Starting phenix.real_space_refine on Wed Sep 25 21:18:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6t_10105/09_2024/6s6t_10105.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6t_10105/09_2024/6s6t_10105.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6t_10105/09_2024/6s6t_10105.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6t_10105/09_2024/6s6t_10105.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6t_10105/09_2024/6s6t_10105.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s6t_10105/09_2024/6s6t_10105.cif" } resolution = 4.1 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= 0.018 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 Fe 36 7.16 5 P 10 5.49 5 S 331 5.16 5 C 35335 2.51 5 N 10164 2.21 5 O 10667 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 194 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 56543 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 11337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1472, 11337 Classifications: {'peptide': 1472} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1409} Chain: "B" Number of atoms: 11337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1472, 11337 Classifications: {'peptide': 1472} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1409} Chain: "C" Number of atoms: 11337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1472, 11337 Classifications: {'peptide': 1472} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1409} Chain: "D" Number of atoms: 11337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1472, 11337 Classifications: {'peptide': 1472} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1409} Chain: "E" Number of atoms: 3612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3612 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 20, 'TRANS': 451} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 3612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3612 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 20, 'TRANS': 451} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 3612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3612 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 20, 'TRANS': 451} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'F3S': 1, 'FMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'F3S': 1, 'FMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'F3S': 1, 'FMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'F3S': 1, 'FMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'FAD': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'FAD': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'FAD': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8585 SG CYS A1113 58.027 148.354 67.636 1.00 48.66 S ATOM 8499 SG CYS A1102 61.549 144.976 67.678 1.00 46.01 S ATOM 8548 SG CYS A1108 62.702 149.858 69.310 1.00 55.93 S ATOM 19922 SG CYS B1113 28.054 85.130 107.898 1.00119.77 S ATOM 19836 SG CYS B1102 31.865 82.064 109.858 1.00122.54 S ATOM 19922 SG CYS B1113 28.054 85.130 107.898 1.00119.77 S ATOM 19885 SG CYS B1108 30.476 82.708 104.296 1.00120.39 S ATOM 31259 SG CYS C1113 136.590 57.080 71.108 1.00 48.85 S ATOM 31173 SG CYS C1102 131.933 60.711 69.603 1.00 42.66 S ATOM 31222 SG CYS C1108 130.767 55.276 72.698 1.00 53.14 S ATOM 42596 SG CYS D1113 165.955 122.538 106.625 1.00 73.28 S ATOM 42510 SG CYS D1102 161.140 125.000 108.192 1.00 68.94 S ATOM 42559 SG CYS D1108 163.205 124.318 102.894 1.00 70.77 S ATOM 45743 SG CYS E 51 58.874 150.120 56.792 1.00 53.57 S ATOM 45743 SG CYS E 51 58.874 150.120 56.792 1.00 53.57 S ATOM 45778 SG CYS E 56 58.104 149.749 51.934 1.00 48.22 S ATOM 45722 SG CYS E 48 56.197 154.189 54.940 1.00 61.73 S ATOM 46193 SG CYS E 109 53.910 149.087 54.813 1.00 51.65 S ATOM 45810 SG CYS E 60 56.778 146.988 43.514 1.00 53.20 S ATOM 46166 SG CYS E 105 53.494 147.386 45.022 1.00 60.80 S ATOM 45810 SG CYS E 60 56.778 146.988 43.514 1.00 53.20 S ATOM 46117 SG CYS E 99 52.223 145.941 41.534 1.00 63.29 S ATOM 46166 SG CYS E 105 53.494 147.386 45.022 1.00 60.80 S ATOM 49334 SG CYS F 48 137.382 50.603 58.145 1.00 61.51 S ATOM 49355 SG CYS F 51 135.027 54.115 59.686 1.00 51.90 S ATOM 49390 SG CYS F 56 135.511 54.381 55.180 1.00 49.09 S ATOM 49334 SG CYS F 48 137.382 50.603 58.145 1.00 61.51 S ATOM 49805 SG CYS F 109 140.053 54.523 58.014 1.00 53.53 S ATOM 49805 SG CYS F 109 140.053 54.523 