Starting phenix.real_space_refine (version: 1.21rc1) on Wed May 17 08:05:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sid_25141/05_2023/7sid_25141_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sid_25141/05_2023/7sid_25141.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sid_25141/05_2023/7sid_25141.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sid_25141/05_2023/7sid_25141.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sid_25141/05_2023/7sid_25141_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sid_25141/05_2023/7sid_25141_updated.pdb" } resolution = 2.53 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 306 5.16 5 C 28526 2.51 5 N 7588 2.21 5 O 8222 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 58": "OD1" <-> "OD2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 713": "OE1" <-> "OE2" Residue "A PHE 1025": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1312": "NH1" <-> "NH2" Residue "A TYR 1319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1666": "OE1" <-> "OE2" Residue "A ASP 1705": "OD1" <-> "OD2" Residue "A ASP 1758": "OD1" <-> "OD2" Residue "A ASP 2003": "OD1" <-> "OD2" Residue "A TYR 2086": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2216": "OD1" <-> "OD2" Residue "A ASP 2249": "OD1" <-> "OD2" Residue "A ASP 2507": "OD1" <-> "OD2" Residue "A GLU 2570": "OE1" <-> "OE2" Residue "A ARG 2618": "NH1" <-> "NH2" Residue "A ASP 2720": "OD1" <-> "OD2" Residue "A PHE 2831": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2943": "OE1" <-> "OE2" Residue "A GLU 3015": "OE1" <-> "OE2" Residue "C PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 58": "OD1" <-> "OD2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 713": "OE1" <-> "OE2" Residue "C PHE 1025": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1312": "NH1" <-> "NH2" Residue "C TYR 1319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1666": "OE1" <-> "OE2" Residue "C ASP 1705": "OD1" <-> "OD2" Residue "C ASP 1758": "OD1" <-> "OD2" Residue "C ASP 2003": "OD1" <-> "OD2" Residue "C TYR 2086": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 2216": "OD1" <-> "OD2" Residue "C ASP 2249": "OD1" <-> "OD2" Residue "C ASP 2507": "OD1" <-> "OD2" Residue "C GLU 2570": "OE1" <-> "OE2" Residue "C ARG 2618": "NH1" <-> "NH2" Residue "C ASP 2720": "OD1" <-> "OD2" Residue "C PHE 2831": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2943": "OE1" <-> "OE2" Residue "C GLU 3015": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 44650 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 22210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2773, 22210 Classifications: {'peptide': 2773} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 88, 'TRANS': 2684} Chain breaks: 18 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 7, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 112 Chain: "B" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 83 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 22210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2773, 22210 Classifications: {'peptide': 2773} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 88, 'TRANS': 2684} Chain breaks: 18 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 7, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 112 Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 83 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 22.64, per 1000 atoms: 0.51 Number of scatterers: 44650 At special positions: 0 Unit cell: (225.302, 113.19, 216.678, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 306 16.00 P 6 15.00 Mg 2 11.99 O 8222 8.00 N 7588 7.00 C 28526 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.83 Conformation dependent library (CDL) restraints added in 6.4 seconds 10972 Ramachandran restraints generated. 5486 Oldfield, 0 Emsley, 5486 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10708 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 292 helices and 6 sheets defined 67.0% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 15.25 Creating SS restraints... Processing helix chain 'A' and resid 6 through 15 Processing helix chain 'A' and resid 22 through 32 Processing helix chain 'A' and resid 36 through 42 Processing helix chain 'A' and resid 57 through 73 Processing helix chain 'A' and resid 88 through 108 Processing helix chain 'A' and resid 117 through 129 Processing helix chain 'A' and resid 135 through 148 Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 161 through 173 Processing helix chain 'A' and resid 182 through 200 removed outlier: 3.712A pdb=" N VAL A 185 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 222 removed outlier: 3.893A pdb=" N ASP A 211 " --> pdb=" O LYS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 243 Processing helix chain 'A' and resid 248 through 268 Proline residue: A 260 - end of helix Processing helix chain 'A' and resid 273 through 290 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 306 through 323 Processing helix chain 'A' and resid 343 through 356 Processing helix chain 'A' and resid 393 through 402 Processing helix chain 'A' and resid 406 through 408 No H-bonds generated for 'chain 'A' and resid 406 through 408' Processing helix chain 'A' and resid 410 through 422 Processing helix chain 'A' and resid 424 through 426 No H-bonds generated for 'chain 'A' and resid 424 through 426' Processing helix chain 'A' and resid 429 through 443 removed outlier: 4.529A pdb=" N SER A 433 " --> pdb=" O CYS A 430 " (cutoff:3.500A) Proline residue: A 434 - end of helix removed outlier: 3.694A pdb=" N LEU A 439 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER A 440 " --> pdb=" O MET A 437 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU A 443 " --> pdb=" O SER A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 468 removed outlier: 3.665A pdb=" N LYS A 468 " --> pdb=" O LEU A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 492 Processing helix chain 'A' and resid 498 through 513 removed outlier: 5.506A pdb=" N ALA A 502 " --> pdb=" O GLN A 499 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASN A 504 " --> pdb=" O GLN A 501 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N PHE A 505 " --> pdb=" O ALA A 502 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN A 513 " --> pdb=" O