Starting phenix.real_space_refine on Thu Oct 10 19:13:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h7g_34520/10_2024/8h7g_34520.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h7g_34520/10_2024/8h7g_34520.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h7g_34520/10_2024/8h7g_34520.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h7g_34520/10_2024/8h7g_34520.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h7g_34520/10_2024/8h7g_34520.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h7g_34520/10_2024/8h7g_34520.cif" } resolution = 3.7 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= -0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 325 5.16 5 C 33598 2.51 5 N 9102 2.21 5 O 9584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 143 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 52609 Number of models: 1 Model: "" Number of chains: 14 Chain: "C" Number of atoms: 26251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3261, 26251 Classifications: {'peptide': 3261} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 144, 'TRANS': 3116} Chain breaks: 34 Chain: "A" Number of atoms: 9158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1168, 9158 Classifications: {'peptide': 1168} Link IDs: {'PTRANS': 60, 'TRANS': 1107} Chain breaks: 5 Chain: "B" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 383 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "D" Number of atoms: 2595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2595 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 18, 'TRANS': 299} Chain breaks: 6 Chain: "E" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1770 Classifications: {'peptide': 225} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 18} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain breaks: 4 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 29 Chain: "G" Number of atoms: 1505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1505 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 10, 'TRANS': 177} Chain breaks: 2 Chain: "H" Number of atoms: 4084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 4084 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 18, 'TRANS': 495} Chain breaks: 6 Chain: "I" Number of atoms: 1419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1419 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 169} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "K" Number of atoms: 2703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2703 Classifications: {'peptide': 352} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 11} Link IDs: {'PTRANS': 14, 'TRANS': 337} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "M" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 957 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 11, 'TRANS': 107} Chain: "O" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 722 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 5, 'TRANS': 85} Chain breaks: 1 Chain: "R" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 605 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "X" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 95 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "L" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 362 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 2, 'TRANS': 41} Time building chain proxies: 20.97, per 1000 atoms: 0.40 Number of scatterers: 52609 At special positions: 0 Unit cell: (178.2, 293.7, 200.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 325 16.00 O 9584 8.00 N 9102 7.00 C 33598 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C1868 " - pdb=" SG CYS C1874 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 9.30 Conformation dependent library (CDL) restraints added in 5.0 seconds 12840 Ramachandran restraints generated. 6420 Oldfield, 0 Emsley, 6420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12638 Finding SS restraints... Secondary structure from input PDB file: 281 helices and 41 sheets defined 51.8% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.76 Creating SS restraints... Processing helix chain 'C' and resid 24 through 26 No H-bonds generated for 'chain 'C' and resid 24 through 26' Processing helix chain 'C' and resid 27 through 33 Processing helix chain 'C' and resid 39 through 45 removed outlier: 3.686A pdb=" N VAL C 45 " --> pdb=" O MET C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 75 removed outlier: 3.705A pdb=" N PHE C 69 " --> pdb=" O ILE C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 98 removed outlier: 3.938A pdb=" N ARG C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS C 98 " --> pdb=" O LEU C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 111 Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.817A pdb=" N SER C 115 " --> pdb=" O ASN C 112 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL C 116 " --> pdb=" O VAL C 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 112 through 116' Processing helix chain 'C' and resid 130 through 143 removed outlier: 3.689A pdb=" N ARG C 134 " --> pdb=" O LEU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 164 Processing helix chain 'C' and resid 164 through 172 Processing helix chain 'C' and resid 229 through 237 removed outlier: 3.892A pdb=" N VAL C 233 " --> pdb=" O PRO C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 250 removed outlier: 3.940A pdb=" N ALA C 248 " --> pdb=" O HIS C 244 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE C 250 " --> pdb=" O VAL C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 292 removed outlier: 3.503A pdb=" N LEU C 288 " --> pdb=" O GLN C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 319 removed outlier: 3.593A pdb=" N LEU C 316 " --> pdb=" O GLY C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 339 removed outlier: 3.723A pdb=" N LEU C 339 " --> pdb=" O ALA C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 351 removed outlier: 4.007A pdb=" N CYS C 350 " --> pdb=" O PHE C 347 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET C 351 " --> pdb=" O ILE C 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 347 through 351' Processing helix chain 'C' and resid 371 through 387 removed outlier: 3.511A pdb=" N ALA C 375 " --> pdb=" O LEU C 371 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR C 376 " --> pdb=" O ARG C 372 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL C 386 " --> pdb=" O LEU C 382 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG C 387 " --> pdb=" O VAL C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 406 removed outlier: 3.824A pdb=" N LYS C 404 " --> pdb=" O GLN C 400 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN C 405 " --> pdb=" O LEU C 401 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE C 406 " --> pdb=" O PHE C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 437 removed outlier: 3.900A pdb=" N ASN C 425 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL C 427 " --> pdb=" O LEU C 423 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ASP C 428 " --> pdb=" O LEU C 424 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N CYS C 429 " --> pdb=" O ASN C 425 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN C 436 " --> pdb=" O SER C 432 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU C 437 " --> pdb=" O LYS C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 462 removed outlier: 3.612A pdb=" N TYR C 462 " --> pdb=" O THR C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 467 Processing helix chain 'C' and resid 542 through 566 Processing helix chain 'C' and resid 582 through 600 removed outlier: 3.610A pdb=" N THR C 586 " --> pdb=" O GLN C 582 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLN C 598 " --> pdb=" O LYS C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 606 removed outlier: 4.322A pdb=" N VAL C 605 " --> pdb=" O ASP C 601 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN C 606 " --> pdb=" O ILE C 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 601 through 606' Processing helix chain 'C' and resid 626 through 637 Processing helix chain 'C' and resid 643 through 654 Processing helix chain 'C' and resid 654 through 665 Processing helix chain 'C' and resid 667 through 674 removed outlier: 4.220A pdb=" N VAL C 671 " --> pdb=" O ALA C 667 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 677 No H-bonds generated for 'chain 'C' and resid 675 through 677' Processing helix chain 'C' and resid 681 through 696 removed outlier: 3.592A pdb=" N ALA C 686 " --> pdb=" O SER C 682 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N THR C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE C 688 " --> pdb=" O LEU C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 700 Processing helix chain 'C' and resid 704 through 724 Processing helix chain 'C' and resid 728 through 733 Processing helix chain 'C' and resid 735 through 747 removed outlier: 4.240A pdb=" N ILE C 739 " --> pdb=" O HIS C 735 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER C 743 " --> pdb=" O ILE C 739 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N MET C 744 " --> pdb=" O VAL C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 768 removed outlier: 3.564A pdb=" N PHE C 757 " --> pdb=" O PRO C 753 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG C 761 " --> pdb=" O PHE C 757 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA C 762 " --> pdb=" O LEU C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 775 through 780 removed outlier: 3.508A pdb=" N LEU C 780 " --> pdb=" O TYR C 776 " (cutoff:3.500A) Processing helix chain 'C' and resid 782 through 794 removed outlier: 3.878A pdb=" N GLY C 789 " --> pdb=" O ASN C 785 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N MET C 792 " --> pdb=" O GLN C 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 800 through 811 removed outlier: 3.737A pdb=" N ASP C 804 " --> pdb=" O GLN C 800 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 827 Proline residue: C 825 - end of helix Processing helix chain 'C' and resid 828 through 835 Processing helix chain 'C' and resid 838 through 855 removed outlier: 3.699A pdb=" N SER C 843 " --> pdb=" O GLN C 839 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASN C 855 " --> pdb=" O LEU C 851 " (cutoff:3.500A) Processing helix chain 'C' and resid 857 through 866 removed outlier: 3.675A pdb=" N LEU C 861 " --> pdb=" O GLN C 857 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 879 Processing helix chain 'C' and resid 887 through 898 removed outlier: 3.608A pdb=" N PHE C 898 " --> pdb=" O VAL C 894 " (cutoff:3.500A) Processing helix chain 'C' and resid 939 through 951 removed outlier: 3.701A pdb=" N GLU C 944 " --> pdb=" O GLU C 940 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 975 removed outlier: 3.572A pdb=" N ARG C 960 " --> pdb=" O GLU C 956 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET C 975 " --> pdb=" O LEU C 971 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 989 removed outlier: 3.552A pdb=" N GLN C 986 " --> pdb=" O HIS C 982 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1029 removed outlier: 3.568A pdb=" N LYS C1016 " --> pdb=" O THR C1012 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR C1017 " --> pdb=" O PRO C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1038 through 1057 Processing helix chain 'C' and resid 1063 through 1067 removed outlier: 4.003A pdb=" N GLN C1067 " --> pdb=" O PRO C1064 " (cutoff:3.500A) Processing helix chain 'C' and resid 1073 through 1077 Processing helix chain 'C' and resid 1090 through 1101 removed outlier: 3.993A pdb=" N ASP C1094 " --> pdb=" O LEU C1090 " (cutoff:3.500A) Processing helix chain 'C' and resid 1107 through 1125 Processing helix chain 'C' and resid 1128 through 1134 removed outlier: 3.779A pdb=" N GLN C1134 " --> pdb=" O GLU C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1136 through 1147 removed outlier: 3.850A pdb=" N TYR C1140 " --> pdb=" O PRO C1136 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU C1143 " --> pdb=" O SER C1139 " (cutoff:3.500A) Processing helix chain 'C' and resid 1148 through 1150 No H-bonds generated for 'chain 'C' and resid 1148 through 1150' Processing helix chain 'C' and resid 1154 through 1171 removed outlier: 3.688A pdb=" N LEU C1171 " --> pdb=" O LEU C1167 " (cutoff:3.500A) Processing helix chain 'C' and resid 1172 through 1179 removed outlier: 3.670A pdb=" N VAL C1176 " --> pdb=" O PRO C1172 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN C1178 " --> pdb=" O THR C1174 " (cutoff:3.500A) Processing helix chain 'C' and resid 1179 through 1194 removed outlier: 3.860A pdb=" N VAL C1190 " --> pdb=" O ALA C1186 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N MET C1191 " --> pdb=" O LEU C1187 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET C1192 " --> pdb=" O LEU C1188 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C1194 " --> pdb=" O VAL C1190 " (cutoff:3.500A) Processing helix chain 'C' and resid 1202 through 1218 Processing helix chain 'C' and resid 1227 through 1246 removed outlier: 3.658A pdb=" N ASP C1244 " --> pdb=" O HIS C1240 " (cutoff:3.500A) Processing helix chain 'C' and resid 1253 through 1271 Processing helix chain 'C' and resid 1282 through 1287 removed outlier: 4.305A pdb=" N LEU C1286 " --> pdb=" O HIS C1282 " (cutoff:3.500A) Processing helix chain 'C' and resid 1301 through 1316 Processing helix chain 'C' and resid 1331 through 1341 removed outlier: 3.963A pdb=" N PHE C1335 " --> pdb=" O GLU C1331 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C1339 " --> pdb=" O PHE C1335 " (cutoff:3.500A) Processing helix chain 'C' and resid 1362 through 1376 removed outlier: 3.870A pdb=" N ARG C1366 " --> pdb=" O LEU C1362 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA C1369 " --> pdb=" O LEU C1365 " (cutoff:3.500A) Processing helix chain 'C' and resid 1383 through 1395 Processing helix chain 'C' and resid 1398 through 1413 Processing helix chain 'C' and resid 1419 through 1427 removed outlier: 3.552A pdb=" N ILE C1423 " --> pdb=" O GLU C1419 " (cutoff:3.500A) Processing helix chain 'C' and resid 1427 through 1433 removed outlier: 3.564A pdb=" N LEU C1431 " --> pdb=" O MET C1427 " (cutoff:3.500A) Processing helix chain 'C' and resid 1441 through 1452 Processing helix chain 'C' and resid 1460 through 1482 removed outlier: 3.699A pdb=" N VAL C1479 " --> pdb=" O MET C1475 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE C1480 " --> pdb=" O GLU C1476 " (cutoff:3.500A) Processing helix chain 'C' and resid 1510 through 1524 removed outlier: 3.509A pdb=" N CYS C1514 " --> pdb=" O GLU C1510 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE C1518 " --> pdb=" O CYS C1514 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE C1521 " --> pdb=" O ILE C1517 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N HIS C1522 " --> pdb=" O ILE C1518 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU C1523 " --> pdb=" O ASN C1519 " (cutoff:3.500A) Processing helix chain 'C' and resid 1528 through 1530 No H-bonds generated for 'chain 'C' and resid 1528 through 1530' Processing helix chain 'C' and resid 1531 through 1547 Processing helix chain 'C' and resid 1555 through 1563 removed outlier: 3.624A pdb=" N LYS C1560 " --> pdb=" O GLU C1556 " (cutoff:3.500A) Processing helix chain 'C' and resid 1565 through 1574 removed outlier: 3.685A pdb=" N THR C1569 " --> pdb=" O HIS C1565 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU