Starting phenix.real_space_refine on Fri Dec 8 07:55:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zb5_14584/12_2023/7zb5_14584.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zb5_14584/12_2023/7zb5_14584.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zb5_14584/12_2023/7zb5_14584.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zb5_14584/12_2023/7zb5_14584.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zb5_14584/12_2023/7zb5_14584.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zb5_14584/12_2023/7zb5_14584.pdb" } resolution = 2.8 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= 0.010 sd= 0.037 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: 6 Type Number sf(0) Gaussians P 144 5.49 5 S 134 5.16 5 C 17687 2.51 5 N 5057 2.21 5 O 5528 1.98 5 H 27856 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 1412": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 56406 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 1122 Classifications: {'DNA': 36} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 35} Chain: "B" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 1112 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "D" Number of atoms: 2907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 2907 Classifications: {'peptide': 178} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 169} Chain: "E" Number of atoms: 23043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1447, 23043 Classifications: {'peptide': 1447} Link IDs: {'PTRANS': 73, 'TRANS': 1373} Chain breaks: 9 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "G" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 2908 Classifications: {'peptide': 178} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 169} Chain: "H" Number of atoms: 23080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1449, 23080 Classifications: {'peptide': 1449} Link IDs: {'PTRANS': 73, 'TRANS': 1375} Chain breaks: 9 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "C" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 1122 Classifications: {'DNA': 36} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 35} Chain: "F" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 1112 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Time building chain proxies: 19.92, per 1000 atoms: 0.35 Number of scatterers: 56406 At special positions: 0 Unit cell: (168.381, 190.62, 115.431, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 134 16.00 P 144 15.00 O 5528 8.00 N 5057 7.00 C 17687 6.00 H 27856 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: 35.79 Conformation dependent library (CDL) restraints added in 4.3 seconds 6416 Ramachandran restraints generated. 3208 Oldfield, 0 Emsley, 3208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6180 Finding SS restraints... Secondary structure from input PDB file: 171 helices and 6 sheets defined 67.1% alpha, 6.2% beta 47 base pairs and 114 stacking pairs defined. Time for finding SS restraints: 20.52 Creating SS restraints... Processing helix chain 'D' and resid 96 through 104 Processing helix chain 'D' and resid 143 through 161 Processing helix chain 'D' and resid 186 through 194 Processing helix chain 'D' and resid 234 through 252 removed outlier: 3.769A pdb=" N ILE D 238 " --> pdb=" O VAL D 234 " (cutoff:3.500A) Proline residue: D 247 - end of helix Processing helix chain 'E' and resid 3 through 15 removed outlier: 3.912A pdb=" N ARG E 7 " --> pdb=" O THR E 3 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR E 10 " --> pdb=" O ASP E 6 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE E 11 " --> pdb=" O ARG E 7 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU E 12 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLU E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 35 Processing helix chain 'E' and resid 38 through 47 removed outlier: 3.803A pdb=" N LEU E 42 " --> pdb=" O GLU E 38 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG E 45 " --> pdb=" O ASN E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 52 removed outlier: 3.642A pdb=" N ARG E 51 " --> pdb=" O PRO E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 70 Processing helix chain 'E' and resid 313 through 323 removed outlier: 3.694A pdb=" N ASP E 323 " --> pdb=" O PHE E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 347 removed outlier: 3.585A pdb=" N ARG E 332 " --> pdb=" O GLN E 328 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL E 345 " --> pdb=" O GLU E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 381 Processing helix chain 'E' and resid 395 through 409 Processing helix chain 'E' and resid 413 through 424 Processing helix chain 'E' and resid 447 through 454 removed outlier: 3.785A pdb=" N TYR E 452 " --> pdb=" O VAL E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 457 through 462 Processing helix chain 'E' and resid 465 through 480 removed outlier: 4.960A pdb=" N VAL E 471 " --> pdb=" O MET E 467 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL E 472 " --> pdb=" O ILE E 468 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG E 473 " --> pdb=" O ASP E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 483 through 495 Processing helix chain 'E' and resid 497 through 505 removed outlier: 4.149A pdb=" N ARG E 505 " --> pdb=" O PHE E 501 " (cutoff:3.500A) Processing helix chain 'E' and resid 506 through 522 removed outlier: 4.356A pdb=" N ASP E 510 " --> pdb=" O ARG E 506 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N SER E 511 " --> pdb=" O SER E 507 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 544 removed outlier: 3.931A pdb=" N LYS E 533 " --> pdb=" O ALA E 529 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE E 544 " --> pdb=" O THR E 540 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 555 removed outlier: 3.687A pdb=" N ALA E 555 " --> pdb=" O MET E 551 " (cutoff:3.500A) Processing helix chain 'E' and resid 562 through 567 Processing helix chain 'E' and resid 568 through 576 Proline residue: E 572 - end of helix removed outlier: 3.749A pdb=" N ARG E 575 " --> pdb=" O PRO E 572 " (cutoff:3.500A) Processing helix chain 'E' and resid 578 through 594 removed outlier: 3.519A pdb=" N ARG E 582 " --> pdb=" O ILE E 578 " (cutoff:3.500A) Processing helix chain 'E' and resid 605 through 619 removed outlier: 3.606A pdb=" N LEU E 609 " --> pdb=" O ASN E 605 " (cutoff:3.500A) Processing helix chain 'E' and resid 621 through 643 removed outlier: 3.689A pdb=" N ARG E 642 " --> pdb=" O ARG E 638 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP E 643 " --> pdb=" O LEU E 639 " (cutoff:3.500A) Processing helix chain 'E' and resid 643 through 651 Processing helix chain 'E' and resid 654 through 663 Processing helix chain 'E' and resid 676 through 680 Processing helix chain 'E' and resid 732 through 738 Processing helix chain 'E' and resid 744 through 766 Processing helix chain 'E' and resid 767 through 770 Processing helix chain 'E' and resid 771 through 782 Processing helix chain 'E' and resid 787 through 804 Processing helix chain 'E' and resid 806 through 812 removed outlier: 4.418A pdb=" N ARG E 812 " --> pdb=" O VAL E 809 " (cutoff:3.500A) Processing helix chain 'E' and resid 813 through 823 removed outlier: 3.791A pdb=" N LEU E 817 " --> pdb=" O PHE E 813 " (cutoff:3.500A) Processing helix chain 'E' and resid 829 through 831 No H-bonds generated for 'chain 'E' and resid 829 through 831' Processing helix chain 'E' and resid 832 through 855 