ALA A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 527 removed outlier: 3.541A pdb=" N LYS A 525 " --> pdb=" O ARG A 521 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N PHE A 527 " --> pdb=" O PHE A 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 521 through 527' Processing helix chain 'A' and resid 536 through 547 Processing helix chain 'A' and resid 573 through 580 Processing helix chain 'A' and resid 597 through 600 No H-bonds generated for 'chain 'A' and resid 597 through 600' Processing helix chain 'A' and resid 608 through 616 removed outlier: 3.580A pdb=" N THR A 616 " --> pdb=" O LEU A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 628 Processing helix chain 'A' and resid 646 through 655 Processing helix chain 'A' and resid 684 through 703 Processing helix chain 'A' and resid 712 through 731 removed outlier: 3.605A pdb=" N VAL A 716 " --> pdb=" O SER A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 741 removed outlier: 3.731A pdb=" N TYR A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 737 through 741' Processing helix chain 'A' and resid 744 through 765 removed outlier: 3.936A pdb=" N GLU A 758 " --> pdb=" O GLN A 754 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N SER A 759 " --> pdb=" O CYS A 755 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ILE A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 786 Processing helix chain 'A' and resid 795 through 806 Processing helix chain 'A' and resid 809 through 824 Processing helix chain 'A' and resid 887 through 889 No H-bonds generated for 'chain 'A' and resid 887 through 889' Processing helix chain 'A' and resid 892 through 911 Processing helix chain 'A' and resid 920 through 931 removed outlier: 3.656A pdb=" N LEU A 930 " --> pdb=" O LYS A 926 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE A 931 " --> pdb=" O LEU A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 953 Processing helix chain 'A' and resid 963 through 979 Proline residue: A 972 - end of helix removed outlier: 5.064A pdb=" N ASN A 975 " --> pdb=" O LYS A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 1001 removed outlier: 4.883A pdb=" N HIS A 996 " --> pdb=" O ASN A 992 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N VAL A 997 " --> pdb=" O HIS A 993 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL A 998 " --> pdb=" O VAL A 994 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N LYS A 999 " --> pdb=" O LEU A 995 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ASN A1000 " --> pdb=" O HIS A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1031 removed outlier: 3.784A pdb=" N VAL A1021 " --> pdb=" O GLN A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1052 Processing helix chain 'A' and resid 1070 through 1079 removed outlier: 3.597A pdb=" N THR A1075 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN A1076 " --> pdb=" O GLU A1072 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE A1077 " --> pdb=" O VAL A1073 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU A1078 " --> pdb=" O PHE A1074 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ALA A1079 " --> pdb=" O THR A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1096 removed outlier: 4.992A pdb=" N ASN A1094 " --> pdb=" O ALA A1090 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ARG A1095 " --> pdb=" O GLU A1091 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N LEU A1096 " --> pdb=" O SER A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1132 removed outlier: 3.565A pdb=" N MET A1131 " --> pdb=" O ALA A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1164 Processing helix chain 'A' and resid 1169 through 1182 removed outlier: 4.120A pdb=" N LYS A1181 " --> pdb=" O CYS A1177 " (cutoff:3.500A) Processing helix chain 'A' and resid 1187 through 1201 Processing helix chain 'A' and resid 1206 through 1224 removed outlier: 3.901A pdb=" N HIS A1213 " --> pdb=" O PHE A1209 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ASP A1215 " --> pdb=" O ALA A1211 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N TYR A1216 " --> pdb=" O SER A1212 " (cutoff:3.500A) Processing helix chain 'A' and resid 1237 through 1239 No H-bonds generated for 'chain 'A' and resid 1237 through 1239' Processing helix chain 'A' and resid 1244 through 1261 removed outlier: 6.607A pdb=" N LYS A1253 " --> pdb=" O ARG A1249 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL A1254 " --> pdb=" O SER A1250 " (cutoff:3.500A) Proline residue: A1257 - end of helix Processing helix chain 'A' and resid 1265 through 1273 Processing helix chain 'A' and resid 1279 through 1285 Processing helix chain 'A' and resid 1287 through 1293 removed outlier: 4.029A pdb=" N ASN A1293 " --> pdb=" O LYS A1289 " (cutoff:3.500A) Processing helix chain 'A' and resid 1295 through 1298 No H-bonds generated for 'chain 'A' and resid 1295 through 1298' Processing helix chain 'A' and resid 1306 through 1322 Processing helix chain 'A' and resid 1328 through 1338 removed outlier: 3.634A pdb=" N ILE A1332 " --> pdb=" O GLY A1329 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ASP A1333 " --> pdb=" O LYS A1330 " (cutoff:3.500A) Processing helix chain 'A' and resid 1341 through 1350 removed outlier: 3.702A pdb=" N THR A1350 " --> pdb=" O GLU A1346 " (cutoff:3.500A) Processing helix chain 'A' and resid 1383 through 1396 Processing helix chain 'A' and resid 1404 through 1408 Processing helix chain 'A' and resid 1412 through 1428 removed outlier: 4.663A pdb=" N GLN A1416 " --> pdb=" O PRO A1412 " (cutoff:3.500A) Processing helix chain 'A' and resid 1432 through 1451 Processing helix chain 'A' and resid 1453 through 1455 No H-bonds generated for 'chain 'A' and resid 1453 through 1455' Processing helix chain 'A' and resid 1461 through 1477 Processing helix chain 'A' and resid 1485 through 1508 Processing helix chain 'A' and resid 1517 through 1527 Proline residue: A1526 - end of helix Processing helix chain 'A' and resid 1535 through 1546 Processing helix chain 'A' and resid 1553 through 1560 removed outlier: 3.961A pdb=" N ILE A1557 " --> pdb=" O GLU A1553 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N THR A1558 " --> pdb=" O ASN A1554 " (cutoff:3.500A) Processing helix chain 'A' and resid 1572 through 1582 Processing helix chain 'A' and resid 