58.014 1.00 53.53 S ATOM 49778 SG CYS F 105 139.740 56.307 48.094 1.00 67.49 S ATOM 49422 SG CYS F 60 136.523 56.484 46.732 1.00 54.80 S ATOM 49729 SG CYS F 99 141.358 57.227 44.458 1.00 72.00 S ATOM 49778 SG CYS F 105 139.740 56.307 48.094 1.00 67.49 S ATOM 52967 SG CYS G 51 170.773 132.556 108.282 1.00 91.57 S ATOM 53002 SG CYS G 56 173.444 136.478 110.591 1.00 85.64 S ATOM 52946 SG CYS G 48 176.187 133.012 106.304 1.00 95.89 S ATOM 53417 SG CYS G 109 175.287 131.171 112.069 1.00 83.15 S ATOM 53390 SG CYS G 105 178.036 139.267 116.895 1.00110.02 S ATOM 53034 SG CYS G 60 176.223 142.599 115.825 1.00 98.57 S ATOM 53341 SG CYS G 99 181.158 141.064 119.295 1.00123.37 S ATOM 53390 SG CYS G 105 178.036 139.267 116.895 1.00110.02 S Time building chain proxies: 25.39, per 1000 atoms: 0.45 Number of scatterers: 56543 At special positions: 0 Unit cell: (216.752, 205.344, 171.12, 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) Fe 36 26.01 S 331 16.00 P 10 15.00 O 10667 8.00 N 10164 7.00 C 35335 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 - 3.00 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: 11.26 Conformation dependent library (CDL) restraints added in 6.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S A1502 " pdb="FE1 F3S A1502 " - pdb=" SG CYS A1113 " pdb="FE3 F3S A1502 " - pdb=" SG CYS A1102 " pdb="FE4 F3S A1502 " - pdb=" SG CYS A1108 " pdb=" F3S B1502 " pdb="FE3 F3S B1502 " - pdb=" SG CYS B1102 " pdb="FE4 F3S B1502 " - pdb=" SG CYS B1108 " pdb="FE1 F3S B1502 " - pdb=" SG CYS B1113 " pdb=" F3S C1502 " pdb="FE1 F3S C1502 " - pdb=" SG CYS C1113 " pdb="FE3 F3S C1502 " - pdb=" SG CYS C1102 " pdb="FE4 F3S C1502 " - pdb=" SG CYS C1108 " pdb=" F3S D1502 " pdb="FE3 F3S D1502 " - pdb=" SG CYS D1102 " pdb="FE4 F3S D1502 " - pdb=" SG CYS D1108 " pdb="FE1 F3S D1502 " - pdb=" SG CYS D1113 " pdb=" SF4 E 501 " pdb="FE1 SF4 E 501 " - pdb=" SG CYS E 51 " pdb="FE4 SF4 E 501 " - pdb=" SG CYS E 109 " pdb="FE3 SF4 E 501 " - pdb=" SG CYS E 48 " pdb="FE2 SF4 E 501 " - pdb=" SG CYS E 56 " pdb=" SF4 E 502 " pdb="FE1 SF4 E 502 " - pdb=" SG CYS E 105 " pdb="FE2 SF4 E 502 " - pdb=" SG CYS E 60 " pdb="FE4 SF4 E 502 " - pdb=" SG CYS E 99 " pdb=" SF4 F 501 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 48 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 51 " pdb="FE2 SF4 F 501 " - pdb=" SG CYS F 56 " pdb="FE4 SF4 F 501 " - pdb=" SG CYS F 109 " pdb=" SF4 F 502 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 105 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 60 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 99 " pdb=" SF4 G 501 " pdb="FE4 SF4 G 501 " - pdb=" SG CYS G 109 " pdb="FE2 SF4 G 501 " - pdb=" SG CYS G 56 " pdb="FE1 SF4 G 501 " - pdb=" SG CYS G 51 " pdb="FE3 SF4 G 501 " - pdb=" SG CYS G 48 " pdb=" SF4 G 502 " pdb="FE1 SF4 G 502 " - pdb=" SG CYS G 105 " pdb="FE2 SF4 G 502 " - pdb=" SG CYS G 60 " pdb="FE4 SF4 G 502 " - pdb=" SG CYS G 99 " Number of angles added : 99 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13166 Finding SS restraints... Secondary structure from input PDB file: 306 helices and 59 sheets defined 41.4% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.35 Creating SS restraints... Processing helix chain 'A' and resid 15 through 26 Processing helix chain 'A' and resid 51 through 63 removed outlier: 3.599A pdb=" N PHE A 55 " --> pdb=" O PRO A 51 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 98 removed outlier: 3.581A pdb=" N ALA A 88 " --> pdb=" O ASP A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 123 removed outlier: 3.797A pdb=" N ASN A 122 " --> pdb=" O GLY A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 162 Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 193 through 197 Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'A' and resid 240 through 248 Processing helix chain 'A' and resid 253 through 264 removed outlier: 3.635A pdb=" N PHE A 256 " --> pdb=" O HIS A 253 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N THR A 258 " --> pdb=" O ALA A 255 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS A 264 " --> pdb=" O GLN A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 286 Processing helix chain 'A' and resid 290 through 299 Processing helix chain 'A' and resid 310 through 324 removed outlier: 3.712A pdb=" N MET A 324 " --> pdb=" O CYS A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 