removed outlier: 4.133A pdb=" N PHE E 850 " --> pdb=" O LEU E 846 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG E 851 " --> pdb=" O ILE E 847 " (cutoff:3.500A) Processing helix chain 'E' and resid 880 through 899 removed outlier: 3.782A pdb=" N ASP E 891 " --> pdb=" O VAL E 887 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N PHE E 892 " --> pdb=" O VAL E 888 " (cutoff:3.500A) Processing helix chain 'E' and resid 902 through 947 Proline residue: E 909 - end of helix Processing helix chain 'E' and resid 955 through 967 removed outlier: 3.860A pdb=" N LYS E 959 " --> pdb=" O SER E 955 " (cutoff:3.500A) Processing helix chain 'E' and resid 970 through 992 removed outlier: 3.581A pdb=" N GLN E 986 " --> pdb=" O ALA E 982 " (cutoff:3.500A) Processing helix chain 'E' and resid 994 through 1008 Processing helix chain 'E' and resid 1017 through 1022 removed outlier: 3.656A pdb=" N HIS E1021 " --> pdb=" O GLU E1017 " (cutoff:3.500A) Processing helix chain 'E' and resid 1028 through 1032 Processing helix chain 'E' and resid 1047 through 1072 removed outlier: 4.095A pdb=" N LYS E1051 " --> pdb=" O ALA E1047 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA E1052 " --> pdb=" O ARG E1048 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG E1054 " --> pdb=" O ALA E1050 " (cutoff:3.500A) Processing helix chain 'E' and resid 1074 through 1079 Processing helix chain 'E' and resid 1080 through 1092 Proline residue: E1089 - end of helix Processing helix chain 'E' and resid 1099 through 1104 Processing helix chain 'E' and resid 1108 through 1124 removed outlier: 4.232A pdb=" N VAL E1114 " --> pdb=" O GLY E1110 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL E1119 " --> pdb=" O ASP E1115 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE E1120 " --> pdb=" O ALA E1116 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ARG E1121 " --> pdb=" O MET E1117 " (cutoff:3.500A) Processing helix chain 'E' and resid 1125 through 1127 No H-bonds generated for 'chain 'E' and resid 1125 through 1127' Processing helix chain 'E' and resid 1128 through 1130 No H-bonds generated for 'chain 'E' and resid 1128 through 1130' Processing helix chain 'E' and resid 1131 through 1148 Proline residue: E1140 - end of helix removed outlier: 3.523A pdb=" N LYS E1144 " --> pdb=" O PRO E1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 1150 through 1168 Processing helix chain 'E' and resid 1168 through 1180 Processing helix chain 'E' and resid 1181 through 1186 removed outlier: 4.056A pdb=" N ASN E1185 " --> pdb=" O PRO E1182 " (cutoff:3.500A) Processing helix chain 'E' and resid 1189 through 1208 removed outlier: 4.105A pdb=" N ILE E1200 " --> pdb=" O ALA E1196 " (cutoff:3.500A) Processing helix chain 'E' and resid 1209 through 1213 Proline residue: E1213 - end of helix Processing helix chain 'E' and resid 1214 through 1226 removed outlier: 4.953A pdb=" N VAL E1220 " --> pdb=" O ILE E1216 " (cutoff:3.500A) Proline residue: E1221 - end of helix Processing helix chain 'E' and resid 1230 through 1248 removed outlier: 3.642A pdb=" N THR E1243 " --> pdb=" O THR E1239 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LYS E1246 " --> pdb=" O ALA E1242 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU E1247 " --> pdb=" O THR E1243 " (cutoff:3.500A) Processing helix chain 'E' and resid 1249 through 1254 removed outlier: 4.320A pdb=" N ALA E1252 " --> pdb=" O PRO E1249 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE E1254 " --> pdb=" O GLU E1251 " (cutoff:3.500A) Processing helix chain 'E' and resid 1261 through 1280 removed outlier: 3.928A pdb=" N GLN E1277 " --> pdb=" O THR E1273 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU E1278 " --> pdb=" O PHE E1274 " (cutoff:3.500A) Processing helix chain 'E' and resid 1298 through 1315 removed outlier: 3.716A pdb=" N TYR E1314 " --> pdb=" O PHE E1310 " (cutoff:3.500A) Processing helix chain 'E' and resid 1327 through 1349 removed outlier: 3.939A pdb=" N GLN E1331 " --> pdb=" O GLY E1327 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA E1348 " --> pdb=" O ALA E1344 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG E1349 " --> pdb=" O GLU E1345 " (cutoff:3.500A) Processing helix chain 'E' and resid 1365 through 1367 No H-bonds generated for 'chain 'E' and resid 1365 through 1367' Processing helix chain 'E' and resid 1368 through 1380 Processing helix chain 'E' and resid 1393 through 1405 removed outlier: 5.905A pdb=" N ASP E1400 " --> pdb=" O ALA E1397 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR E1405 " --> pdb=" O LEU E1402 " (cutoff:3.500A) Processing helix chain 'E' and resid 1412 through 1418 Processing helix chain 'E' and resid 1418 through 1423 Processing helix chain 'E' and resid 1434 through 1439 removed outlier: 3.595A pdb=" N LYS E1439 " --> pdb=" O HIS E1436 " (cutoff:3.500A) Processing helix chain 'E' and resid 1443 through 1450 Processing helix chain 'E' and resid 1468 through 1480 removed outlier: 4.084A pdb=" N LEU E1472 " --> pdb=" O ASN E1468 " (cutoff:3.500A) Processing helix chain 'E' and resid 1486 through 1494 Processing helix chain 'E' and resid 1494 through 1501 Processing helix chain 'E' and resid 1510 through 1525 Processing helix chain 'E' and resid 1533 through 1538 removed outlier: 3.593A pdb=" N VAL E1537 " --> pdb=" O LEU E1533 " (cutoff:3.500A) Processing helix chain 'E' and resid 1554 through 1567 removed outlier: 4.158A pdb=" N LYS E1566 " --> pdb=" O GLU E1562 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG E1567 " --> pdb=" O ASP E1563 " (cutoff:3.500A) Processing helix chain 'E' and resid 1586 through 1599 removed outlier: 3.841A pdb=" N ALA E1590 " --> pdb=" O HIS E1586 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASN E1599 " --> pdb=" O ARG E1595 " (cutoff:3.500A) Processing helix chain 'E' and resid 1635 through 1645 Processing helix chain 'E' and resid 1673 through 1678 Processing helix chain 'E' and resid 1702 through 1716 removed outlier: 3.815A pdb=" N GLN E1707 " --> pdb=" O ALA E1703 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP E1708 " --> pdb=" O ASN E1704 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER E1715 " --> pdb=" O ASN E1711 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP E1716 " --> pdb=" O LYS E1712 " (cutoff:3.500A) Processing helix chain 'E' and resid 1749 through 1759 removed outlier: 3.682A pdb=" N ASP E1753 " --> pdb=" O ASN E1749 " (cutoff:3.500A) Processing helix chain 'E' and resid 1779 through 1799 removed outlier: 4.119A pdb=" N LYS E1783 " --> pdb=" O THR E1779 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL E1798 " --> pdb=" O VAL E1794 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL E1799 " --> pdb=" O ALA E1795 " (cutoff:3.500A) Processing helix chain 'E' and resid 1810 through 1814 Processing helix chain 'G' and resid 96 through 104 Processing helix chain 'G' and resid 143 through 161 Processing helix chain 'G' and resid 186 through 194 Processing helix chain 'G' and resid 234 through 252 removed outlier: 3.768A pdb=" N ILE G 238 " --> pdb=" O VAL G 234 " (cutoff:3.500A) Proline residue: G 247 - end of helix Processing helix chain 'H' and resid 3 through 15 removed outlier: 3.999A pdb=" N ARG H 7 " --> pdb=" O THR H 3 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE H 11 " --> pdb=" O ARG H 7 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU H 12 " --> pdb=" O LEU H 8 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU H 13 " --> pdb=" O VAL