C1571 " --> pdb=" O SER C1567 " (cutoff:3.500A) Processing helix chain 'C' and resid 1575 through 1580 Processing helix chain 'C' and resid 1581 through 1593 Processing helix chain 'C' and resid 1597 through 1606 removed outlier: 3.544A pdb=" N ASP C1602 " --> pdb=" O ARG C1598 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N VAL C1603 " --> pdb=" O PRO C1599 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU C1604 " --> pdb=" O LEU C1600 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA C1605 " --> pdb=" O ARG C1601 " (cutoff:3.500A) Processing helix chain 'C' and resid 1607 through 1616 removed outlier: 4.436A pdb=" N PHE C1611 " --> pdb=" O ASN C1607 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU C1616 " --> pdb=" O ILE C1612 " (cutoff:3.500A) Processing helix chain 'C' and resid 1636 through 1652 removed outlier: 3.627A pdb=" N ILE C1646 " --> pdb=" O ALA C1642 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER C1647 " --> pdb=" O ILE C1643 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE C1648 " --> pdb=" O LYS C1644 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASN C1652 " --> pdb=" O ILE C1648 " (cutoff:3.500A) Processing helix chain 'C' and resid 1661 through 1674 removed outlier: 4.243A pdb=" N SER C1665 " --> pdb=" O HIS C1661 " (cutoff:3.500A) Processing helix chain 'C' and resid 1675 through 1677 No H-bonds generated for 'chain 'C' and resid 1675 through 1677' Processing helix chain 'C' and resid 1691 through 1704 removed outlier: 3.867A pdb=" N ALA C1697 " --> pdb=" O PRO C1693 " (cutoff:3.500A) Processing helix chain 'C' and resid 1732 through 1740 removed outlier: 3.676A pdb=" N MET C1736 " --> pdb=" O LEU C1732 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU C1737 " --> pdb=" O LYS C1733 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE C1740 " --> pdb=" O MET C1736 " (cutoff:3.500A) Processing helix chain 'C' and resid 1752 through 1758 removed outlier: 4.150A pdb=" N PHE C1756 " --> pdb=" O LEU C1752 " (cutoff:3.500A) Processing helix chain 'C' and resid 1766 through 1784 removed outlier: 3.578A pdb=" N ILE C1776 " --> pdb=" O VAL C1772 " (cutoff:3.500A) Proline residue: C1779 - end of helix removed outlier: 4.033A pdb=" N SER C1784 " --> pdb=" O ALA C1780 " (cutoff:3.500A) Processing helix chain 'C' and resid 1806 through 1815 removed outlier: 4.101A pdb=" N VAL C1810 " --> pdb=" O SER C1806 " (cutoff:3.500A) Processing helix chain 'C' and resid 1827 through 1842 Processing helix chain 'C' and resid 1858 through 1865 Processing helix chain 'C' and resid 1876 through 1891 removed outlier: 3.608A pdb=" N HIS C1884 " --> pdb=" O LYS C1880 " (cutoff:3.500A) Processing helix chain 'C' and resid 1899 through 1904 removed outlier: 3.675A pdb=" N VAL C1904 " --> pdb=" O ILE C1900 " (cutoff:3.500A) Processing helix chain 'C' and resid 1904 through 1909 removed outlier: 4.695A pdb=" N LEU C1909 " --> pdb=" O PHE C1905 " (cutoff:3.500A) Processing helix chain 'C' and resid 1916 through 1925 removed outlier: 4.907A pdb=" N GLN C1922 " --> pdb=" O ALA C1918 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA C1925 " --> pdb=" O ARG C1921 " (cutoff:3.500A) Processing helix chain 'C' and resid 1941 through 1952 removed outlier: 3.997A pdb=" N TRP C1945 " --> pdb=" O MET C1941 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE C1949 " --> pdb=" O TRP C1945 " (cutoff:3.500A) Processing helix chain 'C' and resid 1961 through 1964 Processing helix chain 'C' and resid 1965 through 1971 Processing helix chain 'C' and resid 1981 through 1993 removed outlier: 3.639A pdb=" N SER C1987 " --> pdb=" O GLN C1983 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY C1993 " --> pdb=" O MET C1989 " (cutoff:3.500A) Processing helix chain 'C' and resid 2005 through 2020 Processing helix chain 'C' and resid 2092 through 2106 removed outlier: 3.610A pdb=" N THR C2096 " --> pdb=" O GLN C2092 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL C2098 " --> pdb=" O THR C2094 " (cutoff:3.500A) Processing helix chain 'C' and resid 2123 through 2132 Processing helix chain 'C' and resid 2143 through 2148 removed outlier: 3.929A pdb=" N GLN C2147 " --> pdb=" O GLU C2143 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TRP C2148 " --> pdb=" O LEU C2144 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2143 through 2148' Processing helix chain 'C' and resid 2163 through 2180 removed outlier: 3.944A pdb=" N SER C2175 " --> pdb=" O LEU C2171 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU C2178 " --> pdb=" O LEU C2174 " (cutoff:3.500A) Processing helix chain 'C' and resid 2190 through 2197 Processing helix chain 'C' and resid 2209 through 2220 removed outlier: 3.772A pdb=" N HIS C2213 " --> pdb=" O LEU C2209 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER C2214 " --> pdb=" O ARG C2210 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LEU C2216 " --> pdb=" O VAL C2212 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N SER C2217 " --> pdb=" O HIS C2213 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG C2218 " --> pdb=" O SER C2214 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C2219 " --> pdb=" O LEU C2215 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET C2220 " --> pdb=" O LEU C2216 " (cutoff:3.500A) Processing helix chain 'C' and resid 2237 through 2252 removed outlier: 3.733A pdb=" N ILE C2250 " --> pdb=" O VAL C2246 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR C2251 " --> pdb=" O GLY C2247 " (cutoff:3.500A) Processing helix chain 'C' and resid 2266 through 2282 removed outlier: 3.729A pdb=" N ASN C2282 " --> pdb=" O ALA C2278 " (cutoff:3.500A) Processing helix chain 'C' and resid 2289 through 2305 removed outlier: 3.624A pdb=" N PHE C2293 " --> pdb=" O LEU C2289 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU C2305 " --> pdb=" O VAL C2301 " (cutoff:3.500A) Processing helix chain 'C' and resid 2317 through 2332 removed outlier: 3.694A pdb=" N LEU C2326 " --> pdb=" O GLU C2322 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER C2327 " --> pdb=" O LEU C2323 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU C2328 " --> pdb=" O VAL C2324 " (cutoff:3.500A) Processing helix chain 'C' and resid 2342 through 2357 removed outlier: 5.057A pdb=" N GLN C2348 " --> pdb=" O LYS C2344 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ALA C2349 " --> pdb=" O ASN C2345 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU C2351 " --> pdb=" O ILE C2347 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS C2357 " --> pdb=" O SER C2353 " (cutoff:3.500A) Processing helix chain 'C' and resid 2362 through 2376 Processing helix chain 'C' and resid 2388 through 2399 Processing helix chain 'C' and resid 2412 through 2427 Processing helix chain 'C' and resid 2439 through 2446 removed outlier: 3.686A pdb=" N GLY C2446 " --> pdb=" O ALA C2442 " (cutoff:3.500A) Processing helix chain 'C' and resid 2451 through 2464 removed outlier: 3.741A pdb=" N VAL C2461 " --> pdb=" O LYS C2457 " (cutoff:3.500A) Processing helix chain 'C' and resid 2469 through 2477 removed outlier: 3.788A pdb=" N ARG C2473 " --> pdb=" O ARG C2469 " (cutoff:3.500A) Processing helix chain 'C' and resid 2491 through 2501 removed outlier: 3.543A pdb=" N CYS C2495 " --> pdb=" O TRP C2491 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU C2497 " --> pdb=" O LYS C2493 " (cutoff:3.500A) Processing helix chain 'C' and resid 2522 through 2527 removed outlier: 3.734A pdb=" N ASN C2526 " --> pdb=" O THR C2522 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU C2527 " --> pdb=" O ASN C2523 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2522 through 2527' Processing helix chain 'C' and resid 2587 through 2603 Processing helix chain 'C' and resid 2607 through 2621 removed outlier: 3.887A pdb=" N SER C2612 " --> pdb=" O GLY C2608 " (cutoff:3.500A) Processing helix chain 'C' and resid 2621 through 2640 Proline residue: C2634 - end of helix removed outlier: 3.813A pdb=" N ILE C2639 " --> pdb=" O ARG C2635 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU C2640 " --> pdb=" O LEU C2636 " (cutoff:3.500A) Processing helix chain 'C' and resid 2644 through 2657 removed outlier: 3.860A pdb=" N SER C2653 " --> pdb=" O ALA C2649 " (cutoff:3.500A) Proline residue: C2654 - end of helix Processing helix chain 'C' and resid 2662 through 2666 removed outlier: 4.395A pdb=" N ASP C2666 " --> pdb=" O VAL C2663 " (cutoff:3.500A) Processing helix chain 'C' and resid 2672 through 2679 removed outlier: 3.668A pdb=" N MET C2679 " --> pdb=" O PHE C2675 " (cutoff:3.500A) Processing helix chain 'C' and resid 2690 through 2700 removed outlier: 3.900A pdb=" N LYS C2694 " --> pdb=" O PRO C2690 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR C2695 " --> pdb=" O CYS C2691 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS C2698 " --> pdb=" O LYS C2694 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR C2699 " --> pdb=" O TYR C2695 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS C2700 " --> pdb=" O LEU C2696 " (cutoff:3.500A) Processing helix chain 'C' and resid 2702 through 2714 Processing helix chain 'C' and resid 2742 through 2755 Processing helix chain 'C' and resid 2757 through 2769 removed outlier: 3.665A pdb=" N LYS C2767 " --> pdb=" O GLY C2763 " (cutoff:3.500A) Processing helix chain 'C' and resid 2773 through 2783 removed outlier: 4.093A pdb=" N HIS C2783 " --> pdb=" O ALA C2779 " (cutoff:3.500A) Processing helix chain 'C' and resid 2785 through 2807 removed outlier: 3.647A pdb=" N GLU C2805 " --> pdb=" O LYS C2801 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ARG C2806 " --> pdb=" O LYS C2802 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER C2807 " --> pdb=" O GLU C2803 " (cutoff:3.500A) Processing helix chain 'C' and resid 2814 through 2830 removed outlier: 4.323A pdb=" N GLN C2818 " --> pdb=" O PHE C2814 " (cutoff:3.500A) Processing helix chain 'C' and resid 2833 through 2841 removed outlier: 3.580A pdb=" N LEU C2837 " --> pdb=" O GLN C2833 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY C2841 " --> pdb=" O LEU C2837 " (cutoff:3.500A) Processing helix chain 'C' and resid 2848 through 2856 Processing helix chain 'C' and resid 2857 through 2859 No H-bonds generated for 'chain 'C' and resid 2857 through 2859' Processing helix chain 'C' and resid 2862 through 2868 removed outlier: 3.847A pdb=" N LYS C2866 " --> pdb=" O TRP C2862 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU C2867 " --> pdb=" O THR C2863 " (cutoff:3.500A) Processing helix chain 'C' and resid 2869 through 2875 Processing helix chain 'C' and resid 2880 through 2894 removed outlier: 4.137A pdb=" N VAL C2884 " --> pdb=" O MET C2880 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY C2889 " --> pdb=" O ASN C2885 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR C2890 " --> pdb=" O MET C2886 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU C2891 " --> pdb=" O TYR C2887 " (cutoff:3.500A) Processing helix chain 'C' and resid 2903 through 2920 Processing helix chain 'C' and resid 2927 through 2929 No H-bonds generated for 'chain 'C' and resid 2927 through 2929' Processing helix chain 'C' and resid 2930 through 2953 removed outlier: 4.313A pdb=" N GLN C2938 " --> pdb=" O LEU C2934 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLN C2939 " --> pdb=" O GLN C2935 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN C2944 " --> pdb=" O ILE C2940 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN C2948 " --> pdb=" O GLN C2944 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE C2949 " --> pdb=" O GLU C2945 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASN C2950 " --> pdb=" O ALA C2946 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA C2951 " --> pdb=" O ALA C2947 " (cutoff:3.500A) Processing helix chain 'C' and resid 2954 through 2958 removed outlier: 3.655A pdb=" N LEU C2958 " --> pdb=" O PRO C2955 " (cutoff:3.500A) Processing helix chain 'C' and resid 2960 through 2963 Processing helix chain 'C' and resid 2964 through 2977 removed outlier: 3.503A pdb=" N ARG C2977 " --> pdb=" O THR C2973 " (cutoff:3.500A) Processing helix chain 'C' and resid 2984 through 3000 removed outlier: 3.653A pdb=" N TRP C2988 " --> pdb=" O ASP C2984 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N HIS C2998 " --> pdb=" O TRP C2994 " (cutoff:3.500A) Processing helix chain 'C' and resid 3001 through 3007 removed outlier: 4.007A pdb=" N TRP C3005 " --> pdb=" O GLY C3001 " (cutoff:3.500A) Processing helix chain 'C' and resid 3028 through 3051 Processing helix chain 'C' and resid 3054 through 3062 Processing helix chain 'C' and resid 3063 through 3067 Processing helix chain 'C' and resid 3071 through 3089 Processing helix chain 'C' and resid 3097 through 3104 Processing helix chain 'C' and resid 3119 through 3131 removed outlier: 3.687A pdb=" N ALA C3123 " --> pdb=" O ALA C3119 " (cutoff:3.500A) Processing helix chain 'C' and resid 3137 through 3147 removed outlier: 3.997A pdb=" N ALA C3141 " --> pdb=" O GLU C3137 " (cutoff:3.500A) Processing helix chain 'C' and resid 3152 through 3167 removed outlier: 3.561A pdb=" N ILE C3166 " --> pdb=" O TYR C3162 " (cutoff:3.500A) Processing helix chain 'C' and resid 3172 through 3174 No H-bonds generated for 'chain 'C' and resid 3172 through 3174' Processing helix chain 'C' and resid 3175 through 3187 removed outlier: 3.658A pdb=" N ALA C3179 " --> pdb=" O LEU C3175 " (cutoff:3.500A) Processing helix chain 'C' and resid 3195 through 3207 removed outlier: 3.803A pdb=" N SER C3207 " --> pdb=" O LEU C3203 " (cutoff:3.500A) Processing helix chain 'C' and resid 3213 through 3223 Processing helix chain 'C' and resid 3227 through 3232 removed outlier: 3.759A pdb=" N GLN C3230 " --> pdb=" O PRO C3227 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU C3232 " --> pdb=" O ILE C3229 " (cutoff:3.500A) Processing helix chain 'C' and resid 3234 through 3244 removed outlier: 3.759A pdb=" N GLY C3244 " --> pdb=" O THR C3240 " (cutoff:3.500A) Processing helix chain 'C' and resid 3247 through 3249 No H-bonds generated for 'chain 'C' and resid 3247 through 3249' Processing helix chain 'C' and resid 3250 through 3261 removed outlier: 3.535A pdb=" N ILE C3254 " --> pdb=" O LEU C3250 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL C3260 " --> pdb=" O GLN C3256 " (cutoff:3.500A) Processing helix chain 'C' and resid 3266 through 3283 removed outlier: 3.902A pdb=" N ARG C3283 " --> pdb=" O GLU C3279 " (cutoff:3.500A) Processing helix chain 'C' and resid 3294 through 3309 removed outlier: 4.158A pdb=" N GLU C3309 " --> pdb=" O HIS C3305 " (cutoff:3.500A) Processing helix chain 'C' and resid 3311 through 3324 Processing helix chain 'C' and resid 3325 through 3329 removed outlier: 3.848A pdb=" N ARG C3329 " --> pdb=" O VAL C3326 " (cutoff:3.500A) Processing helix chain 'C' and resid 3331 through 3354 Processing helix chain 'C' and resid 3364 through 3379 Processing helix chain 'C' and resid 3419 through 3425 removed outlier: 4.333A pdb=" N ASP C3423 " --> pdb=" O GLN C3419 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP C3425 " --> pdb=" O THR C3421 " (cutoff:3.500A) Processing helix chain 'C' and resid 3434 through 3452 removed outlier: 3.825A pdb=" N LYS C3440 " --> pdb=" O ASN C3436 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LYS C3443 " --> pdb=" O SER C3439 " (cutoff:3.500A) Processing helix chain 'C' and resid 3453 through 3455 No H-bonds generated for 'chain 'C' and resid 3453 through 