1590 through 1602 removed outlier: 3.724A pdb=" N VAL A1602 " --> pdb=" O LEU A1598 " (cutoff:3.500A) Processing helix chain 'A' and resid 1607 through 1622 removed outlier: 4.514A pdb=" N GLU A1612 " --> pdb=" O THR A1609 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A1614 " --> pdb=" O LEU A1611 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU A1622 " --> pdb=" O ARG A1619 " (cutoff:3.500A) Processing helix chain 'A' and resid 1625 through 1636 removed outlier: 3.543A pdb=" N GLN A1636 " --> pdb=" O MET A1632 " (cutoff:3.500A) Processing helix chain 'A' and resid 1639 through 1641 No H-bonds generated for 'chain 'A' and resid 1639 through 1641' Processing helix chain 'A' and resid 1643 through 1658 Processing helix chain 'A' and resid 1664 through 1677 Processing helix chain 'A' and resid 1694 through 1702 Processing helix chain 'A' and resid 1706 through 1723 removed outlier: 4.430A pdb=" N VAL A1723 " --> pdb=" O ASN A1719 " (cutoff:3.500A) Processing helix chain 'A' and resid 1727 through 1741 Processing helix chain 'A' and resid 1744 through 1755 removed outlier: 3.606A pdb=" N ILE A1752 " --> pdb=" O SER A1748 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N MET A1755 " --> pdb=" O GLU A1751 " (cutoff:3.500A) Processing helix chain 'A' and resid 1759 through 1764 Processing helix chain 'A' and resid 1786 through 1789 No H-bonds generated for 'chain 'A' and resid 1786 through 1789' Processing helix chain 'A' and resid 1792 through 1795 No H-bonds generated for 'chain 'A' and resid 1792 through 1795' Processing helix chain 'A' and resid 1802 through 1815 Processing helix chain 'A' and resid 1824 through 1832 removed outlier: 4.113A pdb=" N LYS A1828 " --> pdb=" O GLN A1825 " (cutoff:3.500A) Proline residue: A1829 - end of helix Processing helix chain 'A' and resid 1835 through 1851 Proline residue: A1843 - end of helix Processing helix chain 'A' and resid 1858 through 1875 Processing helix chain 'A' and resid 1903 through 1918 removed outlier: 3.752A pdb=" N ARG A1918 " --> pdb=" O ASP A1914 " (cutoff:3.500A) Processing helix chain 'A' and resid 1929 through 1932 Processing helix chain 'A' and resid 1938 through 1947 Processing helix chain 'A' and resid 1951 through 1973 Processing helix chain 'A' and resid 1986 through 1996 Processing helix chain 'A' and resid 2001 through 2012 Processing helix chain 'A' and resid 2016 through 2019 Processing helix chain 'A' and resid 2029 through 2038 Processing helix chain 'A' and resid 2042 through 2051 Processing helix chain 'A' and resid 2057 through 2070 Processing helix chain 'A' and resid 2074 through 2087 Processing helix chain 'A' and resid 2093 through 2106 Processing helix chain 'A' and resid 2124 through 2136 Processing helix chain 'A' and resid 2140 through 2160 Processing helix chain 'A' and resid 2166 through 2168 No H-bonds generated for 'chain 'A' and resid 2166 through 2168' Processing helix chain 'A' and resid 2170 through 2190 removed outlier: 3.839A pdb=" N GLU A2187 " --> pdb=" O GLU A2183 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU A2188 " --> pdb=" O SER A2184 " (cutoff:3.500A) Processing helix chain 'A' and resid 2195 through 2211 Processing helix chain 'A' and resid 2217 through 2236 Proline residue: A2222 - end of helix Processing helix chain 'A' and resid 2243 through 2264 Processing helix chain 'A' and resid 2269 through 2281 removed outlier: 3.561A pdb=" N TYR A2281 " --> pdb=" O GLN A2277 " (cutoff:3.500A) Processing helix chain 'A' and resid 2290 through 2301 Processing helix chain 'A' and resid 2305 through 2322 removed outlier: 3.902A pdb=" N ALA A2321 " --> pdb=" O LYS A2317 " (cutoff:3.500A) Processing helix chain 'A' and resid 2328 through 2348 Processing helix chain 'A' and resid 2353 through 2359 Processing helix chain 'A' and resid 2361 through 2370 removed outlier: 3.512A pdb=" N VAL A2365 " --> pdb=" O LEU A2361 " (cutoff:3.500A) Processing helix chain 'A' and resid 2378 through 2405 Processing helix chain 'A' and resid 2408 through 2421 Processing helix chain 'A' and resid 2437 through 2476 Processing helix chain 'A' and resid 2481 through 2494 removed outlier: 3.611A pdb=" N PHE A2485 " --> pdb=" O MET A2482 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N CYS A2488 " --> pdb=" O PHE A2485 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU A2492 " --> pdb=" O SER A2489 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU A2493 " --> pdb=" O LEU A2490 " (cutoff:3.500A) Processing helix chain 'A' and resid 2498 through 2510 removed outlier: 4.608A pdb=" N MET A2509 " --> pdb=" O LYS A2505 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LYS A2510 " --> pdb=" O ARG A2506 " (cutoff:3.500A) Processing helix chain 'A' and resid 2513 through 2526 Proline residue: A2518 - end of helix removed outlier: 5.094A pdb=" N TYR A2521 " --> pdb=" O PRO A2518 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A2523 " --> pdb=" O MET A2520 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA A2524 " --> pdb=" O TYR A2521 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A2525 " --> pdb=" O GLN A2522 " (cutoff:3.500A) Processing helix chain 'A' and resid 2537 through 2551 Processing helix chain 'A' and resid 2553 through 2564 removed outlier: 5.794A pdb=" N PHE A2558 " --> pdb=" O HIS A2554 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ILE A2559 " --> pdb=" O HIS A2555 " (cutoff:3.500A) Processing helix chain 'A' and resid 2568 through 2572 Processing helix chain 'A' and resid 2593 through 2610 Processing helix chain 'A' and resid 2614 through 2631 Processing helix chain 'A' and resid 2652 through 2654 No H-bonds generated for 'chain 'A' and resid 2652 through 2654' Processing helix chain 'A' and resid 2723 through 2740 Processing helix chain 'A' and resid 2743 through 2747 Processing helix chain 'A' and resid 2776 through 2781 Processing helix chain 'A' and resid 2787 through 2791 Processing helix chain 'A' and resid 2798 through 2806 Processing helix chain 'A' and resid 2813 through 2825 Processing helix chain 'A' and resid 2831 through 2833 No H-bonds generated for 'chain 'A' and resid 2831 through 2833' Processing helix chain 'A' and resid 2842 through 2866 Processing helix chain 'A' and resid 2873 through 2875 No H-bonds generated for 'chain 'A' and resid 2873 through 