H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 35 Processing helix chain 'H' and resid 38 through 47 removed outlier: 4.012A pdb=" N LEU H 42 " --> pdb=" O GLU H 38 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU H 43 " --> pdb=" O LEU H 39 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG H 45 " --> pdb=" O ASN H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 52 removed outlier: 3.609A pdb=" N ARG H 51 " --> pdb=" O PRO H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 70 Processing helix chain 'H' and resid 313 through 323 removed outlier: 3.662A pdb=" N ASP H 323 " --> pdb=" O PHE H 319 " (cutoff:3.500A) Processing helix chain 'H' and resid 328 through 347 removed outlier: 3.644A pdb=" N ARG H 332 " --> pdb=" O GLN H 328 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL H 345 " --> pdb=" O GLU H 341 " (cutoff:3.500A) Processing helix chain 'H' and resid 357 through 381 Processing helix chain 'H' and resid 395 through 409 Processing helix chain 'H' and resid 413 through 424 removed outlier: 3.847A pdb=" N LEU H 424 " --> pdb=" O ILE H 420 " (cutoff:3.500A) Processing helix chain 'H' and resid 447 through 456 Processing helix chain 'H' and resid 457 through 462 Processing helix chain 'H' and resid 465 through 480 removed outlier: 5.274A pdb=" N VAL H 471 " --> pdb=" O MET H 467 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL H 472 " --> pdb=" O ILE H 468 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG H 473 " --> pdb=" O ASP H 469 " (cutoff:3.500A) Processing helix chain 'H' and resid 483 through 495 Processing helix chain 'H' and resid 497 through 505 removed outlier: 4.350A pdb=" N MET H 503 " --> pdb=" O LYS H 499 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ARG H 505 " --> pdb=" O PHE H 501 " (cutoff:3.500A) Processing helix chain 'H' and resid 506 through 522 removed outlier: 4.288A pdb=" N ASP H 510 " --> pdb=" O ARG H 506 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER H 511 " --> pdb=" O SER H 507 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN H 522 " --> pdb=" O GLU H 518 " (cutoff:3.500A) Processing helix chain 'H' and resid 529 through 544 removed outlier: 3.946A pdb=" N LYS H 533 " --> pdb=" O ALA H 529 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE H 544 " --> pdb=" O THR H 540 " (cutoff:3.500A) Processing helix chain 'H' and resid 544 through 555 removed outlier: 3.875A pdb=" N ALA H 555 " --> pdb=" O MET H 551 " (cutoff:3.500A) Processing helix chain 'H' and resid 562 through 567 Processing helix chain 'H' and resid 568 through 576 Proline residue: H 572 - end of helix removed outlier: 3.681A pdb=" N ARG H 575 " --> pdb=" O PRO H 572 " (cutoff:3.500A) Processing helix chain 'H' and resid 578 through 594 Processing helix chain 'H' and resid 599 through 604 removed outlier: 4.333A pdb=" N TRP H 603 " --> pdb=" O THR H 599 " (cutoff:3.500A) Processing helix chain 'H' and resid 605 through 619 removed outlier: 3.668A pdb=" N LEU H 609 " --> pdb=" O ASN H 605 " (cutoff:3.500A) Processing helix chain 'H' and resid 621 through 643 removed outlier: 3.702A pdb=" N ARG H 642 " --> pdb=" O ARG H 638 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP H 643 " --> pdb=" O LEU H 639 " (cutoff:3.500A) Processing helix chain 'H' and resid 643 through 651 Processing helix chain 'H' and resid 654 through 663 Processing helix chain 'H' and resid 676 through 680 Processing helix chain 'H' and resid 732 through 738 Processing helix chain 'H' and resid 744 through 766 Processing helix chain 'H' and resid 767 through 770 Processing helix chain 'H' and resid 771 through 782 Processing helix chain 'H' and resid 786 through 804 removed outlier: 3.683A pdb=" N GLN H 790 " --> pdb=" O TYR H 786 " (cutoff:3.500A) Processing helix chain 'H' and resid 806 through 812 removed outlier: 4.406A pdb=" N ARG H 812 " --> pdb=" O VAL H 809 " (cutoff:3.500A) Processing helix chain 'H' and resid 813 through 822 removed outlier: 3.675A pdb=" N ILE H 821 " --> pdb=" O LEU H 817 " (cutoff:3.500A) Processing helix chain 'H' and resid 829 through 831 No H-bonds generated for 'chain 'H' and resid 829 through 831' Processing helix chain 'H' and resid 832 through 848 Processing helix chain 'H' and resid 848 through 854 Processing helix chain 'H' and resid 880 through 899 removed outlier: 3.838A pdb=" N ASP H 891 " --> pdb=" O VAL H 887 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N PHE H 892 " --> pdb=" O VAL H 888 " (cutoff:3.500A) Processing helix chain 'H' and resid 902 through 947 Proline residue: H 909 - end of helix Processing helix chain 'H' and resid 955 through 967 removed outlier: 4.041A pdb=" N LYS H 959 " --> pdb=" O SER H 955 " (cutoff:3.500A) Processing helix chain 'H' and resid 970 through 992 removed outlier: 3.526A pdb=" N GLN H 986 " --> pdb=" O ALA H 982 " (cutoff:3.500A) Processing helix chain 'H' and resid 994 through 1008 removed outlier: 3.694A pdb=" N GLU H 998 " --> pdb=" O ARG H 994 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS H 999 " --> pdb=" O GLY H 995 " (cutoff:3.500A) Processing helix chain 'H' and resid 1017 through 1022 removed outlier: 3.522A pdb=" N HIS H1021 " --> pdb=" O GLU H1017 " (cutoff:3.500A) Processing helix chain 'H' and resid 1046 through 1072 removed outlier: 3.904A pdb=" N LYS H1051 " --> pdb=" O ALA H1047 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA H1052 " --> pdb=" O ARG H1048 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG H1054 " --> pdb=" O ALA H1050 " (cutoff:3.500A) Processing helix chain 'H' and resid 1074 through 1079 Processing helix chain 'H' and resid 1079 through 1092 removed outlier: 4.133A pdb=" N ARG H1083 " --> pdb=" O VAL H1079 " (cutoff:3.500A) Proline residue: H1089 - end of helix Processing helix chain 'H' and resid 1099 through 1104 Processing helix chain 'H' and resid 1108 through 1124 removed outlier: 4.270A pdb=" N VAL H1114 " --> pdb=" O GLY H1110 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL H1119 " --> pdb=" O ASP H1115 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE H1120 " --> pdb=" O ALA H1116 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ARG H1121 " --> pdb=" O MET H1117 " (cutoff:3.500A) Processing helix chain 'H' and resid 1125 through 1127 No H-bonds generated for 'chain 'H' and resid 1125 through 1127' Processing helix chain 'H' and resid 1128 through 1130 No H-bonds generated for 'chain 'H' and resid 1128 through 1130' Processing helix chain 'H' and resid 1131 through 1148 Proline residue: H1140 - end of helix removed outlier: 3.694A pdb=" N LYS H1144 " --> pdb=" O PRO H1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 1150 through 1168 Processing helix chain 'H' and resid 1168 through 1180 Processing helix chain 'H' and resid 1181 through 1186 removed outlier: 4.033A pdb=" N ASN H1185 " --> pdb=" O PRO H1182 " (cutoff:3.500A) Processing helix chain 'H' and resid 1189 through 1208 removed outlier: 4.010A pdb=" N ILE H1200 " --> pdb=" O ALA H1196 " (cutoff:3.500A) Processing helix chain 'H' and resid 1209 through 1213 Proline residue: H1213 - end of helix Processing helix chain 'H' and resid 1214 through 1226 removed outlier: 4.882A pdb=" N VAL H1220 " --> pdb=" O ILE H1216 " (cutoff:3.500A) Proline residue: H1221 - end of helix Processing helix chain 'H' and resid 1230 through 1245 Processing helix chain 'H' and resid 1247 through 1254 removed outlier: 4.356A pdb=" N ALA H1252 " --> pdb=" O PRO H1249 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE H1254 " --> pdb=" O GLU H1251 " (cutoff:3.500A) Processing helix chain 'H' and resid 1261 through 1279 removed outlier: 3.966A pdb=" N GLN H1277 " --> pdb=" O THR H1273 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU H1278 " --> pdb=" O PHE H1274 " (cutoff:3.500A) Processing helix chain 'H' and resid 1298 through 1315 removed outlier: 3.719A pdb=" N TYR H1314 " --> pdb=" O PHE H1310 " (cutoff:3.500A) Processing helix chain 'H' and resid 1327 through 1350 removed outlier: 3.907A pdb=" N GLN H1331 " --> pdb=" O GLY H1327 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA H1348 " --> pdb=" O ALA H1344 " (cutoff:3.500A) Processing helix chain 'H' and resid 1365 through 1367 No H-bonds generated for 'chain 'H' and resid 1365 through 1367' Processing helix chain 'H' and resid 1368 through 1380 Processing helix chain 'H' and resid 1393 through 1404 removed outlier: 3.534A pdb=" N LYS H1399 " --> pdb=" O ARG H1396 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ASP H1400 " --> pdb=" O ALA H1397 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU H1402 " --> pdb=" O LYS H1399 " (cutoff:3.500A) Processing helix chain 'H' and resid 1412 through 1418 Processing helix chain 'H' and resid 1418 through 1423 Processing helix chain 'H' and resid 1434 through 1439 Processing helix chain 'H' and resid 1443 through 1450 Processing helix chain 'H' and resid 1468 through 1480 removed outlier: 4.088A pdb=" N LEU H1472 " --> pdb=" O ASN H1468 " (cutoff:3.500A) Processing helix chain 'H' and resid 1486 through 1494 Processing helix chain 'H' and resid 1494 through 1501 Processing helix chain 'H' and resid 1510 through 1525 Processing helix chain 'H' and resid 1533 through 1538 removed outlier: 3.610A pdb=" N VAL H1537 " --> pdb=" O LEU H1533 " (cutoff:3.500A) Processing helix chain 'H' and resid 1554 through 1567 removed outlier: 4.187A pdb=" N LYS H1566 " --> pdb=" O GLU H1562 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG H1567 " --> pdb=" O ASP H1563 " (cutoff:3.500A) Processing helix chain 'H' and resid 1586 through 1598 removed outlier: 3.836A pdb=" N ALA H1590 " --> pdb=" O HIS H1586 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU H1591 " --> pdb=" O ILE H1587 " (cutoff:3.500A) Processing helix chain 'H' and resid 1635 through 1645 removed outlier: 3.534A pdb=" N VAL H1643 " --> pdb=" O ARG H1639 " (cutoff:3.500A) Processing helix chain 'H' and resid 1673 through 1679 Processing helix chain 'H' and resid 1702 through 1716 removed outlier: 3.726A pdb=" N GLN H1707 " --> pdb=" O ALA H1703 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP H1708 " --> pdb=" O ASN H1704 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP H1716 " --> pdb=" O LYS H1712 " (cutoff:3.500A) Processing helix chain 'H' and resid 1749 through 1759 removed outlier: 3.691A pdb=" N ASP H1753 " --> pdb=" O ASN H1749 " (cutoff:3.500A) Processing helix chain 'H' and resid 1779 through 1799 removed outlier: 4.087A pdb=" N LYS H1783 " --> pdb=" O THR H1779 " (cutoff:3.500A) Processing helix chain 'H' and resid 1810 through 1814 Processing sheet with id=AA1, first strand: chain 'D' and resid 107 through 109 removed outlier: 3.622A pdb=" N GLY D 140 " --> pdb=" O ILE D 85 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ILE D 85 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL D 176 " --> pdb=" O GLN D 83 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE D 85 " --> pdb=" O ASN D 174 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASN D 174 " --> pdb=" O ILE D 85 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA D 87 " --> pdb=" O ILE D 172 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE D 172 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL D 89 " --> pdb=" O PHE D 170 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N PHE D 170 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ILE D 175 " --> pdb=" O GLY D 231 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY D 231 " --> pdb=" O ILE D 175 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 1318 through 1320 removed outlier: 4.200A pdb=" N GLY E1318 " --> pdb=" O ARG E1457 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASN E1428 " --> pdb=" O HIS E1456 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LEU E1458 " --> pdb=" O ASN E1428 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N CYS E1430 " --> pdb=" O LEU E1458 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N LEU E1460 " --> pdb=" O CYS E1430 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU E1432 " --> pdb=" O LEU E1460 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N SER E1360 " --> pdb=" O VAL E1408 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N THR E1410 " --> pdb=" O SER E1360 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE E1362 " --> pdb=" O THR E1410 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N THR E1386 " --> pdb=" O ILE E1409 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N SER E1411 " --> pdb=" O THR E1386 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 1544 through 1551 removed outlier: 6.509A pdb=" N ILE E1545 " --> pdb=" O VAL E1771 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N ARG E1773 " --> pdb=" O ILE E1545 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N GLN E1547 " --> pdb=" O ARG E1773 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ILE E1775 " --> pdb=" O GLN E1547 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N TYR E1549 " --> pdb=" O ILE E1775 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU E1668 " --> pdb=" O ILE E1742 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ALA E1667 " --> pdb=" O LEU E1722 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N LEU E1724 " --> pdb=" O ALA E1667 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ILE E1669 " --> pdb=" O LEU E1724 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU E1695 " --> pdb=" O LEU E1723 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 107 through 109 removed outlier: 3.504A pdb=" N ILE G 121 " --> pdb=" O THR G 126 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR G 126 " --> pdb=" O ILE G 121 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY G 140 " --> pdb=" O ILE G 85 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ILE G 85 " --> pdb=" O GLY G 140 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LEU G 82 " --> pdb=" O SER G 178 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N SER G 178 " --> pdb=" O LEU G 82 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N THR G 88 " --> pdb=" O ILE G 172 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ILE G 172 " --> pdb=" O THR G 88 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ASN G 90 " --> pdb=" O PHE G 170 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N PHE G 170 " --> pdb=" O ASN G 90 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ILE G 175 " --> pdb=" O GLY G 231 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY G 231 " --> pdb=" O ILE G 175 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 1318 through 1321 removed outlier: 4.220A pdb=" N GLY H1318 " --> pdb=" O ARG H1457 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR H1461 " --> pdb=" O LEU H1320 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ASN H1428 " --> pdb=" O HIS H1456 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N LEU H1458 " --> pdb=" O ASN H1428 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N CYS H1430 " --> pdb=" O LEU H1458 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N LEU H1460 " --> pdb=" O CYS H1430 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU H1432 " --> pdb=" O LEU H1460 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER H1360 " --> pdb=" O VAL H1408 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N THR H1410 " --> pdb=" O SER H1360 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE H1362 " --> pdb=" O THR H1410 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR H1386 " --> pdb=" O ILE H1409 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N SER H1411 " --> pdb=" O THR H1386 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N TYR H1388 " --> pdb=" O SER H1411 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 1544 through 1551 removed outlier: 3.648A pdb=" N CYS H1551 " --> pdb=" O ILE H1775 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU H1668 " --> pdb=" O ILE H1742 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ALA H1667 " --> pdb=" O LEU H1722 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N LEU H1724 " --> pdb=" O ALA H1667 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ILE H1669 " --> pdb=" O LEU H1724 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU H1695 " --> pdb=" O LEU H1723 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N THR H1725 " --> pdb=" O LEU H1695 " (cutoff:3.500A) 1435 hydrogen bonds defined for protein. 4104 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 120 hydrogen bonds 240 hydrogen bond angles 0 basepair planarities 47 basepair parallelities 114 stacking parallelities Total time for adding SS restraints: 22.69 Time building geometry restraints manager: 37.47 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: 27814 1.03 - 1.23: 78 1.23 - 1.42: 11962 1.42 - 1.62: 17132 1.62 - 1.81: 228 Bond restraints: 57214 Sorted by residual: bond pdb=" C PHE D 205 " pdb=" N PRO D 206 " ideal model delta sigma weight residual 1.334 1.354 -0.021 8.40e-03 1.42e+04 6.17e+00 bond pdb=" C ILE E 495 " pdb=" N PRO E 496 " ideal model delta sigma weight residual 1.337 1.362 -0.025 1.24e-02 6.50e+03 4.17e+00 bond pdb=" C ILE E1289 " pdb=" N PRO E1290 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.96e+00 bond pdb=" N ALA E 2 " pdb=" CA ALA E 2 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N ALA H 2 " pdb=" CA ALA H 2 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.85e+00 ... (remaining 57209 not shown) Histogram of bond angle deviations from ideal: 99.71 - 106.56: 1951 106.56 - 113.42: 67761 113.42 - 120.28: 18770 120.28 - 127.13: 14791 127.13 - 133.99: 560 Bond angle restraints: 103833 Sorted by residual: angle pdb=" C LEU H1247 " pdb=" N VAL H1248 " pdb=" CA VAL H1248 " ideal model delta sigma weight residual 120.24 123.07 -2.83 6.30e-01 2.52e+00 2.02e+01 angle pdb=" C ASN H1682 " pdb=" N THR H1683 " pdb=" CA THR H1683 " ideal model delta sigma weight residual 121.70 129.78 -8.08 1.80e+00 3.09e-01 2.02e+01 angle pdb=" C GLU H1434 " pdb=" N GLY H1435 " pdb=" CA GLY H1435 " ideal model delta sigma weight residual 119.99 123.92 -3.93 1.13e+00 7.83e-01 1.21e+01 angle pdb=" N VAL E 454 " pdb=" CA VAL E 454 " pdb=" C VAL E 454 " ideal model delta sigma weight residual 109.29 104.40 4.89 1.42e+00 4.96e-01 1.18e+01 angle pdb=" C VAL H1248 " pdb=" CA VAL H1248 " pdb=" CB VAL H1248 " ideal model delta sigma weight residual 114.35 110.78 3.57 1.06e+00 8.90e-01 1.13e+01 ... (remaining 103828 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.06: 24561 34.06 - 68.11: 899 68.11 - 102.17: 86 102.17 - 136.22: 0 136.22 - 170.28: 8 Dihedral angle restraints: 25554 sinusoidal: 14815 harmonic: 10739 Sorted by residual: dihedral pdb=" CA GLU H 500 " pdb=" C GLU H 500 " pdb=" N PHE H 501 " pdb=" CA PHE H 501 " ideal model delta harmonic sigma weight residual 180.00 158.16 21.84 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA PHE H1494 " pdb=" C PHE H1494 " pdb=" N ALA H1495 " pdb=" CA ALA H1495 " ideal model delta harmonic sigma weight residual 180.00 -159.41 -20.59 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA PHE E1494 " pdb=" C PHE E1494 " pdb=" N ALA E1495 " pdb=" CA ALA E1495 " ideal model delta harmonic sigma weight residual -180.00 -159.46 -20.54 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 25551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 3096 0.035 - 0.069: 1111 0.069 - 0.104: 332 0.104 - 0.138: 130 0.138 - 0.173: 15 Chirality restraints: 4684 Sorted by residual: chirality pdb=" CA GLU E1088 " pdb=" N GLU E1088 " pdb=" C GLU E1088 " pdb=" CB GLU E1088 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.49e-01 chirality pdb=" P DC B 35 " pdb=" OP1 DC B 35 " pdb=" OP2 DC B 35 " pdb=" O5' DC B 35 " both_signs ideal model delta sigma weight residual True 2.35 -2.51 -0.17 2.00e-01 2.50e+01 6.98e-01 chirality pdb=" P DC F 35 " pdb=" OP1 DC F 35 " pdb=" OP2 DC F 35 " pdb=" O5' DC F 35 " both_signs ideal model delta sigma weight residual True 2.35 -2.51 -0.17 2.00e-01 2.50e+01 6.94e-01 ... (remaining 4681 not shown) Planarity restraints: 7849 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL H1139 " -0.040 5.00e-02 4.00e+02 6.08e-02 5.91e+00 pdb=" N PRO H1140 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO H1140 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO H1140 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E1139 " 0.040 5.00e-02 4.00e+02 6.02e-02 5.79e+00 pdb=" N PRO E1140 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO E1140 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E1140 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E1079 " -0.039 5.00e-02 4.00e+02 5.82e-02 5.42e+00 pdb=" N PRO E1080 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO E1080 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO E1080 " -0.032 5.00e-02 4.00e+02 ... (remaining 7846 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 6691 2.26 - 2.85: 126631 2.85 - 3.43: 145505 3.43 - 4.02: 198216 4.02 - 4.60: 307662 Nonbonded interactions: 784705 Sorted by model distance: nonbonded pdb=" OP1 DG B 25 " pdb=" H LYS E1674 " model vdw 1.680 1.850 nonbonded pdb=" H PHE H1018 " pdb=" OE1 GLN H1111 " model vdw 1.687 1.850 nonbonded pdb=" OD1 ASN E 78 " pdb="HD21 ASN E 361 " model vdw 1.696 1.850 nonbonded pdb=" OD1 ASP E1339 " pdb="HD22 ASN E1428 " model vdw 1.696 1.850 nonbonded pdb=" H PHE E1018 " pdb=" OE1 GLN E1111 " model vdw 1.698 1.850 ... (remaining 784700 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'D' selection = (chain 'G' and (resid 76 through 194 or (resid 195 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 196 through 253)) } ncs_group { reference = (chain 'E' and (resid 2 through 427 or resid 446 through 1817)) selection = (chain 'H' and (resid 2 through 1032 or resid 1046 through 1648 or resid 1664 th \ rough 1817)) } 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.720 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: 0.590 Extract box with map and model: 9.130 Check model and map are aligned: 0.640 Set scattering table: 0.420 Process input model: 160.870 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.180 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:10.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 185.