_start: 0.8504 (OUTLIER) cc_final: 0.7501 (t80) REVERT: B 263 MET cc_start: 0.8686 (tmm) cc_final: 0.8357 (tmm) outliers start: 6 outliers final: 4 residues processed: 87 average time/residue: 0.7045 time to fit residues: 86.8474 Evaluate side-chains 84 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 79 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 295 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 0.9980 chunk 142 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 112 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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: 0.8136 moved from start: 0.5503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13100 Z= 0.184 Angle : 0.461 7.336 17731 Z= 0.239 Chirality : 0.033 0.141 2038 Planarity : 0.003 0.027 2260 Dihedral : 2.990 17.362 1720 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.43 % Allowed : 6.29 % 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: 2.98 (0.22), residues: 1569 helix: 2.97 (0.15), residues: 1167 sheet: None (None), residues: 0 loop : -1.24 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 674 HIS 0.008 0.001 HIS A1674 PHE 0.012 0.001 PHE A 745 TYR 0.013 0.001 TYR A1089 ARG 0.005 0.000 ARG A 985 *********************** 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 82 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 76 time to evaluate : 2.175 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: A 1 MET cc_start: 0.6425 (ppp) cc_final: 0.6170 (ppp) REVERT: A 483 MET cc_start: 0.8749 (mmm) cc_final: 0.8098 (mmm) REVERT: B 251 TYR cc_start: 0.8483 (OUTLIER) cc_final: 0.7542 (t80) REVERT: B 263 MET cc_start: 0.8782 (tmm) cc_final: 0.8498 (tmm) outliers start: 6 outliers final: 4 residues processed: 82 average time/residue: 0.6879 time to fit residues: 79.5139 Evaluate side-chains 81 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 2.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 295 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 0.4980 chunk 71 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 158 optimal weight: 6.9990 chunk 145 optimal weight: 8.9990 chunk 126 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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: 0.8156 moved from start: 0.5842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13100 Z= 0.193 Angle : 0.476 10.130 17731 Z= 0.247 Chirality : 0.033 0.149 2038 Planarity : 0.003 0.028 2260 Dihedral : 3.150 17.774 1720 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.43 % Allowed : 6.36 % Favored : 93.21 % 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: 2.84 (0.22), residues: 1569 helix: 2.89 (0.15), residues: 1167 sheet: None (None), residues: 0 loop : -1.35 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 331 HIS 0.005 0.001 HIS A 425 PHE 0.011 0.001 PHE A 745 TYR 0.014 0.001 TYR A1089 ARG 0.004 0.000 ARG A 985 ********************** 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 84 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 2.079 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: A 1 MET cc_start: 0.6564 (ppp) cc_final: 0.6322 (ppp) REVERT: A 483 MET cc_start: 0.8793 (mmm) cc_final: 0.8058 (mmm) REVERT: A 1233 HIS cc_start: 0.8621 (p-80) cc_final: 0.8346 (p-80) REVERT: A 1338 PHE cc_start: 0.7725 (m-80) cc_final: 0.7165 (t80) REVERT: B 251 TYR cc_start: 0.8476 (OUTLIER) cc_final: 0.7544 (t80) REVERT: B 263 MET cc_start: 0.8783 (tmm) cc_final: 0.8484 (tmm) outliers start: 6 outliers final: 5 residues processed: 84 average time/residue: 0.7077 time to fit residues: 83.6377 Evaluate side-chains 82 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 76 time to evaluate : 2.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 295 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 0.0670 chunk 116 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 126 optimal weight: 0.0970 chunk 52 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 7 optimal weight: 9.9990 overall best weight: 0.5116 ------------------------------------------------------------------------------- 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 = 0.3965 r_free = 0.3965 target = 0.075878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.057286 restraints weight = 200165.720| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 4.84 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.5812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13100 Z= 0.116 Angle : 0.448 9.743 17731 Z= 0.226 Chirality : 0.032 0.138 2038 Planarity : 0.003 0.027 2260 Dihedral : 2.966 18.244 1720 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.50 % Allowed : 6.29 % Favored : 93.21 % 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: 3.22 (0.22), residues: 1569 helix: 3.17 (0.15), residues: 1169 sheet: None (None), residues: 0 loop : -1.24 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1296 HIS 0.003 0.001 HIS A1068 PHE 0.010 0.001 PHE A1404 TYR 0.015 0.001 TYR A1089 ARG 0.004 0.000 ARG A 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4636.85 seconds wall clock time: 84 minutes 5.10 seconds (5045.10 seconds total)