2875' Processing helix chain 'A' and resid 2896 through 2898 No H-bonds generated for 'chain 'A' and resid 2896 through 2898' Processing helix chain 'A' and resid 2912 through 2918 removed outlier: 3.875A pdb=" N MET A2918 " --> pdb=" O ILE A2914 " (cutoff:3.500A) Processing helix chain 'A' and resid 2926 through 2940 Processing helix chain 'A' and resid 2942 through 2953 Processing helix chain 'A' and resid 2964 through 2970 Processing helix chain 'A' and resid 3002 through 3017 Processing helix chain 'A' and resid 3028 through 3039 Processing helix chain 'A' and resid 3042 through 3047 removed outlier: 3.609A pdb=" N ARG A3047 " --> pdb=" O LYS A3043 " (cutoff:3.500A) Processing helix chain 'A' and resid 3050 through 3052 No H-bonds generated for 'chain 'A' and resid 3050 through 3052' Processing helix chain 'C' and resid 6 through 15 Processing helix chain 'C' and resid 22 through 32 Processing helix chain 'C' and resid 36 through 42 Processing helix chain 'C' and resid 57 through 73 Processing helix chain 'C' and resid 88 through 108 Processing helix chain 'C' and resid 117 through 129 Processing helix chain 'C' and resid 135 through 148 Processing helix chain 'C' and resid 153 through 158 Processing helix chain 'C' and resid 161 through 173 Processing helix chain 'C' and resid 182 through 200 removed outlier: 3.712A pdb=" N VAL C 185 " --> pdb=" O VAL C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 222 removed outlier: 3.893A pdb=" N ASP C 211 " --> pdb=" O LYS C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 243 Processing helix chain 'C' and resid 248 through 268 Proline residue: C 260 - end of helix Processing helix chain 'C' and resid 273 through 290 Processing helix chain 'C' and resid 298 through 300 No H-bonds generated for 'chain 'C' and resid 298 through 300' Processing helix chain 'C' and resid 306 through 323 Processing helix chain 'C' and resid 343 through 356 Processing helix chain 'C' and resid 393 through 402 Processing helix chain 'C' and resid 406 through 408 No H-bonds generated for 'chain 'C' and resid 406 through 408' Processing helix chain 'C' and resid 410 through 422 Processing helix chain 'C' and resid 424 through 426 No H-bonds generated for 'chain 'C' and resid 424 through 426' Processing helix chain 'C' and resid 429 through 443 removed outlier: 4.529A pdb=" N SER C 433 " --> pdb=" O CYS C 430 " (cutoff:3.500A) Proline residue: C 434 - end of helix removed outlier: 3.695A pdb=" N LEU C 439 " --> pdb=" O LEU C 436 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER C 440 " --> pdb=" O MET C 437 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU C 443 " --> pdb=" O SER C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 468 removed outlier: 3.665A pdb=" N LYS C 468 " --> pdb=" O LEU C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 492 Processing helix chain 'C' and resid 498 through 513 removed outlier: 5.506A pdb=" N ALA C 502 " --> pdb=" O GLN C 499 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASN C 504 " --> pdb=" O GLN C 501 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N PHE C 505 " --> pdb=" O ALA C 502 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN C 513 " --> pdb=" O ALA C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 527 removed outlier: 3.541A pdb=" N LYS C 525 " --> pdb=" O ARG C 521 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU C 526 " --> pdb=" O GLU C 522 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N PHE C 527 " --> pdb=" O PHE C 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 521 through 527' Processing helix chain 'C' and resid 536 through 547 Processing helix chain 'C' and resid 573 through 580 Processing helix chain 'C' and resid 597 through 600 No H-bonds generated for 'chain 'C' and resid 597 through 600' Processing helix chain 'C' and resid 608 through 616 removed outlier: 3.580A pdb=" N THR C 616 " --> pdb=" O LEU C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 628 Processing helix chain 'C' and resid 646 through 655 Processing helix chain 'C' and resid 684 through 703 Processing helix chain 'C' and resid 712 through 731 removed outlier: 3.605A pdb=" N VAL C 716 " --> pdb=" O SER C 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 741 removed outlier: 3.731A pdb=" N TYR C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 737 through 741' Processing helix chain 'C' and resid 744 through 765 removed outlier: 3.936A pdb=" N GLU C 758 " --> pdb=" O GLN C 754 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N SER C 759 " --> pdb=" O CYS C 755 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ILE C 760 " --> pdb=" O ALA C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 786 Processing helix chain 'C' and resid 795 through 806 Processing helix chain 'C' and resid 809 through 824 Processing helix chain 'C' and resid 887 through 889 No H-bonds generated for 'chain 'C' and resid 887 through 889' Processing helix chain 'C' and resid 892 through 911 Processing helix chain 'C' and resid 920 through 931 removed outlier: 3.656A pdb=" N LEU C 930 " --> pdb=" O LYS C 926 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE C 931 " --> pdb=" O LEU C 927 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 953 Processing helix chain 'C' and resid 963 through 979 Proline residue: C 972 - end of helix removed outlier: 5.064A pdb=" N ASN C 975 " --> pdb=" O LYS C 971 " (cutoff:3.500A) Processing helix chain 'C' and resid 984 through 1001 removed outlier: 4.883A pdb=" N HIS C 996 " --> pdb=" O ASN C 992 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N VAL C 997 " --> pdb=" O HIS C 993 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL C 998 " --> pdb=" O VAL C 994 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N LYS C 999 " --> pdb=" O LEU C 995 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ASN C1000 " --> pdb=" O HIS C 996 " (cutoff:3.500A) Processing helix chain 'C' and resid 1009 through 1031 removed outlier: 3.784A pdb=" N VAL C1021 " --> pdb=" O GLN C1017 " (cutoff:3.500A) Processing helix chain 'C' and resid 1036 through 1052 Processing helix chain 'C' and resid 1070 through 1079 removed outlier: 3.597A pdb=" N THR C1075 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN C1076 " --> pdb=" O GLU C1072 