3455' Processing helix chain 'C' and resid 3535 through 3539 Processing helix chain 'C' and resid 3540 through 3553 removed outlier: 3.659A pdb=" N ARG C3544 " --> pdb=" O ARG C3540 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL C3545 " --> pdb=" O ARG C3541 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU C3546 " --> pdb=" O GLU C3542 " (cutoff:3.500A) Processing helix chain 'C' and resid 3554 through 3557 Processing helix chain 'C' and resid 3560 through 3565 removed outlier: 3.956A pdb=" N ARG C3565 " --> pdb=" O GLU C3561 " (cutoff:3.500A) Processing helix chain 'C' and resid 3593 through 3604 removed outlier: 3.658A pdb=" N LYS C3604 " --> pdb=" O ARG C3600 " (cutoff:3.500A) Processing helix chain 'C' and resid 3609 through 3624 removed outlier: 3.502A pdb=" N SER C3613 " --> pdb=" O ASP C3609 " (cutoff:3.500A) Processing helix chain 'C' and resid 3630 through 3645 removed outlier: 3.627A pdb=" N LEU C3634 " --> pdb=" O SER C3630 " (cutoff:3.500A) Processing helix chain 'C' and resid 3649 through 3659 removed outlier: 3.522A pdb=" N GLU C3653 " --> pdb=" O SER C3649 " (cutoff:3.500A) Processing helix chain 'C' and resid 3661 through 3686 removed outlier: 3.553A pdb=" N LEU C3678 " --> pdb=" O ILE C3674 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU C3686 " --> pdb=" O ALA C3682 " (cutoff:3.500A) Processing helix chain 'C' and resid 3732 through 3740 removed outlier: 3.753A pdb=" N THR C3740 " --> pdb=" O SER C3736 " (cutoff:3.500A) Processing helix chain 'C' and resid 3745 through 3761 removed outlier: 3.668A pdb=" N THR C3749 " --> pdb=" O SER C3745 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET C3752 " --> pdb=" O LEU C3748 " (cutoff:3.500A) Processing helix chain 'C' and resid 3766 through 3785 removed outlier: 3.762A pdb=" N ASP C3776 " --> pdb=" O THR C3772 " (cutoff:3.500A) Processing helix chain 'C' and resid 3804 through 3824 removed outlier: 4.018A pdb=" N VAL C3808 " --> pdb=" O SER C3804 " (cutoff:3.500A) Processing helix chain 'C' and resid 3834 through 3843 removed outlier: 3.900A pdb=" N ASN C3843 " --> pdb=" O VAL C3839 " (cutoff:3.500A) Processing helix chain 'C' and resid 3844 through 3849 removed outlier: 3.521A pdb=" N LEU C3848 " --> pdb=" O SER C3844 " (cutoff:3.500A) Processing helix chain 'C' and resid 3852 through 3856 Processing helix chain 'A' and resid 429 through 433 Processing helix chain 'A' and resid 620 through 624 removed outlier: 3.749A pdb=" N CYS A 624 " --> pdb=" O PRO A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 827 Processing helix chain 'A' and resid 838 through 845 removed outlier: 3.512A pdb=" N LEU A 843 " --> pdb=" O ALA A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 853 Processing helix chain 'A' and resid 1134 through 1152 removed outlier: 3.819A pdb=" N HIS A1138 " --> pdb=" O SER A1134 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A1141 " --> pdb=" O ASP A1137 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER A1150 " --> pdb=" O MET A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1165 Processing helix chain 'A' and resid 1178 through 1185 removed outlier: 4.189A pdb=" N ASN A1183 " --> pdb=" O GLU A1180 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET A1185 " --> pdb=" O PHE A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1197 Processing helix chain 'A' and resid 1200 through 1216 removed outlier: 4.118A pdb=" N ARG A1212 " --> pdb=" O LEU A1208 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR A1215 " --> pdb=" O ILE A1211 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 40 Processing helix chain 'B' and resid 41 through 43 No H-bonds generated for 'chain 'B' and resid 41 through 43' Processing helix chain 'B' and resid 46 through 57 removed outlier: 3.727A pdb=" N GLU B 57 " --> pdb=" O PHE B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 71 Processing helix chain 'D' and resid 3 through 22 removed outlier: 3.571A pdb=" N ARG D 22 " --> pdb=" O SER D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 48 removed outlier: 3.756A pdb=" N TYR D 41 " --> pdb=" O PHE D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 67 removed outlier: 3.664A pdb=" N LYS D 66 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 67' Processing helix chain 'D' and resid 67 through 72 Processing helix chain 'D' and resid 121 through 131 removed outlier: 3.971A pdb=" N VAL D 125 " --> pdb=" O PRO D 121 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS D 130 " --> pdb=" O ASP D 126 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER D 131 " --> pdb=" O LEU D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 182 removed outlier: 4.208A pdb=" N LEU D 173 " --> pdb=" O THR D 169 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL D 177 " --> pdb=" O LEU D 173 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N HIS D 178 " --> pdb=" O ILE D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 203 Processing helix chain 'D' and resid 213 through 225 removed outlier: 4.254A pdb=" N CYS D 217 " --> pdb=" O ILE D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 238 Processing helix chain 'D' and resid 244 through 248 Processing helix chain 'D' and resid 263 through 273 Processing helix chain 'D' and resid 398 through 416 removed outlier: 3.672A pdb=" N ALA D 402 " --> pdb=" O SER D 398 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU D 403 " --> pdb=" O LYS D 399 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG D 404 " --> pdb=" O THR D 400 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN D 415 " --> pdb=" O GLU D 411 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 34 Processing helix chain 'E' and resid 35 through 37 No H-bonds generated for 'chain 'E' and resid 35 through 37' Processing helix chain 'E' and resid 45 through 74 removed outlier: 3.999A pdb=" N GLU E 68 " --> pdb=" O GLN E 64 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL E 69 " --> pdb=" O GLN E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 87 removed outlier: 3.787A pdb=" N MET E 87 " --> pdb=" O LEU E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 103 Processing helix chain 'E' and resid 111 through 124 removed outlier: 3.633A pdb=" N ASP E 115 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU E 124 " --> pdb=" O LEU E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 175 Processing helix chain 'E' and resid 181 through 188 Processing helix chain 'E' and resid 197 through 204 Processing helix chain 'E' and resid 216 through 245 removed outlier: 3.501A pdb=" N ALA E 222 " --> pdb=" O MET E 218 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP E 242 " --> pdb=" O LEU E 238 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET E 243 " --> pdb=" O VAL E 239 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL E 244 " --> pdb=" O ARG E 240 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR E 245 " --> pdb=" O GLN E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 295 removed outlier: 4.076A pdb=" N ILE E 286 " --> pdb=" O GLN E 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 112 removed outlier: 3.756A pdb=" N HIS G 111 " --> pdb=" O LYS G 108 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG G 112 " --> pdb=" O PHE G 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 108 through 112' Processing helix chain 'G' and resid 147 through 163 removed outlier: 3.955A pdb=" N GLY G 153 " --> pdb=" O GLY G 149 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG G 154 " --> pdb=" O GLN G 150 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLU G 161 " --> pdb=" O VAL G 157 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N HIS G 162 " --> pdb=" O THR G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 193 removed outlier: 3.537A pdb=" N ARG G 193 " --> pdb=" O SER G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 218 through 228 Processing helix chain 'G' and resid 252 through 262 Processing helix chain 'G' and resid 276 through 288 removed outlier: 3.962A pdb=" N LEU G 280 " --> pdb=" O ASN G 276 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE G 281 " --> pdb=" O MET G 277 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN G 285 " --> pdb=" O PHE G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 307 removed outlier: 4.220A pdb=" N LEU G 299 " --> pdb=" O THR G 295 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN G 300 " --> pdb=" O VAL G 296 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU G 302 " --> pdb=" O ALA G 298 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG G 303 " --> pdb=" O LEU G 299 " (cutoff:3.500A) Processing helix chain 'G' and resid 312 through 327 removed outlier: 3.720A pdb=" N LEU G 316 " --> pdb=" O ASN G 312 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN G 317 " --> pdb=" O HIS G 313 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN G 318 " --> pdb=" O GLU G 314 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA G 327 " --> pdb=" O ARG G 323 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 20 removed outlier: 3.580A pdb=" N ILE H 9 " --> pdb=" O ARG H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 50 removed outlier: 3.937A pdb=" N MET H 42 " --> pdb=" O THR H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 82 removed outlier: 3.558A pdb=" N ARG H 78 " --> pdb=" O PHE H 74 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 94 No H-bonds generated for 'chain 'H' and resid 92 through 94' Processing helix chain 'H' and resid 95 through 111 removed outlier: 3.738A pdb=" N LEU H 99 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL H 101 " --> pdb=" O TYR H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 123 removed outlier: 3.637A pdb=" N PHE H 123 " --> pdb=" O PHE H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 143 Processing helix chain 'H' and resid 145 through 152 Processing helix chain 'H' and resid 154 through 160 Processing helix chain 'H' and resid 169 through 179 Processing helix chain 'H' and resid 184 through 194 removed outlier: 3.860A pdb=" N VAL H 190 " --> pdb=" O ALA H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 237 through 247 removed outlier: 3.594A pdb=" N VAL H 241 " --> pdb=" O ALA H 237 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 85 removed outlier: 4.135A pdb=" N LEU I 79 " --> pdb=" O ARG I 75 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA I 85 " --> pdb=" O ALA I 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 150 through 170 removed outlier: 3.687A pdb=" N GLN I 156 " --> pdb=" O HIS I 152 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY I 170 " --> pdb=" O LEU I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 175 through 205 removed outlier: 3.654A pdb=" N LEU I 179 " --> pdb=" O ASN I 175 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU I 204 " --> pdb=" O ALA I 200 " (cutoff:3.500A) Processing helix chain 'I' and resid 214 through 224 removed outlier: 3.576A pdb=" N PHE I 220 " --> pdb=" O MET I 216 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS I 221 " --> pdb=" O GLU I 217 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU I 222 " --> pdb=" O GLN I 218 " (cutoff:3.500A) Processing helix chain 'I' and resid 228 through 239 removed outlier: 4.258A pdb=" N GLN I 232 " --> pdb=" O VAL I 228 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS I 233 " --> pdb=" O LEU I 229 " (cutoff:3.500A) Processing helix chain 'I' and resid 239 through 261 Processing helix chain 'K' and resid 14 through 25 Processing helix chain 'K' and resid 32 through 56 removed outlier: 3.813A pdb=" N PHE K 54 " --> pdb=" O ASN K 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 74 removed outlier: 3.855A pdb=" N PHE K 68 " --> pdb=" O THR K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 167 Processing helix chain 'K' and resid 175 through 186 Processing helix chain 'K' and resid 193 through 204 Processing helix chain 'K' and resid 212 through 225 Processing helix chain 'K' and resid 235 through 247 removed outlier: 4.032A pdb=" N GLY K 240 " --> pdb=" O ARG K 236 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N SER K 241 " --> pdb=" O CYS K 237 " (cutoff:3.500A) Processing helix chain 'K' and resid 261 through 278 removed outlier: 3.550A pdb=" N ASP K 265 " --> pdb=" O TRP K 261 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N HIS K 278 " --> pdb=" O ILE K 274 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 298 removed outlier: 3.663A pdb=" N LEU K 293 " --> pdb=" O ILE K 289 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN K 294 " --> pdb=" O LEU K 290 " (cutoff:3.500A) Processing helix chain 'K' and resid 303 through 309 Processing helix chain 'K' and resid 314 through 318 removed outlier: 3.905A pdb=" N LEU K 317 " --> pdb=" O LEU K 314 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY K 318 " --> pdb=" O HIS K 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 314 through 318' Processing helix chain 'K' and resid 322 through 327 Processing helix chain 'K' and resid 333 through 338 removed outlier: 3.677A pdb=" N LEU K 337 " --> pdb=" O TYR K 333 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN K 338 " --> pdb=" O TRP K 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 333 through 338' Processing helix chain 'K' and resid 353 through 360 removed outlier: 3.660A pdb=" N LYS K 357 " --> pdb=" O ALA K 353 " (cutoff:3.500A) Processing helix chain 'K' and resid 362 through 370 Processing helix chain 'K' and resid 401 through 410 removed outlier: 3.659A pdb=" N GLY K 410 " --> pdb=" O SER K 406 " (cutoff:3.500A) Processing helix chain 'K' and resid 414 through 419 removed outlier: 3.548A pdb=" N LEU K 419 " --> pdb=" O PHE K 415 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 26 removed outlier: 3.688A pdb=" N MET M 18 " --> pdb=" O LYS M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 32 through 61 removed outlier: 4.353A pdb=" N ILE M 36 " --> pdb=" O GLU M 32 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASN M 37 " --> pdb=" O PRO M 33 " (cutoff:3.500A) Processing helix chain 'M' and resid 68 through 82 removed outlier: 3.579A pdb=" N GLN M 81 " --> pdb=" O CYS M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 90 through 100 removed outlier: 3.519A pdb=" N ASP M 94 " --> pdb=" O ASP M 90 " (cutoff:3.500A) Processing helix chain 'O' and resid 118 through 126 removed outlier: 3.710A pdb=" N GLN O 122 " --> pdb=" O ASP O 118 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU O 124 " --> pdb=" O LEU O 120 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR O 126 " --> pdb=" O GLN O 122 " (cutoff:3.500A) Processing helix chain 'O' and resid 131 through 143 removed outlier: 3.648A pdb=" N THR O 135 " --> pdb=" O PRO O 131 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR O 137 " --> pdb=" O ALA O 133 " (cutoff:3.500A) Processing helix chain 'O' and resid 153 through 175 removed outlier: 3.589A pdb=" N ILE O 166 " --> pdb=" O PHE O 162 " (cutoff:3.500A) Processing helix chain 'O' and resid 196 through 200 Processing helix chain 'R' and resid 63 through 69 removed outlier: 3.505A pdb=" N VAL R 67 " --> pdb=" O LEU R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 104 removed outlier: 3.586A pdb=" N GLU R 81 " --> pdb=" O ASP R 77 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU R 82 " --> pdb=" O GLU R 78 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N MET R 83 " --> pdb=" O ASP R 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 121 Processing