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 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 : 0.004 0.054 29358 Z= 0.267 Angle : 0.652 8.200 40351 Z= 0.355 Chirality : 0.042 0.173 4684 Planarity : 0.005 0.061 4661 Dihedral : 15.876 170.281 11377 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.64 % Allowed : 3.90 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: 0.79 (0.15), residues: 3208 helix: 1.03 (0.12), residues: 1840 sheet: -0.11 (0.34), residues: 231 loop : 0.01 (0.19), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 55 HIS 0.004 0.001 HIS H 418 PHE 0.012 0.001 PHE H1382 TYR 0.019 0.002 TYR H1155 ARG 0.005 0.000 ARG H 410 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6416 Ramachandran restraints generated. 3208 Oldfield, 0 Emsley, 3208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6416 Ramachandran restraints generated. 3208 Oldfield, 0 Emsley, 3208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Residue THR 1174 is missing expected H atoms. Skipping. Residue SER 1261 is missing expected H atoms. Skipping. Residue SER 507 is missing expected H atoms. Skipping. Residue THR 1174 is missing expected H atoms. Skipping. Residue SER 1261 is missing expected H atoms. Skipping. Evaluate side-chains 683 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 665 time to evaluate : 3.767 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 outliers start: 18 outliers final: 6 residues processed: 677 average time/residue: 2.2097 time to fit residues: 1786.1769 Evaluate side-chains 365 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 359 time to evaluate : 3.258 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 3 average time/residue: 1.5115 time to fit residues: 9.9401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 282 optimal weight: 1.9990 chunk 253 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 261 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 159 optimal weight: 8.9990 chunk 194 optimal weight: 4.9990 chunk 303 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 828 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 858 GLN ** H 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1803 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 29358 Z= 0.354 Angle : 0.648 6.296 40351 Z= 0.361 Chirality : 0.043 0.180 4684 Planarity : 0.006 0.054 4661 Dihedral : 18.280 174.621 5028 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.44 % Allowed : 15.14 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: 0.68 (0.15), residues: 3208 helix: 1.06 (0.12), residues: 1889 sheet: -0.28 (0.34), residues: 245 loop : -0.31 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 603 HIS 0.009 0.001 HIS E 853 PHE 0.013 0.002 PHE H1528 TYR 0.015 0.002 TYR H1388 ARG 0.007 0.001 ARG D 113 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6416 Ramachandran restraints generated. 3208 Oldfield, 0 Emsley, 3208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6416 Ramachandran restraints generated. 3208 Oldfield, 0 Emsley, 3208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Residue THR 1174 is missing expected H atoms. Skipping. Residue SER 1261 is missing expected H atoms. Skipping. Residue SER 507 is missing expected H atoms. Skipping. Residue THR 1174 is missing expected H atoms. Skipping. Residue SER 1261 is missing expected H atoms. Skipping. Evaluate side-chains 423 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 327 time to evaluate : 3.310 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 outliers start: 96 outliers final: 37 residues processed: 392 average time/residue: 2.0683 time to fit residues: 983.3981 Evaluate side-chains 326 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 289 time to evaluate : 3.263 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 32 residues processed: 5 average time/residue: 0.8326 time to fit residues: 10.3910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 168 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 252 optimal weight: 5.9990 chunk 206 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 303 optimal weight: 2.9990 chunk 328 optimal weight: 10.0000 chunk 270 optimal weight: 4.9990 chunk 301 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 243 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 601 GLN ** E 828 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 601 GLN H 828 HIS ** H1026 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1803 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 29358 Z= 0.282 Angle : 0.599 6.298 40351 Z= 0.331 Chirality : 0.041 0.155 4684 Planarity : 0.005 0.056 4661 Dihedral : 18.376 173.821 5028 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.08 % Allowed : 16.03 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: 0.76 (0.15), residues: 3208 helix: 1.21 (0.12), residues: 1892 sheet: -0.21 (0.34), residues: 245 loop : -0.47 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 603 HIS 0.007 0.001 HIS E 853 PHE 0.012 0.001 PHE E 850 TYR 0.012 0.001 TYR E 774 ARG 0.008 0.000 ARG E1054 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6416 Ramachandran restraints generated. 3208 Oldfield, 0 Emsley, 3208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6416 Ramachandran restraints generated. 3208 Oldfield, 0 Emsley, 3208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Residue THR 1174 is missing expected H atoms. Skipping. Residue SER 1261 is missing expected H atoms. Skipping. Residue SER 507 is missing expected H atoms. Skipping. Residue THR 1174 is missing expected H atoms. Skipping. Residue SER 1261 is missing expected H atoms. Skipping. Evaluate side-chains 401 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 315 time to evaluate : 3.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 86 outliers final: 48 residues processed: 381 average time/residue: 1.9928 time to fit residues: 940.8635 Evaluate side-chains 330 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 282 time to evaluate : 3.339 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 42 residues processed: 6 average time/residue: 0.7351 time to fit residues: 11.2823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 300 optimal weight: 2.9990 chunk 228 optimal weight: 7.9990 chunk 157 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 145 optimal weight: 4.9990 chunk 204 optimal weight: 7.9990 chunk 304 optimal weight: 8.9990 chunk 322 optimal weight: 6.9990 chunk 159 optimal weight: 6.9990 chunk 289 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 828 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN ** H 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1026 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 29358 Z= 0.484 Angle : 0.697 6.429 40351 Z= 0.389 Chirality : 0.046 0.202 4684 Planarity : 0.006 0.080 4661 Dihedral : 18.592 172.484 5028 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.47 % Allowed : 16.07 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -0.08 (0.14), residues: 3208 helix: 0.60 (0.12), residues: 1891 sheet: -0.34 (0.35), residues: 225 loop : -1.01 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 632 HIS 0.006 0.001 HIS E 853 PHE 0.016 0.002 PHE D 183 TYR 0.019 0.002 TYR H 774 ARG 0.008 0.001 ARG E 473 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6416 Ramachandran restraints generated. 3208 Oldfield, 0 Emsley, 3208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6416 Ramachandran restraints generated. 