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE C1077 " --> pdb=" O VAL C1073 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU C1078 " --> pdb=" O PHE C1074 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ALA C1079 " --> pdb=" O THR C1075 " (cutoff:3.500A) Processing helix chain 'C' and resid 1083 through 1096 removed outlier: 4.992A pdb=" N ASN C1094 " --> pdb=" O ALA C1090 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ARG C1095 " --> pdb=" O GLU C1091 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N LEU C1096 " --> pdb=" O SER C1092 " (cutoff:3.500A) Processing helix chain 'C' and resid 1113 through 1132 removed outlier: 3.565A pdb=" N MET C1131 " --> pdb=" O ALA C1127 " (cutoff:3.500A) Processing helix chain 'C' and resid 1144 through 1164 Processing helix chain 'C' and resid 1169 through 1182 removed outlier: 4.120A pdb=" N LYS C1181 " --> pdb=" O CYS C1177 " (cutoff:3.500A) Processing helix chain 'C' and resid 1187 through 1201 Processing helix chain 'C' and resid 1206 through 1224 removed outlier: 3.901A pdb=" N HIS C1213 " --> pdb=" O PHE C1209 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ASP C1215 " --> pdb=" O ALA C1211 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N TYR C1216 " --> pdb=" O SER C1212 " (cutoff:3.500A) Processing helix chain 'C' and resid 1237 through 1239 No H-bonds generated for 'chain 'C' and resid 1237 through 1239' Processing helix chain 'C' and resid 1244 through 1261 removed outlier: 6.607A pdb=" N LYS C1253 " --> pdb=" O ARG C1249 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL C1254 " --> pdb=" O SER C1250 " (cutoff:3.500A) Proline residue: C1257 - end of helix Processing helix chain 'C' and resid 1265 through 1273 Processing helix chain 'C' and resid 1279 through 1285 Processing helix chain 'C' and resid 1287 through 1293 removed outlier: 4.029A pdb=" N ASN C1293 " --> pdb=" O LYS C1289 " (cutoff:3.500A) Processing helix chain 'C' and resid 1295 through 1298 No H-bonds generated for 'chain 'C' and resid 1295 through 1298' Processing helix chain 'C' and resid 1306 through 1322 Processing helix chain 'C' and resid 1328 through 1338 removed outlier: 3.634A pdb=" N ILE C1332 " --> pdb=" O GLY C1329 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ASP C1333 " --> pdb=" O LYS C1330 " (cutoff:3.500A) Processing helix chain 'C' and resid 1341 through 1350 removed outlier: 3.702A pdb=" N THR C1350 " --> pdb=" O GLU C1346 " (cutoff:3.500A) Processing helix chain 'C' and resid 1383 through 1396 Processing helix chain 'C' and resid 1404 through 1408 Processing helix chain 'C' and resid 1412 through 1428 removed outlier: 4.663A pdb=" N GLN C1416 " --> pdb=" O PRO C1412 " (cutoff:3.500A) Processing helix chain 'C' and resid 1432 through 1451 Processing helix chain 'C' and resid 1453 through 1455 No H-bonds generated for 'chain 'C' and resid 1453 through 1455' Processing helix chain 'C' and resid 1461 through 1477 Processing helix chain 'C' and resid 1485 through 1508 Processing helix chain 'C' and resid 1517 through 1527 Proline residue: C1526 - end of helix Processing helix chain 'C' and resid 1535 through 1546 Processing helix chain 'C' and resid 1553 through 1560 removed outlier: 3.961A pdb=" N ILE C1557 " --> pdb=" O GLU C1553 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N THR C1558 " --> pdb=" O ASN C1554 " (cutoff:3.500A) Processing helix chain 'C' and resid 1572 through 1582 Processing helix chain 'C' and resid 1590 through 1602 removed outlier: 3.724A pdb=" N VAL C1602 " --> pdb=" O LEU C1598 " (cutoff:3.500A) Processing helix chain 'C' and resid 1607 through 1622 removed outlier: 4.514A pdb=" N GLU C1612 " --> pdb=" O THR C1609 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU C1614 " --> pdb=" O LEU C1611 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU C1622 " --> pdb=" O ARG C1619 " (cutoff:3.500A) Processing helix chain 'C' and resid 1625 through 1636 removed outlier: 3.543A pdb=" N GLN C1636 " --> pdb=" O MET C1632 " (cutoff:3.500A) Processing helix chain 'C' and resid 1639 through 1641 No H-bonds generated for 'chain 'C' and resid 1639 through 1641' Processing helix chain 'C' and resid 1643 through 1658 Processing helix chain 'C' and resid 1664 through 1677 Processing helix chain 'C' and resid 1694 through 1702 Processing helix chain 'C' and resid 1706 through 1723 removed outlier: 4.430A pdb=" N VAL C1723 " --> pdb=" O ASN C1719 " (cutoff:3.500A) Processing helix chain 'C' and resid 1727 through 1741 Processing helix chain 'C' and resid 1744 through 1755 removed outlier: 3.606A pdb=" N ILE C1752 " --> pdb=" O SER C1748 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N MET C1755 " --> pdb=" O GLU C1751 " (cutoff:3.500A) Processing helix chain 'C' and resid 1759 through 1764 Processing helix chain 'C' and resid 1786 through 1789 No H-bonds generated for 'chain 'C' and resid 1786 through 1789' Processing helix chain 'C' and resid 1792 through 1795 No H-bonds generated for 'chain 'C' and resid 1792 through 1795' Processing helix chain 'C' and resid 1802 through 1815 Processing helix chain 'C' and resid 1824 through 1832 removed outlier: 4.113A pdb=" N LYS C1828 " --> pdb=" O GLN C1825 " (cutoff:3.500A) Proline residue: C1829 - end of helix Processing helix chain 'C' and resid 1835 through 1851 Proline residue: C1843 - end of helix Processing helix chain 'C' and resid 1858 through 1875 Processing helix chain 'C' and resid 1903 through 1918 removed outlier: 3.752A pdb=" N ARG C1918 " --> pdb=" O ASP C1914 " (cutoff:3.500A) Processing helix chain 'C' and resid 1929 through 1932 Processing helix chain 'C' and resid 1938 through 1947 Processing helix chain 'C' and resid 1951 through 1973 Processing helix chain 'C' and resid 1986 through 1996 Processing helix chain 'C' and resid 2001 through 2012 Processing helix chain 'C' and resid 2016 through 2019 Processing helix chain 'C' and resid 2029 through 2038 Processing helix chain 'C' and resid 2042 through 2051 Processing helix chain 'C' and resid 2057 through 2070 Processing helix chain 'C' and resid 2074 through 2087 Processing helix chain 'C' and resid 2093 through 2106 Processing helix chain 'C' and resid 2124 through 2136 Processing helix chain 'C' and resid 2140 through 2160 Processing helix chain 'C' and resid 2166 through 2168 No H-bonds generated for 