helix chain 'X' and resid 3 through 7 removed outlier: 4.098A pdb=" N UNK X 7 " --> pdb=" O UNK X 4 " (cutoff:3.500A) Processing helix chain 'L' and resid 541 through 549 Processing sheet with id=AA1, first strand: chain 'C' and resid 749 through 750 removed outlier: 4.341A pdb=" N ALA C 750 " --> pdb=" O SER C1199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 923 through 927 Processing sheet with id=AA3, first strand: chain 'C' and resid 3498 through 3505 removed outlier: 6.926A pdb=" N MET C3500 " --> pdb=" O ARG C3519 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ARG C3519 " --> pdb=" O MET C3500 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ARG C3502 " --> pdb=" O TYR C3517 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR C3517 " --> pdb=" O ARG C3502 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG C3514 " --> pdb=" O VAL C3530 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 3590 through 3592 Processing sheet with id=AA5, first strand: chain 'A' and resid 1105 through 1107 removed outlier: 3.527A pdb=" N GLN A1105 " --> pdb=" O VAL A1118 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR A1107 " --> pdb=" O SER A1116 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A1117 " --> pdb=" O LEU A1129 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU A 3 " --> pdb=" O ILE A1174 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 16 through 20 removed outlier: 3.582A pdb=" N VAL A 31 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY A 20 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A 29 " --> pdb=" O GLY A 20 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 30 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 41 " --> pdb=" O ILE A 30 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL A 32 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLU A 39 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU A 38 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N THR A 55 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU A 40 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ARG A 42 " --> pdb=" O HIS A 51 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N HIS A 51 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 62 through 68 removed outlier: 6.633A pdb=" N GLY A 81 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LEU A 65 " --> pdb=" O VAL A 79 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N VAL A 79 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ALA A 67 " --> pdb=" O TYR A 77 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N TYR A 77 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL A 80 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL A 88 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N SER A 82 " --> pdb=" O ARG A 86 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ARG A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE A 87 " --> pdb=" O GLN A 104 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLN A 104 " --> pdb=" O ILE A 87 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE A 89 " --> pdb=" O ILE A 102 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N MET A 98 " --> pdb=" O GLN A 93 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 120 through 123 removed outlier: 4.169A pdb=" N PHE A 120 " --> pdb=" O SER A 133 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A 133 " --> pdb=" O PHE A 120 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 120 through 123 removed outlier: 4.169A pdb=" N PHE A 120 " --> pdb=" O SER A 133 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A 133 " --> pdb=" O PHE A 120 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL A 141 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 165 through 173 removed outlier: 6.736A pdb=" N LEU A 185 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N VAL A 170 " --> pdb=" O ALA A 183 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ALA A 183 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N GLY A 172 " --> pdb=" O MET A 181 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N MET A 181 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE A 182 " --> pdb=" O TYR A 211 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR A 207 " --> pdb=" O GLU A 186 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU A 208 " --> pdb=" O SER A 225 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N SER A 225 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N PHE A 210 " --> pdb=" O LYS A 223 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N HIS A 219 " --> pdb=" O ASP A 214 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 232 through 237 removed outlier: 4.582A pdb=" N PHE A 234 " --> pdb=" O CYS A 251 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 249 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL A 248 " --> pdb=" O LYS A 259 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR A 255 " --> pdb=" O SER A 252 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A 256 " --> pdb=" O CYS A 269 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS A 269 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR A 258 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 267 " --> pdb=" O TYR A 258 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 273 through 274 removed outlier: 6.121A pdb=" N ARG A 273 " --> pdb=" O PHE A 387 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 287 through 293 removed outlier: 4.211A pdb=" N CYS A 289 " --> pdb=" O GLN A 304 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN A 304 " --> pdb=" O CYS A 289 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N HIS A 293 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N PHE A 300 " --> pdb=" O HIS A 293 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE A 301 " --> pdb=" O ILE A 313 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE A 311 " --> pdb=" O ALA A 303 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ASP A 309 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ILE A 310 " --> pdb=" O PHE A 330 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE A 330 " --> pdb=" O ILE A 310 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 287 through 293 removed outlier: 4.211A pdb=" N CYS A 289 " --> pdb=" O GLN A 304 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN A 304 " --> pdb=" O CYS A 289 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N HIS A 293 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N PHE A 300 " --> pdb=" O HIS A 293 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE A 301 " --> pdb=" O ILE A 313 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE A 311 " --> pdb=" O ALA A 303 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ASP A 309 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LYS A 312 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU A 327 " --> pdb=" O LYS A 312 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR A 314 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ILE A 325 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N GLU A 316 " --> pdb=" O THR A 323 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 336 through 342 removed outlier: 3.800A pdb=" N ALA A 338 " --> pdb=" O ALA A 350 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 350 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL A 349 " --> pdb=" O TYR A 357 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N TYR A 357 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP A 399 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLN A 360 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU A 397 " --> pdb=" O GLN A 360 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 407 through 413 removed outlier: 3.932A pdb=" N PHE A 409 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA A 413 " --> pdb=" O GLN A 422 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 423 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N CYS A 427 " --> pdb=" O SER A 434 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL A 437 " --> pdb=" O VAL A 777 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL A 777 " --> pdb=" O VAL A 437 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 445 through 450 removed outlier: 5.885A pdb=" N GLU A 446 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA A 766 " --> pdb=" O GLU A 446 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ALA A 448 " --> pdb=" O ILE A 764 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR A 761 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG A 763 " --> pdb=" O ALA A 756 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 756 " --> pdb=" O ARG A 763 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 757 " --> pdb=" O PHE A 741 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N PHE A 741 " --> pdb=" O ILE A 757 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 458 through 463 removed outlier: 6.834A pdb=" N ALA A 458 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL A 476 " --> pdb=" O ALA A 458 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TRP A 460 " --> pdb=" O ILE A 474 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE A 474 " --> pdb=" O TRP A 460 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N VAL A 462 " --> pdb=" O ALA A 472 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 474 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 476 " --> pdb=" O LEU A 483 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 508 through 509 removed outlier: 3.602A pdb=" N SER A 509 " --> pdb=" O VAL A 517 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 517 " --> pdb=" O SER A 509 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN A 518 " --> pdb=" O ARG A 525 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG A 525 " --> pdb=" O GLN A 518 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR A 520 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN A 534 " --> pdb=" O HIS A 526 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 544 through 549 removed outlier: 4.564A pdb=" N LYS A 546 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ALA A 557 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A 564 " --> pdb=" O ILE A 556 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 587 through 591 removed outlier: 4.042A pdb=" N CYS A 589 " --> pdb=" O GLY A 608 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER A 591 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ALA A 606 " --> pdb=" O SER A 591 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL A 607 " --> pdb=" O ARG A 615 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ARG A 615 " --> pdb=" O VAL A 607 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LEU A 609 " --> pdb=" O THR A 613 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N THR A 613 " --> pdb=" O LEU A 609 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 637 through 643 Processing sheet with id=AC5, first strand: chain 'A' and resid 702 through 706 removed outlier: 3.807A pdb=" N LEU A 713 " --> pdb=" O PHE A 702 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 704 " --> pdb=" O ALA A 711 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET A 706 " --> pdb=" O GLN A 709 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER A 719 " --> pdb=" O LEU A 734 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 785 through 790 removed outlier: 7.408A pdb=" N ILE A 800 " --> pdb=" O ARG A 786 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE A 788 " --> pdb=" O ILE A 798 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE A 798 " --> pdb=" O PHE A 788 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET A 869 " --> pdb=" O LEU A 797 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A 866 " --> pdb=" O VAL A 880 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 880 " --> pdb=" O ILE A 866 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL A 868 " --> pdb=" O ASP A 878 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASP A 878 " --> pdb=" O VAL A 868 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 886 through 887 removed outlier: 3.609A pdb=" N VAL A 905 " --> pdb=" O TYR A 928 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLY A 922 " --> pdb=" O LYS A 911 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N THR A 927 " --> pdb=" O LEU A 940 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU A 940 " --> pdb=" O THR A 927 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 891 through 894 removed outlier: 3.609A pdb=" N VAL A 905 " --> pdb=" O TYR A 928 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLY A 922 " --> pdb=" O LYS A 911 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 949 through 952 removed outlier: 5.059A pdb=" N ALA A 951 " --> pdb=" O GLY A 962 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY A 962 " --> pdb=" O ALA A 951 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 959 " --> pdb=" O TYR A 970 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE A 961 " --> pdb=" O ARG A 968 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG A 968 " --> pdb=" O ILE A 961 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU A 967 " --> pdb=" O GLU A 982 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLU A 982 " --> pdb=" O LEU A 967 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL A 969 " --> pdb=" O LYS A 980 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 990 through 995 removed outlier: 7.515A pdb=" N TRP A1011 " --> pdb=" O PHE A1024 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE A1024 " --> pdb=" O TRP A1011 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ALA A1089 " --> pdb=" O PHE A1024 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ASP A1026 " --> pdb=" O ALA A1089 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N VAL A1091 " --> pdb=" O ASP A1026 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N VAL A1091 " --> pdb=" O ARG A1057 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ARG A1057 " --> pdb=" O VAL A1091 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N MET A1093 " --> pdb=" O VAL A1055 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS A1054 " --> pdb=" O GLY A1046 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL A1044 " --> pdb=" O VAL A1056 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 86 through 89 removed outlier: 3.747A pdb=" N GLY D 86 " --> pdb=" O TYR D 81 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL D 141 " --> pdb=" O LEU D 166 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA D 143 " --> pdb=" O ILE D 164 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE D 164 " --> pdb=" O ALA D 143 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 394 through 396 removed outlier: 3.505A pdb=" N TYR D 363 " --> pdb=" O ILE D 396 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU D 352 " --> pdb=" O TYR D 337 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER D 426 " --> pdb=" O ASP D 336 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER D 424 " --> pdb=" O VAL D 338 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 199 through 200 removed outlier: 4.148A pdb=" N PHE G 204 " --> pdb=" O ARG G 200 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 163 through 168 removed outlier: 5.876A pdb=" N TYR H 163 " --> pdb=" O HIS H 196 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ASP H 