3208 Oldfield, 0 Emsley, 3208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Residue THR 1174 is missing expected H atoms. Skipping. Residue SER 1261 is missing expected H atoms. Skipping. Residue SER 507 is missing expected H atoms. Skipping. Residue THR 1174 is missing expected H atoms. Skipping. Residue SER 1261 is missing expected H atoms. Skipping. Evaluate side-chains 425 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 300 time to evaluate : 3.301 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 outliers start: 125 outliers final: 66 residues processed: 387 average time/residue: 1.9432 time to fit residues: 923.5389 Evaluate side-chains 333 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 267 time to evaluate : 3.323 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 54 residues processed: 12 average time/residue: 0.6456 time to fit residues: 16.9974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 268 optimal weight: 0.9990 chunk 183 optimal weight: 0.6980 chunk 4 optimal weight: 8.9990 chunk 240 optimal weight: 5.9990 chunk 133 optimal weight: 2.9990 chunk 275 optimal weight: 1.9990 chunk 223 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 164 optimal weight: 2.9990 chunk 289 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 601 GLN E 853 HIS H 601 GLN H 853 HIS ** H1026 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1373 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29358 Z= 0.195 Angle : 0.571 6.337 40351 Z= 0.314 Chirality : 0.039 0.141 4684 Planarity : 0.005 0.049 4661 Dihedral : 18.499 175.156 5028 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.04 % Allowed : 17.93 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: 0.71 (0.15), residues: 3208 helix: 1.27 (0.12), residues: 1890 sheet: -0.24 (0.35), residues: 236 loop : -0.72 (0.19), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 603 HIS 0.007 0.001 HIS D 103 PHE 0.022 0.001 PHE E1094 TYR 0.019 0.001 TYR E1694 ARG 0.005 0.000 ARG E 473 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6416 Ramachandran restraints generated. 3208 Oldfield, 0 Emsley, 3208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6416 Ramachandran restraints generated. 3208 Oldfield, 0 Emsley, 3208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Residue THR 1174 is missing expected H atoms. Skipping. Residue SER 1261 is missing expected H atoms. Skipping. Residue SER 507 is missing expected H atoms. Skipping. Residue THR 1174 is missing expected H atoms. Skipping. Residue SER 1261 is missing expected H atoms. Skipping. Evaluate side-chains 380 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 295 time to evaluate : 3.295 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 outliers start: 85 outliers final: 57 residues processed: 364 average time/residue: 1.9585 time to fit residues: 878.0250 Evaluate side-chains 331 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 274 time to evaluate : 3.314 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 52 residues processed: 8 average time/residue: 0.5532 time to fit residues: 12.0546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 108 optimal weight: 5.9990 chunk 290 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 189 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 323 optimal weight: 7.9990 chunk 268 optimal weight: 4.9990 chunk 149 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 828 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1373 GLN ** H 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1026 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1070 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 29358 Z= 0.413 Angle : 0.650 6.234 40351 Z= 0.361 Chirality : 0.044 0.183 4684 Planarity : 0.005 0.078 4661 Dihedral : 18.561 173.480 5028 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.87 % Allowed : 18.68 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: 0.19 (0.15), residues: 3208 helix: 0.89 (0.12), residues: 1891 sheet: -0.39 (0.35), residues: 233 loop : -1.03 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 632 HIS 0.011 0.001 HIS E 853 PHE 0.015 0.002 PHE G 183 TYR 0.020 0.002 TYR E1694 ARG 0.007 0.001 ARG E 473 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6416 Ramachandran restraints generated. 3208 Oldfield, 0 Emsley, 3208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6416 Ramachandran restraints generated. 3208 Oldfield, 0 Emsley, 3208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Residue THR 1174 is missing expected H atoms. Skipping. Residue SER 1261 is missing expected H atoms. Skipping. Residue SER 507 is missing expected H atoms. Skipping. Residue THR 1174 is missing expected H atoms. Skipping. Residue SER 1261 is missing expected H atoms. Skipping. Evaluate side-chains 378 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 270 time to evaluate : 3.332 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: 108 outliers final: 65 residues processed: 348 average time/residue: 1.9374 time to fit residues: 829.0576 Evaluate side-chains 331 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 266 time to evaluate : 3.288 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 57 residues processed: 10 average time/residue: 0.5482 time to fit residues: 13.8659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 311 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 184 optimal weight: 0.2980 chunk 235 optimal weight: 5.9990 chunk 182 optimal weight: 1.9990 chunk 272 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 chunk 321 optimal weight: 4.9990 chunk 201 optimal weight: 0.8980 chunk 196 optimal weight: 3.9990 chunk 148 optimal weight: 7.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1026 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29358 Z= 0.208 Angle : 0.573 7.376 40351 Z= 0.314 Chirality : 0.039 0.143 4684 Planarity : 0.005 0.065 4661 Dihedral : 18.560 176.206 5028 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.76 % Allowed : 19.54 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: 0.73 (0.15), residues: 3208 helix: 1.31 (0.12), residues: 1893 sheet: -0.31 (0.35), residues: 234 loop : -0.73 (0.19), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 603 HIS 0.014 0.001 HIS H 853 PHE 0.009 0.001 PHE E 850 TYR 0.017 0.001 TYR E 452 ARG 0.008 0.000 ARG E 473 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6416 Ramachandran restraints generated. 3208 Oldfield, 0 Emsley, 3208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6416 Ramachandran restraints generated. 3208 Oldfield, 0 Emsley, 3208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Residue THR 1174 is missing expected H atoms. Skipping. Residue SER 1261 is missing expected H atoms. Skipping. Residue SER 507 is missing expected H atoms. Skipping. Residue THR 1174 is missing expected H atoms. Skipping. Residue SER 1261 is missing expected H atoms. Skipping. Evaluate side-chains 372 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 295 time to evaluate : 3.316 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 outliers start: 77 outliers final: 60 residues processed: 361 average time/residue: 1.8857 time to fit residues: 841.7702 Evaluate side-chains 331 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 271 time to evaluate : 3.264 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 56 residues processed: 6 average time/residue: 0.7468 time to fit residues: 11.1342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 199 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 192 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 204 optimal weight: 10.0000 chunk 219 optimal weight: 7.9990 chunk 159 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 253 optimal weight: 6.