'chain 'C' and resid 2166 through 2168' Processing helix chain 'C' and resid 2170 through 2190 removed outlier: 3.839A pdb=" N GLU C2187 " --> pdb=" O GLU C2183 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU C2188 " --> pdb=" O SER C2184 " (cutoff:3.500A) Processing helix chain 'C' and resid 2195 through 2211 Processing helix chain 'C' and resid 2217 through 2236 Proline residue: C2222 - end of helix Processing helix chain 'C' and resid 2243 through 2264 Processing helix chain 'C' and resid 2269 through 2281 removed outlier: 3.561A pdb=" N TYR C2281 " --> pdb=" O GLN C2277 " (cutoff:3.500A) Processing helix chain 'C' and resid 2290 through 2301 Processing helix chain 'C' and resid 2305 through 2322 removed outlier: 3.902A pdb=" N ALA C2321 " --> pdb=" O LYS C2317 " (cutoff:3.500A) Processing helix chain 'C' and resid 2328 through 2348 Processing helix chain 'C' and resid 2353 through 2359 Processing helix chain 'C' and resid 2361 through 2370 removed outlier: 3.512A pdb=" N VAL C2365 " --> pdb=" O LEU C2361 " (cutoff:3.500A) Processing helix chain 'C' and resid 2378 through 2405 Processing helix chain 'C' and resid 2408 through 2421 Processing helix chain 'C' and resid 2437 through 2476 Processing helix chain 'C' and resid 2481 through 2494 removed outlier: 3.611A pdb=" N PHE C2485 " --> pdb=" O MET C2482 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N CYS C2488 " --> pdb=" O PHE C2485 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU C2492 " --> pdb=" O SER C2489 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU C2493 " --> pdb=" O LEU C2490 " (cutoff:3.500A) Processing helix chain 'C' and resid 2498 through 2510 removed outlier: 4.608A pdb=" N MET C2509 " --> pdb=" O LYS C2505 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LYS C2510 " --> pdb=" O ARG C2506 " (cutoff:3.500A) Processing helix chain 'C' and resid 2513 through 2526 Proline residue: C2518 - end of helix removed outlier: 5.094A pdb=" N TYR C2521 " --> pdb=" O PRO C2518 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C2523 " --> pdb=" O MET C2520 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA C2524 " --> pdb=" O TYR C2521 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C2525 " --> pdb=" O GLN C2522 " (cutoff:3.500A) Processing helix chain 'C' and resid 2537 through 2551 Processing helix chain 'C' and resid 2553 through 2564 removed outlier: 5.794A pdb=" N PHE C2558 " --> pdb=" O HIS C2554 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ILE C2559 " --> pdb=" O HIS C2555 " (cutoff:3.500A) Processing helix chain 'C' and resid 2568 through 2572 Processing helix chain 'C' and resid 2593 through 2610 Processing helix chain 'C' and resid 2614 through 2631 Processing helix chain 'C' and resid 2652 through 2654 No H-bonds generated for 'chain 'C' and resid 2652 through 2654' Processing helix chain 'C' and resid 2723 through 2740 Processing helix chain 'C' and resid 2743 through 2747 Processing helix chain 'C' and resid 2776 through 2781 Processing helix chain 'C' and resid 2787 through 2791 Processing helix chain 'C' and resid 2798 through 2806 Processing helix chain 'C' and resid 2813 through 2825 Processing helix chain 'C' and resid 2831 through 2833 No H-bonds generated for 'chain 'C' and resid 2831 through 2833' Processing helix chain 'C' and resid 2842 through 2866 Processing helix chain 'C' and resid 2873 through 2875 No H-bonds generated for 'chain 'C' and resid 2873 through 2875' Processing helix chain 'C' and resid 2896 through 2898 No H-bonds generated for 'chain 'C' and resid 2896 through 2898' Processing helix chain 'C' and resid 2912 through 2918 removed outlier: 3.875A pdb=" N MET C2918 " --> pdb=" O ILE C2914 " (cutoff:3.500A) Processing helix chain 'C' and resid 2926 through 2940 Processing helix chain 'C' and resid 2942 through 2953 Processing helix chain 'C' and resid 2964 through 2970 Processing helix chain 'C' and resid 3002 through 3017 Processing helix chain 'C' and resid 3028 through 3039 Processing helix chain 'C' and resid 3042 through 3047 removed outlier: 3.609A pdb=" N ARG C3047 " --> pdb=" O LYS C3043 " (cutoff:3.500A) Processing helix chain 'C' and resid 3050 through 3052 No H-bonds generated for 'chain 'C' and resid 3050 through 3052' Processing sheet with id= A, first strand: chain 'A' and resid 1060 through 1063 Processing sheet with id= B, first strand: chain 'A' and resid 2757 through 2759 Processing sheet with id= C, first strand: chain 'A' and resid 2773 through 2775 Processing sheet with id= D, first strand: chain 'C' and resid 1060 through 1063 Processing sheet with id= E, first strand: chain 'C' and resid 2757 through 2759 Processing sheet with id= F, first strand: chain 'C' and resid 2773 through 2775 2446 hydrogen bonds defined for protein. 6780 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: 21.31 Time building geometry restraints manager: 19.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14411 1.34 - 1.46: 9796 1.46 - 1.58: 20819 1.58 - 1.70: 8 1.70 - 1.82: 450 Bond restraints: 45484 Sorted by residual: bond pdb=" O3A ANP C3101 " pdb=" PB ANP C3101 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.16e+01 bond pdb=" O3A ANP A3101 " pdb=" PB ANP A3101 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.16e+01 bond pdb=" N3B ANP A3101 " pdb=" PG ANP A3101 " ideal model delta sigma weight residual 1.795 1.693 0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" N3B ANP C3101 " pdb=" PG ANP C3101 " ideal model delta sigma weight residual 1.795 1.693 0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" O5' ANP A3101 " pdb=" PA ANP A3101 " ideal model delta sigma weight residual 1.655 1.578 0.077 2.00e-02 2.50e+03 1.48e+01 ... (remaining 45479 not shown) Histogram of bond angle deviations from ideal: 99.89 - 106.74: 1064 106.74 - 113.59: 25484 113.59 - 120.44: 17472 120.44 - 127.29: 16982 127.29 - 134.14: 462 Bond angle restraints: 61464 Sorted by residual: angle pdb=" CA GLU A1313 " pdb=" CB GLU A1313 " pdb=" CG GLU A1313 " ideal model delta sigma weight residual 114.10 130.17 -16.07 2.00e+00 2.50e-01 6.46e+01 angle pdb=" CA GLU C1313 " pdb=" CB GLU C1313 " pdb=" CG GLU C1313 " ideal model delta sigma weight residual 114.10 130.17 -16.07 2.00e+00 2.50e-01 6.46e+01 angle pdb=" PB ANP A3101 " pdb=" N3B ANP A3101 " pdb=" PG