412 Processing helix chain 'A' and resid 413 through 415 No H-bonds generated for 'chain 'A' and resid 413 through 415' Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.986A pdb=" N GLN A 421 " --> pdb=" O ASP A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 433 Processing helix chain 'A' and resid 443 through 454 removed outlier: 3.571A pdb=" N PHE A 454 " --> pdb=" O ARG A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 464 removed outlier: 3.738A pdb=" N ILE A 464 " --> pdb=" O ASP A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 471 removed outlier: 3.615A pdb=" N VAL A 469 " --> pdb=" O LEU A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 497 Processing helix chain 'A' and resid 551 through 563 Processing helix chain 'A' and resid 580 through 598 removed outlier: 3.755A pdb=" N ASP A 584 " --> pdb=" O GLU A 580 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU A 594 " --> pdb=" O ARG A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 634 Processing helix chain 'A' and resid 652 through 662 removed outlier: 3.936A pdb=" N GLY A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 681 removed outlier: 3.674A pdb=" N ARG A 681 " --> pdb=" O GLU A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 710 removed outlier: 3.561A pdb=" N GLY A 692 " --> pdb=" O PRO A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 719 Processing helix chain 'A' and resid 731 through 738 Processing helix chain 'A' and resid 750 through 767 removed outlier: 3.802A pdb=" N ILE A 754 " --> pdb=" O GLY A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 805 removed outlier: 3.773A pdb=" N ILE A 795 " --> pdb=" O GLU A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 819 removed outlier: 3.541A pdb=" N PHE A 810 " --> pdb=" O SER A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 828 removed outlier: 3.913A pdb=" N LEU A 828 " --> pdb=" O GLN A 824 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 824 through 828' Processing helix chain 'A' and resid 845 through 851 removed outlier: 3.529A pdb=" N ILE A 849 " --> pdb=" O SER A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 879 removed outlier: 3.984A pdb=" N ILE A 878 " --> pdb=" O ALA A 874 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY A 879 " --> pdb=" O MET A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 919 through 923 Processing helix chain 'A' and resid 950 through 958 Processing helix chain 'A' and resid 976 through 991 Processing helix chain 'A' and resid 1005 through 1016 removed outlier: 4.300A pdb=" N ILE A1009 " --> pdb=" O GLY A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1040 Processing helix chain 'A' and resid 1044 through 1059 removed outlier: 4.037A pdb=" N GLY A1048 " --> pdb=" O PRO A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1061 through 1065 Processing helix chain 'A' and resid 1075 through 1086 removed outlier: 3.825A pdb=" N ILE A1079 " --> pdb=" O THR A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1101 removed outlier: 3.621A pdb=" N LEU A1097 " --> pdb=" O GLY A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1107 through 1111 removed outlier: 3.790A pdb=" N ASN A1111 " --> pdb=" O CYS A1108 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1154 removed outlier: 3.766A pdb=" N VAL A1135 " --> pdb=" O THR A1131 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY A1154 " --> pdb=" O LEU A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1157 through 1161 removed outlier: 3.624A pdb=" N GLU A1160 " --> pdb=" O SER A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1166 No H-bonds generated for 'chain 'A' and resid 1164 through 1166' Processing helix chain 'A' and resid 1183 through 1188 removed outlier: 3.808A pdb=" N LEU A1187 " --> pdb=" O LEU A1183 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A1188 " --> pdb=" O ASN A1184 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1183 through 1188' Processing helix chain 'A' and resid 1211 through 1217 removed outlier: 3.550A pdb=" N ALA A1217 " --> pdb=" O ALA A1213 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1226 removed outlier: 3.813A pdb=" N PHE A1223 " --> pdb=" O ALA A1219 " (cutoff:3.500A) Processing helix chain 'A' and resid 1243 through 1254 Processing helix chain 'A' and resid 1316 through 1320 removed outlier: 4.195A pdb=" N ASN A1320 " --> pdb=" O THR A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1400 through 1405 removed outlier: 3.688A pdb=" N TYR A1404 " --> pdb=" O SER A1400 " (cutoff:3.500A) Processing helix chain 'A' and resid 1417 through 1435 Processing helix chain 'A' and resid 1438 through 1446 Processing helix chain 'A' and resid 1461 through 1463 No H-bonds generated for 'chain 'A' and resid 1461 through 1463' Processing helix chain 'B' and resid 15 through 26 Processing helix chain 'B' and resid 51 through 63 Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 85 through 98 Processing helix chain 'B' and resid 140 through 162 removed outlier: 3.544A pdb=" N GLU B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 192 Processing helix chain 'B' and resid 193 through 197 Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 239 through 248 removed outlier: 3.858A pdb=" N TRP B 243 " --> pdb=" O GLY B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 251 No H-bonds generated for 'chain 'B' and resid 249 through 251' Processing helix chain 'B' and resid 256 through 264 removed outlier: 4.326A pdb=" N HIS B 259 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS B 264 " --> pdb=" O GLN B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 286 Processing helix chain 'B' and resid 290 through 299 Processing helix chain 'B' and resid 310 through 324 removed outlier: 3.785A pdb=" N MET B 324 " --> pdb=" O CYS B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 412 Processing helix chain 'B' and resid 419 through 423 removed outlier: 4.004A pdb=" N THR B 423 " --> pdb=" O VAL B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 432 Processing helix chain 'B' and resid 443 through 454 removed outlier: 3.629A pdb=" N PHE B 454 " --> pdb=" O ARG B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 464 Processing helix chain 'B' and resid 465 through 471 Processing helix chain 'B' and resid 494 through 497 Processing helix chain 'B' and resid 537 through 541 removed outlier: 3.848A pdb=" N ARG B 541 " --> pdb=" O THR B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 562 Processing helix chain 'B' and resid 580 through 599 removed outlier: 3.902A pdb=" N ARG B 598 " --> pdb=" O GLU B 594 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY B 599 " --> pdb=" O ASP B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 634 Processing helix chain 'B' and resid 651 through 660 removed outlier: 4.493A pdb=" N PHE B 655 " --> pdb=" O ASP B 651 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA B 656 " --> pdb=" O THR B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 680 removed outlier: 3.662A pdb=" N GLN B 672 " --> pdb=" O ALA B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 710 Processing helix chain 'B' and resid 715 through 719 Processing helix chain 'B' and resid 731 through 738 Processing helix chain 'B' and resid 751 through 767 Processing helix chain 'B' and resid 791 through 804 Processing helix chain 'B' and resid 807 through 819 Processing helix chain 'B' and resid 824 through 828 removed outlier: 4.170A pdb=" N LEU B 828 " --> pdb=" O GLN B 824 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 824 through 828' Processing helix chain 'B' and resid 845 through 851 Processing helix chain 'B' and resid 864 through 879 removed outlier: 3.660A pdb=" N ILE B 878 " --> pdb=" O ALA B 874 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY B 879 " --> pdb=" O MET B 875 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 894 Processing helix chain 'B' and resid 920 through 924 removed outlier: 3.904A pdb=" N GLN B 924 " --> pdb=" O TYR B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 949 removed outlier: 3.648A pdb=" N LYS B 948 " --> pdb=" O PRO B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 957 Processing helix chain 'B' and resid 976 through 991 removed outlier: 3.690A pdb=" N ASN B 991 " --> pdb=" O LEU B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1005 through 1015 removed outlier: 4.176A pdb=" N ILE B1009 " --> pdb=" O GLY B1005 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS B1015 " --> pdb=" O ALA B1011 " (cutoff:3.500A) Processing helix chain 'B' and resid 1034 through 1040 Processing helix chain 'B' and resid 1044 through 1059 removed outlier: 3.938A pdb=" N GLY B1048 " --> pdb=" O PRO B1044 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN B1054 " --> pdb=" O SER B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1061 through 1065 removed outlier: 3.785A pdb=" N VAL B1065 " --> pdb=" O ARG B1062 " (cutoff:3.500A) Processing helix chain 'B' and resid 1075 through 1086 Processing helix chain 'B' and resid 1093 through 1101 removed outlier: 3.510A pdb=" N LEU B1097 " --> pdb=" O GLY B1093 " (cutoff:3.500A) Processing helix chain 'B' and resid 1107 through 1111 Processing helix chain 'B' and resid 1124 through 1128 removed outlier: 3.506A pdb=" N LYS B1127 " --> pdb=" O LEU B1124 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE B1128 " --> pdb=" O ARG B1125 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1124 through 1128' Processing helix chain 'B' and resid 1131 through 1154 removed outlier: 3.981A pdb=" N VAL B1135 " --> pdb=" O THR B1131 " (cutoff:3.500A) Processing helix chain 'B' and resid 1157 through 1161 removed outlier: 3.586A pdb=" N GLU B1160 " --> pdb=" O SER B1157 " (cutoff:3.500A) Processing helix chain 'B' and resid 1164 through 1166 No H-bonds generated for 'chain 'B' and resid 1164 through 1166' Processing helix chain 'B' and resid 1183 through 1188 removed outlier: 3.554A pdb=" N ALA B1188 " --> pdb=" O ASN B1184 " (cutoff:3.500A) Processing helix chain 'B' and resid 1211 through 1219 Processing helix chain 'B' and resid 1220 through 1225 Processing helix chain 'B' and resid 1243 through 1254 removed outlier: 3.613A pdb=" N SER B1247 " --> pdb=" O GLY B1243 " (cutoff:3.500A) Processing helix chain 'B' and resid 1400 through 1404 Processing helix chain 'B' and resid 1417 through 1436 removed outlier: 3.572A pdb=" N GLU B1421 " --> pdb=" O VAL B1417 " (cutoff:3.500A) Processing helix chain 'B' and resid 1438 through 1446 Processing helix chain 'B' and resid 1446 through 1451 removed outlier: 3.729A pdb=" N GLU B1450 " --> pdb=" O ASP B1446 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL B1451 " --> pdb=" O TRP B1447 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1446 through 1451' Processing helix chain 'B' and resid 1461 through 1463 No H-bonds generated for 'chain 'B' and resid 1461 through 1463' Processing helix chain 'C' and resid 14 through 26 removed outlier: 4.457A pdb=" N VAL C 18 " --> pdb=" O ARG C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 32 removed outlier: 5.445A pdb=" N HIS C 30 " --> pdb=" O ALA C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 63 removed outlier: 3.552A pdb=" N PHE C 55 " --> pdb=" O PRO C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 98 removed outlier: 3.689A pdb=" N ALA C 88 " --> pdb=" O ASP C 84 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU C 98 " --> pdb=" O GLU C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 117 removed outlier: 4.005A pdb=" N ILE C 116 " --> pdb=" O ASN C 113 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE C 117 " --> pdb=" O VAL C 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 113 through 117' Processing helix chain 'C' and resid 118 through 123 Processing helix chain 'C' and resid 140 through 161 Processing helix chain 'C' and resid 187 through 192 Processing helix chain 'C' and resid 193 through 197 Processing helix chain 'C' and resid 218 through 222 removed outlier: 3.594A pdb=" N ALA C 222 " --> pdb=" O TRP C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 248 removed outlier: 3.902A pdb=" N VAL C 241 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASN C 242 " --> pdb=" O LYS C 238 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N TRP C 243 " --> pdb=" O GLY C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 264 removed outlier: 4.118A pdb=" N HIS C 259 " --> pdb=" O PHE C 256 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS C 264 " --> pdb=" O GLN C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 286 Processing helix chain 'C' and resid 290 through 299 Processing helix chain 'C' and resid 310 through 324 removed outlier: 3.529A pdb=" N LYS C 314 " --> pdb=" O PRO C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 412 Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.584A pdb=" N TRP C 419 " --> pdb=" O PRO C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 431 Processing helix chain 'C' and resid 443 through 453 Processing helix chain 'C' and resid 459 through 464 Processing helix chain 'C' and resid 464 through 