198 " --> pdb=" O TYR H 163 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL H 165 " --> pdb=" O ASP H 198 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N GLN H 200 " --> pdb=" O VAL H 165 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU H 167 " --> pdb=" O GLN H 200 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'H' and resid 565 through 570 removed outlier: 4.154A pdb=" N ASN H 565 " --> pdb=" O ILE H 582 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE H 582 " --> pdb=" O ASN H 565 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR H 580 " --> pdb=" O LEU H 567 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL H 569 " --> pdb=" O LEU H 578 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU H 578 " --> pdb=" O VAL H 569 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE H 264 " --> pdb=" O GLY H 581 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N HIS K 130 " --> pdb=" O PHE H 261 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG K 128 " --> pdb=" O ALA H 263 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 273 through 276 removed outlier: 3.772A pdb=" N THR H 273 " --> pdb=" O GLY H 286 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 356 through 357 removed outlier: 3.744A pdb=" N VAL H 378 " --> pdb=" O TYR H 368 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASP H 370 " --> pdb=" O ASN H 376 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ASN H 376 " --> pdb=" O ASP H 370 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 387 through 392 removed outlier: 6.963A pdb=" N GLY H 402 " --> pdb=" O TRP H 388 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N LEU H 390 " --> pdb=" O ALA H 400 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ALA H 400 " --> pdb=" O LEU H 390 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER H 401 " --> pdb=" O ARG H 409 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG H 420 " --> pdb=" O LEU H 410 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 429 through 434 removed outlier: 3.763A pdb=" N SER H 445 " --> pdb=" O THR H 449 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N THR H 449 " --> pdb=" O SER H 445 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG H 462 " --> pdb=" O LEU H 452 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 471 through 476 removed outlier: 3.605A pdb=" N ALA H 475 " --> pdb=" O ALA H 484 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU H 494 " --> pdb=" O LYS H 504 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LYS H 504 " --> pdb=" O LEU H 494 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ASP H 496 " --> pdb=" O LEU H 502 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU H 502 " --> pdb=" O ASP H 496 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 513 through 518 removed outlier: 6.975A pdb=" N ALA H 528 " --> pdb=" O THR H 514 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LEU H 516 " --> pdb=" O ALA H 526 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA H 526 " --> pdb=" O LEU H 516 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N PHE H 518 " --> pdb=" O LEU H 524 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU H 524 " --> pdb=" O PHE H 518 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG H 535 " --> pdb=" O SER H 527 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER H 529 " --> pdb=" O SER H 533 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N SER H 533 " --> pdb=" O SER H 529 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL H 534 " --> pdb=" O VAL H 558 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N VAL H 558 " --> pdb=" O VAL H 534 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL H 536 " --> pdb=" O VAL H 556 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 107 through 108 removed outlier: 3.896A pdb=" N VAL K 107 " --> pdb=" O ALA I 174 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA I 174 " --> pdb=" O VAL K 107 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N CYS I 173 " --> pdb=" O LEU O 195 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'L' and resid 527 through 529 2259 hydrogen bonds defined for protein. 6588 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 26.44 Time building geometry restraints manager: 11.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 17175 1.34 - 1.46: 11626 1.46 - 1.58: 24354 1.58 - 1.70: 3 1.70 - 1.82: 514 Bond restraints: 53672 Sorted by residual: bond pdb=" CG PRO G 273 " pdb=" CD PRO G 273 " ideal model delta sigma weight residual 1.503 1.373 0.130 3.40e-02 8.65e+02 1.45e+01 bond pdb=" C GLN C1319 " pdb=" N PRO C1320 " ideal model delta sigma weight residual 1.335 1.360 -0.025 8.70e-03 1.32e+04 8.08e+00 bond pdb=" CB PRO A 504 " pdb=" CG PRO A 504 " ideal model delta sigma weight residual 1.492 1.620 -0.128 5.00e-02 4.00e+02 6.53e+00 bond pdb=" CB PRO G 273 " pdb=" CG PRO G 273 " ideal model delta sigma weight residual 1.492 1.610 -0.118 5.00e-02 4.00e+02 5.55e+00 bond pdb=" C ILE C 348 " pdb=" N PRO C 349 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.47e+00 ... (remaining 53667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 71762 2.19 - 4.37: 736 4.37 - 6.56: 116 6.56 - 8.74: 16 8.74 - 10.93: 12 Bond angle restraints: 72642 Sorted by residual: angle pdb=" N PRO G 273 " pdb=" CD PRO G 273 " pdb=" CG PRO G 273 " ideal model delta sigma weight residual 103.20 93.05 10.15 1.50e+00 4.44e-01 4.58e+01 angle pdb=" N PRO K 420 " pdb=" CA PRO K 420 " pdb=" CB PRO K 420 " ideal model delta sigma weight residual 103.00 110.41 -7.41 1.10e+00 8.26e-01 4.54e+01 angle pdb=" N PRO K 413 " pdb=" CA PRO K 413 " pdb=" CB PRO K 413 " ideal model delta sigma weight residual 103.25 110.23 -6.98 1.05e+00 9.07e-01 4.42e+01 angle pdb=" CA PRO A 504 " pdb=" N PRO A 504 " pdb=" CD PRO A 504 " ideal model delta sigma weight residual 112.00 102.93 9.07 1.40e+00 5.10e-01 4.19e+01 angle pdb=" CA PRO G 273 " pdb=" N PRO G 273 " pdb=" CD PRO G 273 " ideal model delta sigma weight residual 112.00 103.34 8.66 1.40e+00 5.10e-01 3.82e+01 ... (remaining 72637 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 30392 17.99 - 35.98: 1781 35.98 - 53.97: 350 53.97 - 71.96: 60 71.96 - 89.95: 44 Dihedral angle restraints: 32627 sinusoidal: 13250 harmonic: 19377 Sorted by residual: dihedral pdb=" CA THR K 58 " pdb=" C THR K 58 " pdb=" N LYS K 59 " pdb=" CA LYS K 59 " ideal model delta harmonic sigma weight residual 180.00 150.93 29.07 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA ILE O 152 " pdb=" C ILE O 152 " pdb=" N ARG O 153 " pdb=" CA ARG O 153 " ideal model delta harmonic sigma weight residual 180.00 158.14 21.86 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA LEU K 193 " pdb=" C LEU K 193 " pdb=" N PRO K 194 " pdb=" CA PRO K 194 " ideal model delta harmonic sigma weight residual -180.00 -158.94 -21.06 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 32624 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 6946 0.051 - 0.103: 1158 0.103 - 0.154: 179 0.154 - 0.206: 5 0.206 - 0.257: 2 Chirality restraints: 8290 Sorted by residual: chirality pdb=" CA PRO K 413 " pdb=" N PRO K 413 " pdb=" C PRO K 413 " pdb=" CB PRO K 413 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA PRO K 420 " pdb=" N PRO K 420 " pdb=" C PRO K 420 " pdb=" CB PRO K 420 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CB ILE C2197 " pdb=" CA ILE C2197 " pdb=" CG1 ILE C2197 " pdb=" CG2 ILE C2197 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.20 2.00e-01 2.50e+01 9.88e-01 ... (remaining 8287 not shown) Planarity restraints: 9241 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 503 " -0.084 5.00e-02 4.00e+02 1.21e-01 2.33e+01 pdb=" N PRO A 504 " 0.209 5.00e-02 4.00e+02 pdb=" CA PRO A 504 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO A 504 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU G 272 " -0.078 5.00e-02 4.00e+02 1.12e-01 1.99e+01 pdb=" N PRO G 273 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO G 273 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO G 273 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO H 253 " -0.048 5.00e-02 4.00e+02 6.92e-02 7.66e+00 pdb=" N PRO H 254 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO H 254 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO H 254 " -0.039 5.00e-02 4.00e+02 ... (remaining 9238 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1829 2.73 - 3.27: 51505 3.27 - 3.81: 78491 3.81 - 4.36: 93541 4.36 - 4.90: 159062 Nonbonded interactions: 384428 Sorted by model distance: nonbonded pdb=" OD1 ASP A1040 " pdb=" OG1 THR A1043 " model vdw 2.182 3.040 nonbonded pdb=" O LEU C3739 " pdb=" OG1 THR C3740 " model vdw 2.207 3.040 nonbonded pdb=" O PRO C 583 " pdb=" OG1 THR C 586 " model vdw 2.214 3.040 nonbonded pdb=" O LYS C1771 " pdb=" ND1 HIS C1775 " model vdw 2.225 3.120 nonbonded pdb=" OE2 GLU A 136 " pdb=" OH TYR A 189 " model vdw 2.228 3.040 ... (remaining 384423 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.350 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: 0.060 Extract box with map and model: 1.690 Check model and map are aligned: 0.300 Set scattering table: 0.390 Process input model: 94.940 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.200 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: 0.020 Load rotamer database and sin/cos tables:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5861 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.130 53672 Z= 0.140 Angle : 0.571 10.930 72642 Z= 0.312 Chirality : 0.039 0.257 8290 Planarity : 0.004 0.121 9241 Dihedral : 12.369 89.949 19986 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.34 % Favored : 94.63 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.10), residues: 6420 helix: 0.28 (0.10), residues: 2961 sheet: -0.17 (0.22), residues: 606 loop : -2.26 (0.11), residues: 2853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C1175 HIS 0.006 0.000 HIS H 315 PHE 0.027 0.001 PHE D 136 TYR 0.029 0.001 TYR C2476 ARG 0.008 0.000 ARG C1564 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12840 Ramachandran restraints generated. 6420 Oldfield, 0 Emsley, 6420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12840 Ramachandran restraints generated. 6420 Oldfield, 0 Emsley, 6420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 663 time to evaluate : 4.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 1586 ARG cc_start: 0.6327 (tpp-160) cc_final: 0.5942 (tpp-160) REVERT: C 1905 PHE cc_start: 0.5347 (t80) cc_final: 0.4281 (t80) REVERT: A 131 MET cc_start: 0.1573 (tpp) cc_final: 0.0873 (tpp) REVERT: A 568 MET cc_start: 0.0897 (tpt) cc_final: 0.0690 (tpt) REVERT: A 715 MET cc_start: 0.2670 (mmm) cc_final: 0.2317 (mmm) REVERT: A 823 MET cc_start: -0.1659 (mmt) cc_final: -0.2735 (ppp) REVERT: A 1039 LEU cc_start: 0.2966 (tt) cc_final: 0.2195 (mp) REVERT: B 37 ARG cc_start: 0.4143 (mtt180) cc_final: 0.2943 (ptt90) REVERT: D 144 GLU cc_start: 0.3901 (tm-30) cc_final: 0.3662 (tm-30) REVERT: D 393 TRP cc_start: 0.7025 (m100) cc_final: 0.6550 (m100) REVERT: E 167 MET cc_start: 0.2924 (mmp) cc_final: 0.2069 (ppp) REVERT: E 220 ILE cc_start: 0.6173 (mm) cc_final: 0.5868 (tp) REVERT: G 143 MET cc_start: 0.5730 (mmm) cc_final: 0.5471 (mmt) REVERT: G 198 ARG cc_start: 0.7198 (ptm160) cc_final: 0.6830 (ptm160) REVERT: I 131 HIS cc_start: 0.5872 (t-90) cc_final: 0.5344 (p90) REVERT: K 198 TYR cc_start: 0.3246 (m-80) cc_final: 0.2983 (m-80) REVERT: K 307 HIS cc_start: 0.1360 (t70) cc_final: 0.0950 (m90) REVERT: L 515 HIS cc_start: 0.4389 (t70) cc_final: 0.4055 (p-80) outliers start: 0 outliers final: 0 residues processed: 663 average time/residue: 0.4893 time to fit residues: 554.3393 Evaluate side-chains 452 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 452 time to evaluate : 4.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 550 optimal weight: 0.1980 chunk 494 optimal weight: 4.9990 chunk 274 optimal weight: 7.9990 chunk 168 optimal weight: 2.9990 chunk 333 optimal weight: 6.9990 chunk 264 optimal weight: 4.9990 chunk 511 optimal weight: 10.0000 chunk 197 optimal weight: 4.9990 chunk 310 optimal weight: 3.9990 chunk 380 optimal weight: 8.9990 chunk 592 optimal weight: 5.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 ASN C 140 HIS C 244 HIS C 337 HIS C 604 GLN C 708 ASN C 755 ASN C 936 GLN C 990 HIS C1057 GLN C1262 HIS ** C1299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1424 HIS C1443 ASN C1760 ASN ** C1774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1775 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1842 HIS ** C1884 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2589 HIS C2700 HIS ** C2885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3174 HIS C3522 ASN C3608 HIS C3610 ASN A 5 ASN A 775 ASN B 67 ASN D 134 ASN ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 ASN E 310 ASN G 111 HIS G 182 HIS G 215 GLN ** G 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 294 HIS H 88 HIS H 139 GLN I 65 HIS I 160 GLN I 168 HIS ** I 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 160 GLN R 75 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6404 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 53672 Z= 0.406 Angle : 0.773 10.654 72642 Z= 0.399 Chirality : 0.049 0.207 8290 Planarity : 0.006 0.079 9241 Dihedral : 4.459 34.035 7101 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.74 % Favored : 93.21 % Rotamer: Outliers : 1.26 % Allowed : 7.76 % Favored : 90.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.44 (0.10), residues: 6420 helix: 0.14 (0.09), residues: 3089 sheet: -0.27 (0.21), residues: 622 loop : -2.47 (0.11), residues: 2709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C2703 HIS 0.016 0.002 HIS C2823 PHE 0.045 0.003 PHE C3458 TYR 0.040 0.003 TYR K 198 ARG 0.009 0.001 ARG C3711 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12840 Ramachandran restraints generated. 6420 Oldfield, 0 Emsley, 6420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12840 Ramachandran restraints generated. 6420 Oldfield, 0 Emsley, 6420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 530 time to evaluate : 4.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 290 PHE cc_start: 0.5261 (OUTLIER) cc_final: 0.4880 (m-10) REVERT: C 313 MET cc_start: 0.6477 (ppp) cc_final: 0.6215 (tmm) REVERT: C 354 LEU cc_start: 0.4934 (OUTLIER) cc_final: 0.4655 (pp) REVERT: C 446 MET cc_start: 0.5025 (mmt) cc_final: 0.4817 (mmt) REVERT: C 826 MET cc_start: 0.7839 (mtm) cc_final: 0.7441 (mtt) REVERT: C 1199 SER cc_start: 0.7824 (p) cc_final: 0.7244 (m) REVERT: C 1467 MET cc_start: 0.6651 (mtp) cc_final: 0.6283 (mtp) REVERT: C 1540 MET cc_start: 0.6670 (mtm) cc_final: 0.6413 (mtm) REVERT: C 2220 MET cc_start: 0.5205 (mpp) cc_final: 0.4623 (mpp) REVERT: C 2294 MET cc_start: 0.3827 (mtt) cc_final: 0.3138 (mtp) REVERT: C 2886 MET cc_start: 0.6712 (tpt) cc_final: 0.6504 (tmm) REVERT: C 2917 ARG cc_start: 0.8231 (ttt180) cc_final: 0.7958 (ttt180) REVERT: C 3709 TYR cc_start: 0.7807 (OUTLIER) cc_final: 0.7493 (m-10) REVERT: C 3737 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8625 (tm-30) REVERT: C 3810 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7726 (tt) REVERT: A 38 LEU cc_start: 0.3621 (tp) cc_final: 0.3321 (mt) REVERT: A 706 MET cc_start: 0.0246 (ppp) cc_final: 0.0025 (ptp) REVERT: A 715 MET cc_start: 0.2537 (mmm) cc_final: 0.2171 (mmm) REVERT: A 823 MET cc_start: -0.1380 (mmt) cc_final: -0.2453 (ppp) REVERT: B 37 ARG cc_start: 0.4230 (mtt180) cc_final: 0.3130 (ptt90) REVERT: B 69 MET cc_start: 0.4081 (mmt) cc_final: 0.3593 (tpp) REVERT: D 396 ILE cc_start: 0.7981 (mm) cc_final: 0.7762 (mt) REVERT: E 60 ILE cc_start: 0.8105 (mm) cc_final: 0.7888 (mt) REVERT: I 73 ASN cc_start: 0.5402 (OUTLIER) cc_final: 0.4951 (t0) REVERT: R 59 THR cc_start: 0.4630 (p) cc_final: 0.4374 (m) REVERT: L 515 HIS cc_start: 0.5275 (t70) cc_final: 0.4318 (p-80) outliers start: 73 outliers final: 39 residues processed: 575 average time/residue: 0.4873 time to fit residues: 480.5006 Evaluate side-chains 470 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 425 time to evaluate : 4.