ANP A3101 " ideal model delta sigma weight residual 126.95 109.48 17.47 3.00e+00 1.11e-01 3.39e+01 angle pdb=" PB ANP C3101 " pdb=" N3B ANP C3101 " pdb=" PG ANP C3101 " ideal model delta sigma weight residual 126.95 109.48 17.47 3.00e+00 1.11e-01 3.39e+01 angle pdb=" N GLU C1313 " pdb=" CA GLU C1313 " pdb=" CB GLU C1313 " ideal model delta sigma weight residual 110.28 116.88 -6.60 1.55e+00 4.16e-01 1.81e+01 ... (remaining 61459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 24975 17.98 - 35.96: 2221 35.96 - 53.94: 370 53.94 - 71.92: 104 71.92 - 89.91: 46 Dihedral angle restraints: 27716 sinusoidal: 11298 harmonic: 16418 Sorted by residual: dihedral pdb=" CD ARG A1262 " pdb=" NE ARG A1262 " pdb=" CZ ARG A1262 " pdb=" NH1 ARG A1262 " ideal model delta sinusoidal sigma weight residual 0.00 -88.30 88.30 1 1.00e+01 1.00e-02 9.32e+01 dihedral pdb=" CD ARG C1262 " pdb=" NE ARG C1262 " pdb=" CZ ARG C1262 " pdb=" NH1 ARG C1262 " ideal model delta sinusoidal sigma weight residual 0.00 -88.27 88.27 1 1.00e+01 1.00e-02 9.31e+01 dihedral pdb=" CA LEU C 443 " pdb=" C LEU C 443 " pdb=" N PRO C 444 " pdb=" CA PRO C 444 " ideal model delta harmonic sigma weight residual 180.00 -156.85 -23.15 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 27713 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 6077 0.054 - 0.109: 911 0.109 - 0.163: 51 0.163 - 0.218: 1 0.218 - 0.272: 4 Chirality restraints: 7044 Sorted by residual: chirality pdb=" C3' ANP C3101 " pdb=" C2' ANP C3101 " pdb=" C4' ANP C3101 " pdb=" O3' ANP C3101 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C3' ANP A3101 " pdb=" C2' ANP A3101 " pdb=" C4' ANP A3101 " pdb=" O3' ANP A3101 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA GLU A1313 " pdb=" N GLU A1313 " pdb=" C GLU A1313 " pdb=" CB GLU A1313 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 7041 not shown) Planarity restraints: 7740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1262 " -1.028 9.50e-02 1.11e+02 4.61e-01 1.29e+02 pdb=" NE ARG A1262 " 0.067 2.00e-02 2.50e+03 pdb=" CZ ARG A1262 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A1262 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG A1262 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C1262 " -1.028 9.50e-02 1.11e+02 4.61e-01 1.29e+02 pdb=" NE ARG C1262 " 0.067 2.00e-02 2.50e+03 pdb=" CZ ARG C1262 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG C1262 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG C1262 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 443 " 0.041 5.00e-02 4.00e+02 6.03e-02 5.82e+00 pdb=" N PRO A 444 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 444 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 444 " 0.034 5.00e-02 4.00e+02 ... (remaining 7737 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 302 2.64 - 3.20: 40965 3.20 - 3.77: 68861 3.77 - 4.33: 93270 4.33 - 4.90: 153595 Nonbonded interactions: 356993 Sorted by model distance: nonbonded pdb=" N GLU C1313 " pdb=" OE1 GLU C1313 " model vdw 2.072 2.520 nonbonded pdb=" N GLU A1313 " pdb=" OE1 GLU A1313 " model vdw 2.072 2.520 nonbonded pdb=" O ALA C1309 " pdb=" OE1 GLU C1313 " model vdw 2.244 3.040 nonbonded pdb=" O ALA A1309 " pdb=" OE1 GLU A1313 " model vdw 2.244 3.040 nonbonded pdb=" O PHE C1298 " pdb=" NH2 ARG C1312 " model vdw 2.266 2.520 ... (remaining 356988 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 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: 0.030 Extract box with map and model: 9.680 Check model and map are aligned: 0.590 Set scattering table: 0.370 Process input model: 110.320 Find NCS groups from input model: 2.470 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5911 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 : 0.003 0.144 45484 Z= 0.172 Angle : 0.529 17.475 61464 Z= 0.275 Chirality : 0.036 0.272 7044 Planarity : 0.008 0.461 7740 Dihedral : 14.328 89.906 17008 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.12), residues: 5486 helix: 2.47 (0.09), residues: 3820 sheet: 0.50 (0.61), residues: 62 loop : -0.35 (0.16), residues: 1604 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10972 Ramachandran restraints generated. 5486 Oldfield, 0 Emsley, 5486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10972 Ramachandran restraints generated. 5486 Oldfield, 0 Emsley, 5486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 5058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 605 time to evaluate : 5.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 6 residues processed: 636 average time/residue: 1.7594 time to fit residues: 1359.6507 Evaluate side-chains 369 residues out of total 5058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 363 time to evaluate : 4.735 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 2 average time/residue: 0.4641 time to fit residues: 9.5480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 469 optimal weight: 3.9990 chunk 421 optimal weight: 0.8980 chunk 233 optimal weight: 8.9990 chunk 143 optimal weight: 1.9990 chunk 284 optimal weight: 8.9990 chunk 225 optimal weight: 3.9990 chunk 435 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 chunk 264 optimal weight: 0.9980 chunk 324 optimal weight: 10.0000 chunk 504 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN A 654 GLN A 684 GLN A1223 ASN A1380 HIS A1384 HIS A1578 GLN A1638 ASN A2069 GLN A2108 GLN A2177 GLN A2243 GLN A2358 GLN A2697 ASN C 180 GLN C 654 GLN C1380 HIS C1384 HIS C1578 GLN C1638 ASN C1720 ASN C2069 GLN C2108 GLN C2177 GLN C2243 GLN C2358 GLN C2697 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6065 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 45484 Z= 0.280 Angle : 0.611 9.779 61464 Z= 0.310 Chirality : 0.042 0.249 7044 Planarity : 0.005 0.113 7740 Dihedral : 4.135 49.428 5982 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer Outliers : 2.10 % 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: 1.83 (0.11), residues: 5486 helix: 1.90 (0.08), residues: 3840 sheet: 0.47 (0.59), residues: 62 loop : -0.42 (0.15), residues: 1584 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10972 Ramachandran restraints generated. 5486 Oldfield, 0 Emsley, 5486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10972 Ramachandran restraints generated. 