471 removed outlier: 3.999A pdb=" N MET C 468 " --> pdb=" O ILE C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 489 Processing helix chain 'C' and resid 494 through 497 Processing helix chain 'C' and resid 516 through 520 removed outlier: 3.629A pdb=" N VAL C 519 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 541 removed outlier: 3.534A pdb=" N GLN C 539 " --> pdb=" O ASP C 536 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR C 540 " --> pdb=" O GLU C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 563 Processing helix chain 'C' and resid 576 through 578 No H-bonds generated for 'chain 'C' and resid 576 through 578' Processing helix chain 'C' and resid 580 through 598 removed outlier: 3.924A pdb=" N ASP C 584 " --> pdb=" O GLU C 580 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLU C 594 " --> pdb=" O ARG C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 634 removed outlier: 3.844A pdb=" N ALA C 623 " --> pdb=" O PRO C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 640 removed outlier: 3.527A pdb=" N THR C 640 " --> pdb=" O ARG C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 661 removed outlier: 4.151A pdb=" N PHE C 655 " --> pdb=" O ASP C 651 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 661 " --> pdb=" O VAL C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 680 removed outlier: 4.147A pdb=" N GLN C 672 " --> pdb=" O ALA C 668 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU C 673 " --> pdb=" O TYR C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 710 removed outlier: 3.662A pdb=" N GLY C 692 " --> pdb=" O PRO C 688 " (cutoff:3.500A) Processing helix chain 'C' and resid 715 through 719 removed outlier: 3.619A pdb=" N SER C 718 " --> pdb=" O VAL C 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 731 through 739 Processing helix chain 'C' and resid 751 through 766 Processing helix chain 'C' and resid 791 through 805 Processing helix chain 'C' and resid 806 through 819 Processing helix chain 'C' and resid 824 through 827 Processing helix chain 'C' and resid 839 through 843 Processing helix chain 'C' and resid 845 through 851 Processing helix chain 'C' and resid 864 through 879 removed outlier: 4.223A pdb=" N ILE C 878 " --> pdb=" O ALA C 874 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY C 879 " --> pdb=" O MET C 875 " (cutoff:3.500A) Processing helix chain 'C' and resid 890 through 894 Processing helix chain 'C' and resid 945 through 949 removed outlier: 3.618A pdb=" N LYS C 948 " --> pdb=" O PRO C 945 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL C 949 " --> pdb=" O GLY C 946 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 945 through 949' Processing helix chain 'C' and resid 950 through 958 Processing helix chain 'C' and resid 976 through 991 Processing helix chain 'C' and resid 1005 through 1015 removed outlier: 3.897A pdb=" N ILE C1009 " --> pdb=" O GLY C1005 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS C1015 " --> pdb=" O ALA C1011 " (cutoff:3.500A) Processing helix chain 'C' and resid 1035 through 1040 Processing helix chain 'C' and resid 1044 through 1059 removed outlier: 3.980A pdb=" N GLY C1048 " --> pdb=" O PRO C1044 " (cutoff:3.500A) Processing helix chain 'C' and resid 1075 through 1086 removed outlier: 3.834A pdb=" N ILE C1079 " --> pdb=" O THR C1075 " (cutoff:3.500A) Processing helix chain 'C' and resid 1093 through 1101 Processing helix chain 'C' and resid 1107 through 1111 removed outlier: 3.745A pdb=" N ASN C1111 " --> pdb=" O CYS C1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 1123 through 1127 removed outlier: 3.607A pdb=" N GLN C1126 " --> pdb=" O LYS C1123 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS C1127 " --> pdb=" O LEU C1124 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1123 through 1127' Processing helix chain 'C' and resid 1131 through 1154 removed outlier: 3.910A pdb=" N VAL C1135 " --> pdb=" O THR C1131 " (cutoff:3.500A) Processing helix chain 'C' and resid 1157 through 1161 Processing helix chain 'C' and resid 1164 through 1166 No H-bonds generated for 'chain 'C' and resid 1164 through 1166' Processing helix chain 'C' and resid 1183 through 1187 Processing helix chain 'C' and resid 1211 through 1217 removed outlier: 3.792A pdb=" N ILE C1215 " --> pdb=" O LEU C1211 " (cutoff:3.500A) Processing helix chain 'C' and resid 1219 