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 916 VAL Chi-restraints excluded: chain C residue 1017 THR Chi-restraints excluded: chain C residue 1062 LEU Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1214 LEU Chi-restraints excluded: chain C residue 1297 LEU Chi-restraints excluded: chain C residue 1317 THR Chi-restraints excluded: chain C residue 1552 SER Chi-restraints excluded: chain C residue 1775 HIS Chi-restraints excluded: chain C residue 2273 MET Chi-restraints excluded: chain C residue 2340 MET Chi-restraints excluded: chain C residue 2776 THR Chi-restraints excluded: chain C residue 3053 LEU Chi-restraints excluded: chain C residue 3062 SER Chi-restraints excluded: chain C residue 3249 LEU Chi-restraints excluded: chain C residue 3432 MET Chi-restraints excluded: chain C residue 3709 TYR Chi-restraints excluded: chain C residue 3737 GLU Chi-restraints excluded: chain C residue 3810 LEU Chi-restraints excluded: chain C residue 3828 PHE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 445 SER Chi-restraints excluded: chain H residue 473 SER Chi-restraints excluded: chain I residue 73 ASN Chi-restraints excluded: chain K residue 41 CYS Chi-restraints excluded: chain K residue 263 LEU Chi-restraints excluded: chain K residue 291 LEU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain O residue 120 LEU Chi-restraints excluded: chain R residue 77 ASP Chi-restraints excluded: chain R residue 90 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 329 optimal weight: 5.9990 chunk 183 optimal weight: 0.6980 chunk 492 optimal weight: 0.0010 chunk 403 optimal weight: 20.0000 chunk 163 optimal weight: 0.0980 chunk 593 optimal weight: 9.9990 chunk 640 optimal weight: 0.0770 chunk 528 optimal weight: 0.0570 chunk 588 optimal weight: 3.9990 chunk 202 optimal weight: 5.9990 chunk 475 optimal weight: 0.8980 overall best weight: 0.1862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 ASN C 936 GLN C1282 HIS C3029 ASN C3139 ASN A1105 GLN B 35 GLN B 67 ASN ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 252 GLN ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 122 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6279 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 53672 Z= 0.141 Angle : 0.551 10.075 72642 Z= 0.278 Chirality : 0.041 0.209 8290 Planarity : 0.004 0.059 9241 Dihedral : 3.963 30.058 7101 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.34 % Favored : 94.63 % Rotamer: Outliers : 0.95 % Allowed : 10.37 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.81 (0.10), residues: 6420 helix: 0.84 (0.10), residues: 3082 sheet: -0.09 (0.21), residues: 615 loop : -2.36 (0.11), residues: 2723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C2491 HIS 0.008 0.001 HIS K 288 PHE 0.037 0.001 PHE C1811 TYR 0.024 0.001 TYR C2243 ARG 0.011 0.000 ARG C2906 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12840 Ramachandran restraints generated. 6420 Oldfield, 0 Emsley, 6420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12840 Ramachandran restraints generated. 6420 Oldfield, 0 Emsley, 6420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 478 time to evaluate : 4.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 290 PHE cc_start: 0.5147 (OUTLIER) cc_final: 0.4536 (m-10) REVERT: C 309 MET cc_start: 0.4275 (mpp) cc_final: 0.2675 (tpt) REVERT: C 411 LEU cc_start: 0.3162 (pt) cc_final: 0.2495 (tt) REVERT: C 587 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.7190 (tp40) REVERT: C 826 MET cc_start: 0.7845 (mtm) cc_final: 0.7502 (mtt) REVERT: C 1420 VAL cc_start: 0.5680 (m) cc_final: 0.5421 (m) REVERT: C 1540 MET cc_start: 0.6520 (mtm) cc_final: 0.6270 (mtm) REVERT: C 1586 ARG cc_start: 0.6332 (tpp-160) cc_final: 0.6121 (tpp-160) REVERT: C 2220 MET cc_start: 0.5297 (mpp) cc_final: 0.4772 (mpp) REVERT: C 2294 MET cc_start: 0.3673 (mtt) cc_final: 0.2877 (mtp) REVERT: C 2709 MET cc_start: 0.8305 (mtp) cc_final: 0.8023 (mtp) REVERT: C 3737 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8523 (tm-30) REVERT: A 181 MET cc_start: 0.0416 (mmt) cc_final: -0.0362 (tpt) REVERT: A 715 MET cc_start: 0.2687 (mmm) cc_final: 0.2370 (mmm) REVERT: A 823 MET cc_start: -0.1680 (mmt) cc_final: -0.2767 (ppp) REVERT: B 37 ARG cc_start: 0.4173 (mtt180) cc_final: 0.3051 (ptt180) REVERT: E 60 ILE cc_start: 0.8056 (mm) cc_final: 0.7816 (mt) REVERT: E 167 MET cc_start: 0.4297 (OUTLIER) cc_final: 0.2385 (ppp) REVERT: E 195 LYS cc_start: 0.3024 (ttpp) cc_final: 0.1433 (ttmt) REVERT: H 11 MET cc_start: 0.6193 (tmm) cc_final: 0.5726 (ptt) REVERT: K 176 MET cc_start: 0.5190 (mmm) cc_final: 0.4666 (mmm) REVERT: R 59 THR cc_start: 0.4997 (p) cc_final: 0.4737 (m) REVERT: L 515 HIS cc_start: 0.5110 (t70) cc_final: 0.4210 (p-80) outliers start: 55 outliers final: 35 residues processed: 513 average time/residue: 0.4947 time to fit residues: 437.9884 Evaluate side-chains 458 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 419 time to evaluate : 4.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 587 GLN Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 729 GLU Chi-restraints excluded: chain C residue 1017 THR Chi-restraints excluded: chain C residue 1082 ASN Chi-restraints excluded: chain C residue 1214 LEU Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1552 SER Chi-restraints excluded: chain C residue 1715 PHE Chi-restraints excluded: chain C residue 1775 HIS Chi-restraints excluded: chain C residue 2273 MET Chi-restraints excluded: chain C residue 2859 VAL Chi-restraints excluded: chain C residue 3432 MET Chi-restraints excluded: chain C residue 3433 LYS Chi-restraints excluded: chain C residue 3581 MET Chi-restraints excluded: chain C residue 3710 PHE Chi-restraints excluded: chain C residue 3737 GLU Chi-restraints excluded: chain C residue 3828 PHE Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 1095 TYR Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 167 MET Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain G residue 227 ASN Chi-restraints excluded: chain H residue 445 SER Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain K residue 282 VAL Chi-restraints excluded: chain K residue 291 LEU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain O residue 120 LEU Chi-restraints excluded: chain R residue 77 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 586 optimal weight: 0.0770 chunk 445 optimal weight: 1.9990 chunk 307 optimal weight: 3.9990 chunk 65 optimal weight: 0.0570 chunk 283 optimal weight: 0.9990 chunk 398 optimal weight: 3.9990 chunk 595 optimal weight: 20.0000 chunk 630 optimal weight: 0.0370 chunk 311 optimal weight: 1.9990 chunk 564 optimal weight: 5.9990 chunk 169 optimal weight: 0.8980 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1424 HIS C1522 HIS ** C2304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3139 ASN ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 322 HIS H 79 ASN H 139 GLN M 38 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6282 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 53672 Z= 0.132 Angle : 0.517 10.185 72642 Z= 0.260 Chirality : 0.040 0.208 8290 Planarity : 0.004 0.057 9241 Dihedral : 3.790 32.701 7101 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.76 % Favored : 94.21 % Rotamer: Outliers : 1.47 % Allowed : 11.42 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.11), residues: 6420 helix: 1.16 (0.10), residues: 3088 sheet: 0.03 (0.21), residues: 619 loop : -2.25 (0.11), residues: 2713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C1690 HIS 0.017 0.001 HIS C1424 PHE 0.035 0.001 PHE C1811 TYR 0.024 0.001 TYR C2243 ARG 0.005 0.000 ARG C2906 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12840 Ramachandran restraints generated. 6420 Oldfield, 0 Emsley, 6420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12840 Ramachandran restraints generated. 6420 Oldfield, 0 Emsley, 6420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 458 time to evaluate : 4.642 Fit side-chains REVERT: C 290 PHE cc_start: 0.5135 (OUTLIER) cc_final: 0.4447 (m-10) REVERT: C 309 MET cc_start: 0.4574 (mpp) cc_final: 0.2899 (tpt) REVERT: C 354 LEU cc_start: 0.4617 (OUTLIER) cc_final: 0.4390 (pp) REVERT: C 411 LEU cc_start: 0.3172 (pt) cc_final: 0.2550 (tt) REVERT: C 587 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.7126 (tp40) REVERT: C 826 MET cc_start: 0.7839 (mtm) cc_final: 0.7493 (mtt) REVERT: C 1459 PHE cc_start: 0.4898 (m-80) cc_final: 0.4479 (m-80) REVERT: C 1657 LEU cc_start: 0.6886 (OUTLIER) cc_final: 0.6421 (tt) REVERT: C 2220 MET cc_start: 0.5129 (mpp) cc_final: 0.4720 (mpp) REVERT: C 2953 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.6914 (mt) REVERT: C 3486 MET cc_start: 0.8077 (mmp) cc_final: 0.7850 (mmp) REVERT: C 3737 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8553 (tm-30) REVERT: A 715 MET cc_start: 0.2503 (mmm) cc_final: 0.2256 (mmm) REVERT: A 823 MET cc_start: -0.1623 (mmt) cc_final: -0.2718 (ppp) REVERT: B 37 ARG cc_start: 0.4217 (mtt180) cc_final: 0.3151 (ptt180) REVERT: D 396 ILE cc_start: 0.7989 (mm) cc_final: 0.7777 (mt) REVERT: E 60 ILE cc_start: 0.7894 (mm) cc_final: 0.7680 (mt) REVERT: E 102 PHE cc_start: 0.4700 (m-10) cc_final: 0.4227 (t80) REVERT: K 176 MET cc_start: 0.4965 (mmm) cc_final: 0.4598 (mmm) REVERT: R 59 THR cc_start: 0.5112 (p) cc_final: 0.4864 (m) REVERT: L 515 HIS cc_start: 0.5077 (t70) cc_final: 0.4192 (p-80) outliers start: 85 outliers final: 54 residues processed: 518 average time/residue: 0.5443 time to fit residues: 491.3677 Evaluate side-chains 474 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 414 time to evaluate : 4.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 587 GLN Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 729 GLU Chi-restraints excluded: chain C residue 916 VAL Chi-restraints excluded: chain C residue 1017 THR Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain C residue 1062 LEU Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1124 ILE Chi-restraints excluded: chain C residue 1214 LEU Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1521 PHE Chi-restraints excluded: chain C residue 1552 SER Chi-restraints excluded: chain C residue 1657 LEU Chi-restraints excluded: chain C residue 1775 HIS Chi-restraints excluded: chain C residue 2273 MET Chi-restraints excluded: chain C residue 2328 LEU Chi-restraints excluded: chain C residue 2424 VAL Chi-restraints excluded: chain C residue 2859 VAL Chi-restraints excluded: chain C residue 2884 VAL Chi-restraints excluded: chain C residue 2953 LEU Chi-restraints excluded: chain C residue 3053 LEU Chi-restraints excluded: chain C residue 3062 SER Chi-restraints excluded: chain C residue 3149 HIS Chi-restraints excluded: chain C residue 3432 MET Chi-restraints excluded: chain C residue 3433 LYS Chi-restraints excluded: chain C residue 3581 MET Chi-restraints excluded: chain C residue 3710 PHE Chi-restraints excluded: chain C residue 3737 GLU Chi-restraints excluded: chain C residue 3740 THR Chi-restraints excluded: chain C residue 3812 GLN Chi-restraints excluded: chain C residue 3828 PHE Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 1095 TYR Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain G residue 148 ARG Chi-restraints excluded: chain G residue 227 ASN Chi-restraints excluded: chain G residue 326 LEU Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 445 SER Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain K residue 282 VAL Chi-restraints excluded: chain K residue 314 LEU Chi-restraints excluded: chain M residue 127 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 524 optimal weight: 9.9990 chunk 357 optimal weight: 10.0000 chunk 9 optimal weight: 0.0770 chunk 469 optimal weight: 3.9990 chunk 260 optimal weight: 6.9990 chunk 537 optimal weight: 6.9990 chunk 435 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 321 optimal weight: 0.9980 chunk 565 optimal weight: 10.0000 chunk 159 optimal weight: 6.9990 overall best weight: 3.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 405 ASN C 936 GLN C1057 GLN C1078 HIS ** C1253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1775 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1884 HIS ** C2304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2885 ASN C3029 ASN C3139 ASN C3623 GLN C3734 ASN A 28 GLN ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 ASN A 805 ASN B 67 ASN ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 GLN H 124 HIS ** K 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 119 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6617 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 53672 Z= 0.398 Angle : 0.769 15.913 72642 Z= 0.393 Chirality : 0.049 0.278 8290 Planarity : 0.006 0.067 9241 Dihedral : 4.798 49.500 7101 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.38 % Favored : 92.57 % Rotamer: Outliers : 2.28 % Allowed : 12.28 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.16 (0.10), residues: 6420 helix: 0.46 (0.09), residues: 3119 sheet: -0.10 (0.22), residues: 583 loop : -2.46 (0.11), residues: 2718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 187 HIS 0.016 0.002 HIS C2823 PHE 0.050 0.003 PHE A 745 TYR 0.029 0.002 TYR C3044 ARG 0.009 0.001 ARG C 761 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12840 Ramachandran restraints generated. 6420 Oldfield, 0 Emsley, 6420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12840 Ramachandran restraints generated. 6420 Oldfield, 0 Emsley, 6420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 477 time to evaluate : 4.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 354 LEU cc_start: 0.4877 (OUTLIER) cc_final: 0.4626 (pp) REVERT: C 553 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7712 (tt) REVERT: C 641 MET cc_start: 0.6557 (ptt) cc_final: 0.6200 (ptt) REVERT: C 826 MET cc_start: 0.7983 (mtm) cc_final: 0.7763 (mtm) REVERT: C 939 MET cc_start: 0.7010 (OUTLIER) cc_final: 0.6639 (mtp) REVERT: C 1199 SER cc_start: 0.7684 (p) cc_final: 0.7207 (m) REVERT: C 1522 HIS cc_start: 0.6783 (OUTLIER) cc_final: 0.6234 (t70) REVERT: C 1615 LEU cc_start: 0.4905 (OUTLIER) cc_final: 0.3845 (tp) REVERT: C 1657 LEU cc_start: 0.7037 (OUTLIER) cc_final: 0.6682 (tp) REVERT: C 2220 MET cc_start: 0.5221 (mpp) cc_final: 0.4808 (mpp) REVERT: C 2730 GLU cc_start: 0.5861 (tt0) cc_final: 0.4815 (mm-30) REVERT: C 2953 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7572 (mt) REVERT: C 3306 MET cc_start: 0.7506 (mtp) cc_final: 0.7299 (mtm) REVERT: A 1 MET cc_start: 0.2153 (OUTLIER) cc_final: -0.0165 (mtp) REVERT: A 131 MET cc_start: 0.2161 (tpp) cc_final: 0.1610 (tpp) REVERT: A 1039 LEU cc_start: 0.4469 (tt) cc_final: 0.3883 (mt) REVERT: D 393 TRP cc_start: 0.7433 (m100) cc_final: 0.6804 (m100) REVERT: E 60 ILE cc_start: 0.8137 (mm) cc_final: 0.7915 (mt) REVERT: H 270 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.7962 (pp) REVERT: H 391 ASP cc_start: 0.8277 (p0) cc_final: 0.8075 (p0) REVERT: I 259 ARG cc_start: 0.5255 (mmm-85) cc_final: 0.4574 (ttp80) REVERT: K 111 GLU cc_start: 0.6651 (OUTLIER) cc_final: 0.6120 (mm-30) REVERT: K 133 TYR cc_start: 0.5101 (OUTLIER) cc_final: 0.4749 (p90) outliers start: 132 outliers final: 74 residues processed: 575 average time/residue: 0.5069 time to fit residues: 499.5624 Evaluate side-chains 477 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 392 time to evaluate : 4.