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 828 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1373 GLN ** E1599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1026 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 29358 Z= 0.341 Angle : 0.617 7.336 40351 Z= 0.340 Chirality : 0.042 0.169 4684 Planarity : 0.005 0.057 4661 Dihedral : 18.585 175.343 5028 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.97 % Allowed : 20.08 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: 0.49 (0.15), residues: 3208 helix: 1.14 (0.12), residues: 1895 sheet: -0.28 (0.36), residues: 228 loop : -0.92 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 603 HIS 0.010 0.001 HIS H 853 PHE 0.013 0.001 PHE E1192 TYR 0.017 0.002 TYR E1694 ARG 0.008 0.000 ARG E 473 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6416 Ramachandran restraints generated. 3208 Oldfield, 0 Emsley, 3208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6416 Ramachandran restraints generated. 3208 Oldfield, 0 Emsley, 3208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Residue THR 1174 is missing expected H atoms. Skipping. Residue SER 1261 is missing expected H atoms. Skipping. Residue SER 507 is missing expected H atoms. Skipping. Residue THR 1174 is missing expected H atoms. Skipping. Residue SER 1261 is missing expected H atoms. Skipping. Evaluate side-chains 354 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 271 time to evaluate : 3.342 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: 83 outliers final: 64 residues processed: 335 average time/residue: 1.8465 time to fit residues: 767.8352 Evaluate side-chains 321 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 257 time to evaluate : 3.439 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 58 residues processed: 9 average time/residue: 0.5829 time to fit residues: 13.3443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 292 optimal weight: 2.9990 chunk 308 optimal weight: 0.0970 chunk 281 optimal weight: 4.9990 chunk 299 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 235 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 271 optimal weight: 0.8980 chunk 283 optimal weight: 5.9990 chunk 298 optimal weight: 0.6980 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1026 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29358 Z= 0.200 Angle : 0.571 7.943 40351 Z= 0.310 Chirality : 0.039 0.140 4684 Planarity : 0.004 0.049 4661 Dihedral : 18.578 177.277 5028 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.61 % Allowed : 20.58 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: 0.93 (0.15), residues: 3208 helix: 1.49 (0.12), residues: 1890 sheet: -0.26 (0.36), residues: 232 loop : -0.66 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 603 HIS 0.010 0.001 HIS H 853 PHE 0.010 0.001 PHE E1192 TYR 0.016 0.001 TYR E1694 ARG 0.005 0.000 ARG E 994 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6416 Ramachandran restraints generated. 3208 Oldfield, 0 Emsley, 3208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6416 Ramachandran restraints generated. 3208 Oldfield, 0 Emsley, 3208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Residue THR 1174 is missing expected H atoms. Skipping. Residue SER 1261 is missing expected H atoms. Skipping. Residue SER 507 is missing expected H atoms. Skipping. Residue THR 1174 is missing expected H atoms. Skipping. Residue SER 1261 is missing expected H atoms. Skipping. Evaluate side-chains 354 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 281 time to evaluate : 3.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 56 residues processed: 347 average time/residue: 1.8365 time to fit residues: 791.6414 Evaluate side-chains 328 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 272 time to evaluate : 3.271 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 53 residues processed: 5 average time/residue: 0.5399 time to fit residues: 8.8636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 196 optimal weight: 7.9990 chunk 317 optimal weight: 9.9990 chunk 193 optimal weight: 3.9990 chunk 150 optimal weight: 0.7980 chunk 220 optimal weight: 1.9990 chunk 332 optimal weight: 10.0000 chunk 306 optimal weight: 4.9990 chunk 264 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 204 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 828 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1026 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 29358 Z= 0.231 Angle : 0.576 8.127 40351 Z= 0.313 Chirality : 0.039 0.147 4684 Planarity : 0.004 0.048 4661 Dihedral : 18.548 176.746 5028 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.25 % Allowed : 21.15 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: 0.97 (0.15), residues: 3208 helix: 1.53 (0.12), residues: 1890 sheet: -0.22 (0.36), residues: 232 loop : -0.67 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 603 HIS 0.010 0.001 HIS H 853 PHE 0.009 0.001 PHE H1094 TYR 0.015 0.001 TYR H1694 ARG 0.005 0.000 ARG E1048 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6416 Ramachandran restraints generated. 3208 Oldfield, 0 Emsley, 3208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6416 Ramachandran restraints generated. 3208 Oldfield, 0 Emsley, 3208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Residue THR 1174 is missing expected H atoms. Skipping. Residue SER 1261 is missing expected H atoms. Skipping. Residue SER 507 is missing expected H atoms. Skipping. Residue THR 1174 is missing expected H atoms. Skipping. Residue SER 1261 is missing expected H atoms. Skipping. Evaluate side-chains 340 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 277 time to evaluate : 3.343 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: 63 outliers final: 57 residues processed: 335 average time/residue: 1.8373 time to fit residues: 765.7295 Evaluate side-chains 322 residues out of total 2798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 265 time to evaluate : 3.286 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 55 residues processed: 5 average time/residue: 0.5697 time to fit residues: 9.1271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 210 optimal weight: 7.9990 chunk 282 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 244 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 265 optimal weight: 4.9990 chunk 111 optimal weight: 0.5980 chunk 272 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1026 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.142566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.114485 restraints weight = 142872.074| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.80 r_work: 0.3578 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29358 Z= 0.196 Angle : 0.562 8.590 40351 Z= 0.303 Chirality : 0.039 0.137 4684 Planarity : 0.004 0.049 4661 Dihedral : 18.542 177.444 5028 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.22 % Allowed : 21.30 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: 1.17 (0.15), residues: 3208 helix: 1.67 (0.12), residues: 1887 sheet: -0.14 (0.36), residues: 232 loop : -0.55 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 603 HIS 0.010 0.001 HIS H 853 PHE 0.009 0.001 PHE H1588 TYR 0.016 0.001 TYR E 452 ARG 0.004 0.000 ARG H 353 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15508.56 seconds wall clock time: 267 minutes 6.97 seconds (16026.97 seconds total)