5486 Oldfield, 0 Emsley, 5486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 5058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 380 time to evaluate : 5.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 104 outliers final: 28 residues processed: 452 average time/residue: 1.5475 time to fit residues: 858.8593 Evaluate side-chains 353 residues out of total 5058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 325 time to evaluate : 3.662 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 24 residues processed: 4 average time/residue: 0.8059 time to fit residues: 9.8425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 280 optimal weight: 20.0000 chunk 156 optimal weight: 0.9990 chunk 420 optimal weight: 1.9990 chunk 343 optimal weight: 0.9990 chunk 139 optimal weight: 0.8980 chunk 505 optimal weight: 0.8980 chunk 546 optimal weight: 3.9990 chunk 450 optimal weight: 0.7980 chunk 501 optimal weight: 4.9990 chunk 172 optimal weight: 0.5980 chunk 405 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN A 628 GLN A1640 GLN A1660 ASN A2069 GLN A2177 GLN A2243 GLN A2358 GLN A2697 ASN C 65 GLN C 628 GLN C1223 ASN C1640 GLN C1660 ASN C2069 GLN C2070 ASN C2177 GLN C2243 GLN C2358 GLN C2469 ASN C2697 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6036 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 45484 Z= 0.149 Angle : 0.477 8.968 61464 Z= 0.242 Chirality : 0.037 0.220 7044 Planarity : 0.004 0.053 7740 Dihedral : 3.781 43.204 5982 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer Outliers : 1.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.11), residues: 5486 helix: 2.20 (0.08), residues: 3798 sheet: 0.49 (0.59), residues: 62 loop : -0.34 (0.15), residues: 1626 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10972 Ramachandran restraints generated. 5486 Oldfield, 0 Emsley, 5486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10972 Ramachandran restraints generated. 5486 Oldfield, 0 Emsley, 5486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 5058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 330 time to evaluate : 5.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 98 outliers final: 30 residues processed: 397 average time/residue: 1.5109 time to fit residues: 743.0071 Evaluate side-chains 340 residues out of total 5058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 310 time to evaluate : 3.724 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 26 residues processed: 4 average time/residue: 0.7692 time to fit residues: 9.9239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 499 optimal weight: 0.8980 chunk 380 optimal weight: 0.3980 chunk 262 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 241 optimal weight: 9.9990 chunk 339 optimal weight: 9.9990 chunk 507 optimal weight: 0.9990 chunk 537 optimal weight: 0.9980 chunk 265 optimal weight: 0.8980 chunk 481 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN A1640 GLN A1660 ASN A1951 HIS A2069 GLN A2697 ASN C1640 GLN C1660 ASN C2069 GLN C2358 GLN C2697 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6035 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 45484 Z= 0.146 Angle : 0.466 8.184 61464 Z= 0.237 Chirality : 0.036 0.173 7044 Planarity : 0.003 0.040 7740 Dihedral : 3.685 42.554 5982 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.12), residues: 5486 helix: 2.24 (0.08), residues: 3804 sheet: 0.48 (0.58), residues: 62 loop : -0.36 (0.15), residues: 1620 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10972 Ramachandran restraints generated. 5486 Oldfield, 0 Emsley, 5486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10972 Ramachandran restraints generated. 5486 Oldfield, 0 Emsley, 5486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 5058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 335 time to evaluate : 3.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 100 outliers final: 32 residues processed: 404 average time/residue: 1.7131 time to fit residues: 855.1335 Evaluate side-chains 347 residues out of total 5058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 315 time to evaluate : 5.199 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 30 residues processed: 2 average time/residue: 0.4644 time to fit residues: 9.4557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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: 69.6546 > 50: distance: 63 - 89: 34.670 distance: 70 - 97: 36.675 distance: 78 - 82: 13.213 distance: 79 - 105: 31.998 distance: 82 - 83: 32.551 distance: 83 - 84: 6.771 distance: 83 - 86: 32.454 distance: 84 - 85: 7.942 distance: 84 - 89: 8.737 distance: 85 - 113: 41.589 distance: 86 - 87: 22.634 distance: 86 - 88: 37.858 distance: 89 - 90: 40.708 distance: 90 - 91: 28.060 distance: 90 - 93: 29.211 distance: 91 - 92: 29.159 distance: 91 - 97: 40.113 distance: 92 - 121: 60.713 distance: 93 - 94: 21.822 distance: 94 - 95: 40.370 distance: 98 - 99: 42.086 distance: 99 - 100: 34.098 distance: 99 - 105: 42.165 distance: 100 - 130: 39.369 distance: 105 - 106: 25.964 distance: 106 - 107: 14.424 distance: 106 - 109: 8.868 distance: 107 - 108: 14.545 distance: 107 - 113: 15.047 distance: 108 - 142: 36.065 distance: 109 - 110: 5.534 distance: 110 - 111: 5.832 distance: 110 - 112: 19.572 distance: 113 - 114: 11.930 distance: 114 - 115: 3.664 distance: 114 - 117: 36.579 distance: 115 - 116: 3.249 distance: 116 - 150: 50.739 distance: 117 - 118: 35.890 distance: 118 - 119: 38.897 distance: 118 - 120: 24.661 distance: 121 - 122: 32.258 distance: 122 - 123: 48.373 distance: 122 - 125: 37.509 distance: 123 - 124: 28.251 distance: 123 - 130: 6.991 distance: 125 - 126: 35.663 distance: 126 - 127: 40.803 distance: 127 - 128: 31.954 distance: 128 - 129: 43.505 distance: 130 - 131: 10.044 distance: 131 - 132: 18.402 distance: 131 - 134: 45.791 distance: 132 - 142: 4.595 distance: 135 - 136: 40.249 distance: 135 - 137: 55.673 distance: 138 - 140: 69.141 distance: 143 - 144: 6.043 distance: 144 - 145: 5.030 distance: 144 - 150: 28.403 distance: 147 - 148: 29.785 distance: 150 - 151: 7.727 distance: 151 - 152: 21.389 distance: 151 - 154: 36.806 distance: 152 - 153: 27.471 distance: 152 - 157: 20.911 distance: 154 - 155: 37.387 distance: 154 - 156: 7.783 distance: 158 - 159: 20.006 distance: 158 - 161: 39.268 distance: 159 - 160: 5.757 distance: 159 - 165: 27.948