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 633 GLU Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 729 GLU Chi-restraints excluded: chain C residue 916 VAL Chi-restraints excluded: chain C residue 939 MET Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1082 ASN Chi-restraints excluded: chain C residue 1124 ILE Chi-restraints excluded: chain C residue 1214 LEU Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1340 LEU Chi-restraints excluded: chain C residue 1420 VAL Chi-restraints excluded: chain C residue 1421 ASP Chi-restraints excluded: chain C residue 1522 HIS Chi-restraints excluded: chain C residue 1552 SER Chi-restraints excluded: chain C residue 1615 LEU Chi-restraints excluded: chain C residue 1657 LEU Chi-restraints excluded: chain C residue 1775 HIS Chi-restraints excluded: chain C residue 2273 MET Chi-restraints excluded: chain C residue 2328 LEU Chi-restraints excluded: chain C residue 2340 MET Chi-restraints excluded: chain C residue 2436 THR Chi-restraints excluded: chain C residue 2652 ILE Chi-restraints excluded: chain C residue 2838 THR Chi-restraints excluded: chain C residue 2884 VAL Chi-restraints excluded: chain C residue 2953 LEU Chi-restraints excluded: chain C residue 3053 LEU Chi-restraints excluded: chain C residue 3062 SER Chi-restraints excluded: chain C residue 3117 MET Chi-restraints excluded: chain C residue 3149 HIS Chi-restraints excluded: chain C residue 3294 THR Chi-restraints excluded: chain C residue 3432 MET Chi-restraints excluded: chain C residue 3443 LYS Chi-restraints excluded: chain C residue 3463 GLU Chi-restraints excluded: chain C residue 3688 LEU Chi-restraints excluded: chain C residue 3740 THR Chi-restraints excluded: chain C residue 3752 MET Chi-restraints excluded: chain C residue 3812 GLN Chi-restraints excluded: chain C residue 3828 PHE Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 1017 ASN Chi-restraints excluded: chain A residue 1095 TYR Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 167 MET Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain G residue 148 ARG Chi-restraints excluded: chain G residue 227 ASN Chi-restraints excluded: chain G residue 326 LEU Chi-restraints excluded: chain H residue 88 HIS Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 270 LEU Chi-restraints excluded: chain H residue 445 SER Chi-restraints excluded: chain H residue 473 SER Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain K residue 41 CYS Chi-restraints excluded: chain K residue 111 GLU Chi-restraints excluded: chain K residue 133 TYR Chi-restraints excluded: chain K residue 235 VAL Chi-restraints excluded: chain K residue 282 VAL Chi-restraints excluded: chain K residue 285 LEU Chi-restraints excluded: chain K residue 291 LEU Chi-restraints excluded: chain M residue 84 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain R residue 77 ASP Chi-restraints excluded: chain R residue 90 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 212 optimal weight: 3.9990 chunk 567 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 370 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 630 optimal weight: 6.9990 chunk 523 optimal weight: 3.9990 chunk 292 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 208 optimal weight: 1.9990 chunk 331 optimal weight: 9.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 634 HIS ** C1774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1962 HIS ** C2304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3823 HIS ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1138 HIS B 67 ASN ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 ASN ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 53672 Z= 0.302 Angle : 0.647 10.747 72642 Z= 0.330 Chirality : 0.045 0.318 8290 Planarity : 0.005 0.069 9241 Dihedral : 4.642 58.476 7101 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.96 % Favored : 93.01 % Rotamer: Outliers : 1.95 % Allowed : 13.77 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.00 (0.10), residues: 6420 helix: 0.66 (0.09), residues: 3125 sheet: -0.14 (0.22), residues: 600 loop : -2.47 (0.11), residues: 2695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C1690 HIS 0.014 0.001 HIS C1775 PHE 0.028 0.002 PHE C1811 TYR 0.020 0.002 TYR C2243 ARG 0.007 0.001 ARG A1212 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12840 Ramachandran restraints generated. 6420 Oldfield, 0 Emsley, 6420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12840 Ramachandran restraints generated. 6420 Oldfield, 0 Emsley, 6420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 428 time to evaluate : 4.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 290 PHE cc_start: 0.5188 (OUTLIER) cc_final: 0.4718 (m-10) REVERT: C 354 LEU cc_start: 0.4961 (OUTLIER) cc_final: 0.4714 (pp) REVERT: C 411 LEU cc_start: 0.3705 (pt) cc_final: 0.3433 (tt) REVERT: C 431 ARG cc_start: 0.5009 (mmm160) cc_final: 0.4804 (mmm160) REVERT: C 447 ARG cc_start: 0.6725 (ttm170) cc_final: 0.6410 (ttm170) REVERT: C 553 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7716 (tt) REVERT: C 641 MET cc_start: 0.7044 (ptt) cc_final: 0.6791 (ptp) REVERT: C 675 PHE cc_start: 0.6089 (OUTLIER) cc_final: 0.5455 (t80) REVERT: C 826 MET cc_start: 0.7936 (mtm) cc_final: 0.7690 (mtm) REVERT: C 939 MET cc_start: 0.6744 (OUTLIER) cc_final: 0.6446 (mtp) REVERT: C 1199 SER cc_start: 0.7771 (OUTLIER) cc_final: 0.7310 (m) REVERT: C 1657 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.6566 (tp) REVERT: C 1891 ILE cc_start: 0.6502 (mp) cc_final: 0.6227 (mt) REVERT: C 2220 MET cc_start: 0.5086 (mpp) cc_final: 0.4830 (mpp) REVERT: C 2730 GLU cc_start: 0.5913 (tt0) cc_final: 0.4863 (mm-30) REVERT: C 3306 MET cc_start: 0.7455 (mtp) cc_final: 0.7240 (mtm) REVERT: C 3529 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8721 (mp) REVERT: A 1 MET cc_start: 0.2610 (tpt) cc_final: -0.0076 (mtm) REVERT: A 131 MET cc_start: 0.1631 (tpp) cc_final: 0.1429 (tpp) REVERT: A 1039 LEU cc_start: 0.4800 (tt) cc_final: 0.4321 (mt) REVERT: E 42 ARG cc_start: 0.6631 (ttp-110) cc_final: 0.6368 (ttp-170) REVERT: E 60 ILE cc_start: 0.8138 (mm) cc_final: 0.7937 (mt) REVERT: H 153 PHE cc_start: 0.6297 (m-80) cc_final: 0.6058 (m-80) REVERT: H 391 ASP cc_start: 0.8163 (p0) cc_final: 0.7930 (p0) REVERT: I 259 ARG cc_start: 0.5324 (mmm-85) cc_final: 0.4700 (ttp80) REVERT: K 111 GLU cc_start: 0.6661 (OUTLIER) cc_final: 0.6113 (mm-30) REVERT: K 133 TYR cc_start: 0.5224 (OUTLIER) cc_final: 0.4875 (p90) REVERT: K 198 TYR cc_start: 0.4819 (m-10) cc_final: 0.4308 (m-10) outliers start: 113 outliers final: 72 residues processed: 518 average time/residue: 0.4943 time to fit residues: 443.9598 Evaluate side-chains 470 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 388 time to evaluate : 4.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 766 SER Chi-restraints excluded: chain C residue 916 VAL Chi-restraints excluded: chain C residue 939 MET Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1124 ILE Chi-restraints excluded: chain C residue 1199 SER Chi-restraints excluded: chain C residue 1214 LEU Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1340 LEU Chi-restraints excluded: chain C residue 1536 LEU Chi-restraints excluded: chain C residue 1552 SER Chi-restraints excluded: chain C residue 1657 LEU Chi-restraints excluded: chain C residue 1902 LEU Chi-restraints excluded: chain C residue 2273 MET Chi-restraints excluded: chain C residue 2328 LEU Chi-restraints excluded: chain C residue 2340 MET Chi-restraints excluded: chain C residue 2436 THR Chi-restraints excluded: chain C residue 2884 VAL Chi-restraints excluded: chain C residue 2902 SER Chi-restraints excluded: chain C residue 2953 LEU Chi-restraints excluded: chain C residue 3053 LEU Chi-restraints excluded: chain C residue 3062 SER Chi-restraints excluded: chain C residue 3074 ASP Chi-restraints excluded: chain C residue 3117 MET Chi-restraints excluded: chain C residue 3149 HIS Chi-restraints excluded: chain C residue 3164 GLU Chi-restraints excluded: chain C residue 3432 MET Chi-restraints excluded: chain C residue 3458 PHE Chi-restraints excluded: chain C residue 3529 LEU Chi-restraints excluded: chain C residue 3688 LEU Chi-restraints excluded: chain C residue 3740 THR Chi-restraints excluded: chain C residue 3812 GLN Chi-restraints excluded: chain C residue 3828 PHE Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 1095 TYR Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 185 HIS Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 357 SER Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain G residue 148 ARG Chi-restraints excluded: chain G residue 227 ASN Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 326 LEU Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 88 HIS Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 445 SER Chi-restraints excluded: chain H residue 473 SER Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain K residue 41 CYS Chi-restraints excluded: chain K residue 111 GLU Chi-restraints excluded: chain K residue 133 TYR Chi-restraints excluded: chain K residue 282 VAL Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 77 ASP Chi-restraints excluded: chain R residue 90 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 608 optimal weight: 0.3980 chunk 71 optimal weight: 2.9990 chunk 359 optimal weight: 4.9990 chunk 460 optimal weight: 9.9990 chunk 356 optimal weight: 20.0000 chunk 531 optimal weight: 0.9990 chunk 352 optimal weight: 0.0870 chunk 628 optimal weight: 5.9990 chunk 393 optimal weight: 8.9990 chunk 383 optimal weight: 10.0000 chunk 290 optimal weight: 1.9990 overall best weight: 1.2964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C2304 HIS C3029 ASN C3724 ASN ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 GLN D 220 ASN H 315 HIS ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6575 moved from start: 0.5108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 53672 Z= 0.179 Angle : 0.577 10.439 72642 Z= 0.291 Chirality : 0.042 0.261 8290 Planarity : 0.004 0.070 9241 Dihedral : 4.371 56.329 7101 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.65 % Favored : 93.33 % Rotamer: Outliers : 1.73 % Allowed : 14.63 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.65 (0.11), residues: 6420 helix: 1.02 (0.10), residues: 3092 sheet: -0.09 (0.22), residues: 607 loop : -2.34 (0.11), residues: 2721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C2374 HIS 0.011 0.001 HIS C1775 PHE 0.036 0.001 PHE C1759 TYR 0.020 0.001 TYR C2243 ARG 0.006 0.000 ARG C2906 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12840 Ramachandran restraints generated. 6420 Oldfield, 0 Emsley, 6420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12840 Ramachandran restraints generated. 6420 Oldfield, 0 Emsley, 6420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 414 time to evaluate : 4.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 351 MET cc_start: 0.3924 (ptm) cc_final: 0.3612 (ptm) REVERT: C 354 LEU cc_start: 0.4865 (OUTLIER) cc_final: 0.4605 (pp) REVERT: C 411 LEU cc_start: 0.3526 (pt) cc_final: 0.3245 (tp) REVERT: C 553 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7660 (tt) REVERT: C 641 MET cc_start: 0.7067 (ptt) cc_final: 0.6838 (ptp) REVERT: C 675 PHE cc_start: 0.6265 (OUTLIER) cc_final: 0.5512 (t80) REVERT: C 826 MET cc_start: 0.7866 (mtm) cc_final: 0.7610 (mtm) REVERT: C 1657 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.6491 (tt) REVERT: C 1891 ILE cc_start: 0.6472 (mp) cc_final: 0.6189 (mt) REVERT: C 1924 MET cc_start: 0.5392 (mmp) cc_final: 0.4863 (ppp) REVERT: C 2294 MET cc_start: 0.3904 (mtt) cc_final: 0.3468 (mtp) REVERT: C 2730 GLU cc_start: 0.5878 (tt0) cc_final: 0.4931 (mm-30) REVERT: C 2906 ARG cc_start: 0.6499 (ttp-110) cc_final: 0.6273 (ttp-110) REVERT: C 3463 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8399 (pt0) REVERT: A 1 MET cc_start: 0.2771 (tpt) cc_final: 0.2530 (tpt) REVERT: A 131 MET cc_start: 0.1671 (tpp) cc_final: 0.1456 (tpp) REVERT: A 321 MET cc_start: 0.2676 (OUTLIER) cc_final: 0.2044 (mtt) REVERT: A 544 ILE cc_start: 0.2505 (tt) cc_final: 0.2249 (tt) REVERT: A 823 MET cc_start: -0.1631 (mmt) cc_final: -0.2597 (ppp) REVERT: A 1039 LEU cc_start: 0.4973 (tt) cc_final: 0.4599 (mt) REVERT: D 146 ARG cc_start: 0.5731 (mmt90) cc_final: 0.5480 (mmt90) REVERT: E 42 ARG cc_start: 0.6567 (ttp-110) cc_final: 0.6365 (tmm160) REVERT: E 60 ILE cc_start: 0.8104 (mm) cc_final: 0.7895 (mt) REVERT: E 102 PHE cc_start: 0.5048 (m-10) cc_final: 0.4505 (t80) REVERT: E 209 MET cc_start: 0.2737 (pmm) cc_final: 0.1997 (ptp) REVERT: H 153 PHE cc_start: 0.6326 (m-80) cc_final: 0.6060 (m-80) REVERT: I 259 ARG cc_start: 0.5417 (mmm-85) cc_final: 0.4813 (ttp80) REVERT: K 20 MET cc_start: 0.6517 (ptt) cc_final: 0.6038 (tmm) REVERT: K 111 GLU cc_start: 0.6706 (OUTLIER) cc_final: 0.6241 (mm-30) REVERT: K 133 TYR cc_start: 0.5244 (OUTLIER) cc_final: 0.5037 (p90) REVERT: M 93 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.8000 (mt) outliers start: 100 outliers final: 65 residues processed: 494 average time/residue: 0.5124 time to fit residues: 437.4269 Evaluate side-chains 461 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 387 time to evaluate : 4.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 633 GLU Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 729 GLU Chi-restraints excluded: chain C residue 916 VAL Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1124 ILE Chi-restraints excluded: chain C residue 1214 LEU Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1340 LEU Chi-restraints excluded: chain C residue 1552 SER Chi-restraints excluded: chain C residue 1657 LEU Chi-restraints excluded: chain C residue 1831 TYR Chi-restraints excluded: chain C residue 2273 MET Chi-restraints excluded: chain C residue 2328 LEU Chi-restraints excluded: chain C residue 2340 MET Chi-restraints excluded: chain C residue 2522 THR Chi-restraints excluded: chain C residue 2953 LEU Chi-restraints excluded: chain C residue 3053 LEU Chi-restraints excluded: chain C residue 3062 SER Chi-restraints excluded: chain C residue 3117 MET Chi-restraints excluded: chain C residue 3149 HIS Chi-restraints excluded: chain C residue 3164 GLU Chi-restraints excluded: chain C residue 3432 MET Chi-restraints excluded: chain C residue 3463 GLU Chi-restraints excluded: chain C residue 3688 LEU Chi-restraints excluded: chain C residue 3740 THR Chi-restraints excluded: chain C residue 3812 GLN Chi-restraints excluded: chain C residue 3828 PHE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 1017 ASN Chi-restraints excluded: chain A residue 1095 TYR Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 185 HIS Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 357 SER Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 167 MET Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain G residue 148 ARG Chi-restraints excluded: chain G residue 227 ASN Chi-restraints excluded: chain G residue 326 LEU Chi-restraints excluded: chain H residue 88 HIS Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 445 SER Chi-restraints excluded: chain H residue 473 SER Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain K residue 111 GLU Chi-restraints excluded: chain K residue 133 TYR Chi-restraints excluded: chain K residue 282 VAL Chi-restraints excluded: chain K residue 285 LEU Chi-restraints excluded: chain M residue 93 LEU Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain O residue 201 THR Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 90 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 388 optimal weight: 20.0000 chunk 250 optimal weight: 0.9980 chunk 375 optimal weight: 5.9990 chunk 189 optimal weight: 8.9990 chunk 123 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 399 optimal weight: 30.0000 chunk 428 optimal weight: 10.0000 chunk 310 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 493 optimal weight: 9.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 384 HIS ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.5488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 53672 Z= 0.251 Angle : 0.625 9.703 72642 Z= 0.317 Chirality : 0.044 0.243 8290 Planarity : 0.005 0.066 9241 Dihedral : 4.487 57.338 7101 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.45 % Favored : 92.54 % Rotamer: Outliers : 2.00 % Allowed : 14.73 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.70 (0.11), residues: 6420 helix: 0.98 (0.09), residues: 3099 sheet: -0.11 (0.22), residues: 614 loop : -2.37 (0.11), residues: 2707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C1690 HIS 0.010 0.001 HIS C1661 PHE 0.035 0.002 PHE C1811 TYR 0.021 0.002 TYR A 4 ARG 0.015 0.001 ARG I 203 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12840 Ramachandran restraints generated. 6420 Oldfield, 0 Emsley, 6420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12840 Ramachandran restraints generated. 6420 Oldfield, 0 Emsley, 6420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 421 time to evaluate : 4.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 290 PHE cc_start: 0.5142 (OUTLIER) cc_final: 0.4592 (m-10) REVERT: C 354 LEU cc_start: 0.4885 (OUTLIER) cc_final: 0.4667 (pp) REVERT: C 443 ASP cc_start: 0.7290 (m-30) cc_final: 0.7020 (t0) REVERT: C 641 MET cc_start: 0.7203 (ptt) cc_final: 0.6967 (ptp) REVERT: C 675 PHE cc_start: 0.6813 (OUTLIER) cc_final: 0.5835 (t80) REVERT: C 826 MET cc_start: 0.7888 (mtm) cc_final: 0.7651 (mtm) REVERT: C 1657 LEU cc_start: 0.6824 (OUTLIER) cc_final: 0.6491 (tt) REVERT: C 1924 MET cc_start: 0.5184 (mmp) cc_final: 0.4654 (ppp) REVERT: C 2294 MET cc_start: 0.4114 (mtt) cc_final: 0.3834 (mtp) REVERT: C 2730 GLU cc_start: 0.5917 (tt0) cc_final: 0.4881 (mm-30) REVERT: A 1 MET cc_start: 0.2744 (tpt) cc_final: 0.2507 (tpt) REVERT: A 377 MET cc_start: 0.3189 (ttm) cc_final: 0.2755 (ttt) REVERT: A 544 ILE cc_start: 0.2462 (tt) cc_final: 0.2211 (tt) REVERT: A 690 ARG cc_start: 0.0889 (ttt180) cc_final: 0.0057 (ptp-170) REVERT: A 823 MET cc_start: -0.1598 (mmt) cc_final: -0.2411 (ppp) REVERT: E 42 ARG cc_start: 0.6565 (ttp-110) cc_final: 0.6364 (tmm160) REVERT: E 60 ILE cc_start: 0.8052 (mm) cc_final: 0.7822 (mt) REVERT: E 102 PHE cc_start: 0.5097 (m-10) cc_final: 0.4517 (t80) REVERT: E 209 MET cc_start: 0.3396 (pmm) cc_final: 0.2269 (ptp) REVERT: I 259 ARG cc_start: 0.5593 (mmm-85) cc_final: 0.4947 (ttp80) REVERT: K 100 TYR cc_start: 0.5531 (OUTLIER) cc_final: 0.5258 (m-80) REVERT: K 111 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.6477 (mm-30) outliers start: 116 outliers final: 85 residues processed: 516 average time/residue: 0.4978 time to fit residues: 442.9649 Evaluate side-chains 480 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 389 time to evaluate : 4.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 633 GLU Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 729 GLU Chi-restraints excluded: chain C residue 916 VAL Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1099 CYS Chi-restraints excluded: chain C residue 1124 ILE Chi-restraints excluded: chain C residue 1141 ILE Chi-restraints excluded: chain C residue 1214 LEU Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1340 LEU Chi-restraints excluded: chain C residue 1386 ILE Chi-restraints excluded: chain C residue 1552 SER Chi-restraints excluded: chain C residue 1562 LEU Chi-restraints excluded: chain C residue 1657 LEU Chi-restraints excluded: chain C residue 1776 ILE Chi-restraints excluded: chain C residue 1902 LEU Chi-restraints excluded: chain C residue 2209 LEU Chi-restraints excluded: chain C residue 2273 MET Chi-restraints excluded: chain C residue 2328 LEU Chi-restraints excluded: chain C residue 2340 MET Chi-restraints excluded: chain C residue 2388 THR Chi-restraints excluded: chain C residue 2436 THR Chi-restraints excluded: chain C residue 2522 THR Chi-restraints excluded: chain C residue 2884 VAL Chi-restraints excluded: chain C residue 2902 SER Chi-restraints excluded: chain C residue 3053 LEU Chi-restraints excluded: chain C residue 3062 SER Chi-restraints excluded: chain C residue 3117 MET Chi-restraints excluded: chain C residue 3122 TYR Chi-restraints excluded: chain C residue 3149 HIS Chi-restraints excluded: chain C residue 3164 GLU Chi-restraints excluded: chain C residue 3432 MET Chi-restraints excluded: chain C residue 3433 LYS Chi-restraints excluded: chain C residue 3463 GLU Chi-restraints excluded: chain C residue 3688 LEU Chi-restraints excluded: chain C residue 3740 THR Chi-restraints excluded: chain C residue 3741 THR Chi-restraints excluded: chain C residue 3812 GLN Chi-restraints excluded: chain C residue 3828 PHE Chi-restraints excluded: chain C residue 3838 LEU Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 1017 ASN Chi-restraints excluded: chain A residue 1095 TYR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 185 HIS Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 357 SER Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 90 ASP Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 167 MET Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain G residue 148 ARG Chi-restraints excluded: chain G residue 227 ASN Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 326 LEU Chi-restraints excluded: chain H residue 88 HIS Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 364 MET Chi-restraints excluded: chain H residue 445 SER Chi-restraints excluded: chain H residue 473 SER Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain K residue 41 CYS Chi-restraints excluded: chain K residue 100 TYR Chi-restraints excluded: chain K residue 111 GLU Chi-restraints excluded: chain K residue 282 VAL Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 118 ASP Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain O residue 148 ASP Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 65 ASP Chi-restraints excluded: chain R residue 90 ASP Chi-restraints excluded: chain R residue 117 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 571 optimal weight: 0.8980 chunk 602 optimal weight: 3.9990 chunk 549 optimal weight: 2.9990 chunk 585 optimal weight: 5.9990 chunk 601 optimal weight: 0.9990 chunk 352 optimal weight: 4.9990 chunk 255 optimal weight: 0.7980 chunk 459 optimal weight: 0.1980 chunk 179 optimal weight: 0.0030 chunk 529 optimal weight: 7.9990 chunk 553 optimal weight: 3.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1675 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1778 ASN C3532 ASN ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6555 moved from start: 0.5483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 53672 Z= 0.147 Angle : 0.571 18.084 72642 Z= 0.285 Chirality : 0.041 0.229 8290 Planarity : 0.004 0.072 9241 Dihedral : 4.234 56.321 7101 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.98 % Favored : 94.00 % Rotamer: Outliers : 1.33 % Allowed : 15.78 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.43 (0.11), residues: 6420 helix: 1.23 (0.10), residues: 3105 sheet: -0.01 (0.22), residues: 615 loop : -2.27 (0.11), residues: 2700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C1175 HIS 0.013 0.001 HIS C1775 PHE 0.040 0.001 PHE C1811 TYR 0.021 0.001 TYR C2243 ARG 0.009 0.000 ARG C2906 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12840 Ramachandran restraints generated. 6420 Oldfield, 0 Emsley, 6420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12840 Ramachandran restraints generated. 6420 Oldfield, 0 Emsley, 6420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 425 time to evaluate : 4.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 354 LEU cc_start: 0.4841 (OUTLIER) cc_final: 0.4614 (pp) REVERT: C 625 MET cc_start: 0.6623 (OUTLIER) cc_final: 0.6163 (ppp) REVERT: C 641 MET cc_start: 0.7144 (ptt) cc_final: 0.6921 (ptp) REVERT: C 675 PHE cc_start: 0.6637 (OUTLIER) cc_final: 0.5675 (t80) REVERT: C 826 MET cc_start: 0.7839 (mtm) cc_final: 0.7594 (mtm) REVERT: C 1336 TYR cc_start: 0.7002 (t80) cc_final: 0.6727 (t80) REVERT: C 1657 LEU cc_start: 0.6800 (OUTLIER) cc_final: 0.6498 (tt) REVERT: C 1891 ILE cc_start: 0.6025 (mp) cc_final: 0.5477 (mt) REVERT: C 1924 MET cc_start: 0.5075 (mmp) cc_final: 0.4706 (ppp) REVERT: C 2730 GLU cc_start: 0.5838 (tt0) cc_final: 0.4884 (mm-30) REVERT: C 3279 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7577 (tm-30) REVERT: C 3463 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8400 (pt0) REVERT: C 3812 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.7378 (mt0) REVERT: A 181 MET cc_start: 0.1098 (mmt) cc_final: -0.0341 (tpt) REVERT: A 544 ILE cc_start: 0.2376 (tt) cc_final: 0.2084 (tt) REVERT: A 697 ARG cc_start: 0.1974 (mtp85) cc_final: 0.1455 (mmm160) REVERT: A 823 MET cc_start: -0.1713 (mmt) cc_final: -0.2594 (ppp) REVERT: B 37 ARG cc_start: 0.4038 (mtt180) cc_final: 0.3072 (ptt180) REVERT: D 146 ARG cc_start: 0.5510 (mmt90) cc_final: 0.5297 (mmt90) REVERT: E 60 ILE cc_start: 0.8044 (mm) cc_final: 0.7811 (mt) REVERT: E 102 PHE cc_start: 0.4819 (m-10) cc_final: 0.4486 (t80) REVERT: E 209 MET cc_start: 0.3257 (pmm) cc_final: 0.2225 (ptp) REVERT: I 259 ARG cc_start: 0.5606 (mmm-85) cc_final: 0.4992 (ttp80) REVERT: K 20 MET cc_start: 0.6398 (ptt) cc_final: 0.6063 (tmm) REVERT: K 111 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6377 (mm-30) REVERT: K 114 LEU cc_start: 0.5156 (tt) cc_final: 0.4807 (tp) REVERT: K 291 LEU cc_start: 0.5046 (pp) cc_final: 0.4845 (pp) outliers start: 77 outliers final: 57 residues processed: 487 average time/residue: 0.5026 time to fit residues: 420.6186 Evaluate side-chains 455 residues out of total 5838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 391 time to evaluate : 4.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 625 MET Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 729 GLU Chi-restraints excluded: chain C residue 916 VAL Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain C residue 1099 CYS Chi-restraints excluded: chain C residue 1124 ILE Chi-restraints excluded: chain C residue 1214 LEU Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1340 LEU Chi-restraints excluded: chain C residue 1562 LEU Chi-restraints excluded: chain C residue 1657 LEU Chi-restraints excluded: chain C residue 1695 LEU Chi-restraints excluded: chain C residue 1902 LEU Chi-restraints excluded: chain C residue 2273 MET Chi-restraints excluded: chain C residue 2328 LEU Chi-restraints excluded: chain C residue 2388 THR Chi-restraints excluded: chain C residue 2436 THR Chi-restraints excluded: chain C residue 2522 THR Chi-restraints excluded: chain C residue 2902 SER Chi-restraints excluded: chain C residue 3062 SER Chi-restraints excluded: chain C residue 3117 MET Chi-restraints excluded: chain C residue 3122 TYR Chi-restraints excluded: chain C residue 3149 HIS Chi-restraints excluded: chain C residue 3164 GLU Chi-restraints excluded: chain C residue 3432 MET Chi-restraints excluded: chain C residue 3463 GLU Chi-restraints excluded: chain C residue 3688 LEU Chi-restraints excluded: chain C residue 3740 THR Chi-restraints excluded: chain C residue 3741 THR Chi-restraints excluded: chain C residue 3812 GLN Chi-restraints excluded: chain C residue 3828 PHE Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 1095 TYR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 185 HIS Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain G residue 148 ARG Chi-restraints excluded: chain G residue 227 ASN Chi-restraints excluded: chain G residue 326 LEU Chi-restraints excluded: chain H residue 88 HIS Chi-restraints excluded: chain H residue 445 SER Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain K residue 111 GLU Chi-restraints excluded: chain K residue 282 VAL Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain O residue 199 ASP Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 65 ASP Chi-restraints excluded: chain R residue 90 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.4516 > 50: distance: 88 - 145: 22.777 distance: 91 - 142: 16.174 distance: 116 - 121: 13.250 distance: 121 - 122: 34.744 distance: 122 - 123: 10.322 distance: 122 - 125: 28.910 distance: 123 - 124: 10.217 distance: 123 - 126: 8.326 distance: 126 - 127: 32.017 distance: 127 - 128: 21.163 distance: 127 - 130: 21.661 distance: 128 - 129: 24.414 distance: 128 - 131: 21.029 distance: 131 - 132: 6.438 distance: 132 - 133: 18.607 distance: 132 - 135: 16.418 distance: 133 - 134: 20.471 distance: 133 - 142: 8.829 distance: 134 - 259: 18.152 distance: 135 - 136: 25.577 distance: 136 - 137: 12.678 distance: 137 - 138: 21.273 distance: 138 - 139: 18.740 distance: 139 - 140: 9.719 distance: 139 - 141: 18.791 distance: 142 - 143: 18.132 distance: 143 - 144: 25.495 distance: 143 - 146: 8.357 distance: 144 - 145: 6.107 distance: 144 - 153: 14.470 distance: 146 - 147: 20.897 distance: 147 - 148: 8.042 distance: 148 - 149: 21.832 distance: 149 - 150: 11.259 distance: 150 - 151: 11.245 distance: 150 - 152: 9.398 distance: 153 - 154: 11.970 distance: 153 - 246: 12.774 distance: 154 - 155: 7.194 distance: 154 - 157: 5.827 distance: 155 - 156: 11.194 distance: 155 - 161: 20.515 distance: 156 - 243: 16.372 distance: 157 - 158: 15.914 distance: 162 - 163: 7.131 distance: 162 - 165: 12.189 distance: 163 - 164: 18.558 distance: 163 - 173: 11.446 distance: 165 - 166: 12.221 distance: 166 - 167: 10.207 distance: 166 - 168: 15.029 distance: 167 - 169: 12.725 distance: 168 - 170: 23.140 distance: 169 - 171: 3.247 distance: 170 - 171: 17.206 distance: 171 - 172: 7.798 distance: 173 - 174: 6.816 distance: 173 - 231: 23.711 distance: 174 - 175: 7.954 distance: 174 - 177: 18.478 distance: 175 - 176: 3.049 distance: 175 - 181: 8.467 distance: 176 - 228: 18.096 distance: 177 - 178: 21.716 distance: 177 - 179: 13.610 distance: 178 - 180: 10.813 distance: 181 - 182: 4.168 distance: 182 - 183: 6.835 distance: 183 - 184: 3.093 distance: 183 - 192: 5.686 distance: 185 - 186: 10.658 distance: 186 - 187: 10.742 distance: 187 - 188: 10.133 distance: 188 - 189: 3.433 distance: 189 - 190: 6.440 distance: 189 - 191: 13.025 distance: 192 - 193: 9.225 distance: 193 - 194: 8.435 distance: 194 - 195: 3.130 distance: 194 - 196: 13.306 distance: 196 - 197: 10.606 distance: 197 - 198: 7.819 distance: 197 - 200: 11.877 distance: 198 - 199: 6.861 distance: 198 - 206: 4.424 distance: 200 - 201: 8.537 distance: 201 - 202: 12.321 distance: 201 - 203: 5.586 distance: 202 - 204: 12.211 distance: 203 - 205: 6.491 distance: 204 - 205: 4.978