through 1226 Processing helix chain 'C' and resid 1244 through 1254 Processing helix chain 'C' and resid 1400 through 1404 Processing helix chain 'C' and resid 1417 through 1436 Processing helix chain 'C' and resid 1438 through 1446 removed outlier: 4.116A pdb=" N ASP C1446 " --> pdb=" O GLU C1442 " (cutoff:3.500A) Processing helix chain 'C' and resid 1447 through 1450 Processing helix chain 'C' and resid 1461 through 1463 No H-bonds generated for 'chain 'C' and resid 1461 through 1463' Processing helix chain 'D' and resid 14 through 26 removed outlier: 4.345A pdb=" N VAL D 18 " --> pdb=" O ARG D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 63 removed outlier: 3.553A pdb=" N PHE D 55 " --> pdb=" O PRO D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 98 removed outlier: 4.281A pdb=" N GLN D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLU D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA D 88 " --> pdb=" O ASP D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 161 Processing helix chain 'D' and resid 187 through 192 Processing helix chain 'D' and resid 193 through 197 Processing helix chain 'D' and resid 218 through 222 Processing helix chain 'D' and resid 237 through 248 removed outlier: 3.801A pdb=" N ASN D 242 " --> pdb=" O LYS D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 256 through 264 removed outlier: 3.704A pdb=" N HIS D 259 " --> pdb=" O PHE D 256 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS D 264 " --> pdb=" O GLN D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 286 Processing helix chain 'D' and resid 290 through 299 removed outlier: 3.639A pdb=" N VAL D 294 " --> pdb=" O THR D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 324 removed outlier: 3.508A pdb=" N LYS D 314 " --> pdb=" O PRO D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 413 removed outlier: 3.936A pdb=" N LEU D 413 " --> pdb=" O HIS D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 420 removed outlier: 3.938A pdb=" N TRP D 419 " --> pdb=" O PRO D 415 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL D 420 " --> pdb=" O TRP D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 415 through 420' Processing helix chain 'D' and resid 426 through 432 removed outlier: 3.588A pdb=" N THR D 432 " --> pdb=" O GLU D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 453 Processing helix chain 'D' and resid 459 through 464 Processing helix chain 'D' and resid 465 through 471 Processing helix chain 'D' and resid 494 through 497 Processing helix chain 'D' and resid 516 through 520 removed outlier: 3.529A pdb=" N VAL D 519 " --> pdb=" O GLU D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 563 Processing helix chain 'D' and resid 576 through 578 No H-bonds generated for 'chain 'D' and resid 576 through 578' Processing helix chain 'D' and resid 580 through 600 removed outlier: 3.557A pdb=" N ASP D 584 " --> pdb=" O GLU D 580 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU D 594 " --> pdb=" O ARG D 590 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG D 598 " --> pdb=" O GLU D 594 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY D 599 " --> pdb=" O ASP D 595 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY D 600 " --> pdb=" O ALA D 596 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 634 Processing helix chain 'D' and resid 636 through 640 Processing helix chain 'D' and resid 651 through 660 removed outlier: 4.065A pdb=" N PHE D 655 " --> pdb=" O ASP D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 681 removed outlier: 3.769A pdb=" N GLU D 673 " --> pdb=" O TYR D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 710 Processing helix chain 'D' and resid 715 through 719 Processing helix chain 'D' and resid 731 through 739 Processing helix chain 'D' and resid 750 through 767 removed outlier: 4.328A pdb=" N ILE D 754 " --> pdb=" O GLY D 750 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN D 755 " --> pdb=" O LEU D 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 791 through 805 Processing helix chain 'D' and resid 806 through 819 Processing helix chain 'D' and resid 824 through 827 Processing helix chain 'D' and resid 839 through 843 removed outlier: 3.743A pdb=" N VAL D 843 " --> pdb=" O VAL D 840 " (cutoff:3.500A) Processing helix chain 'D' and resid 846 through 851 Processing helix chain 'D' and resid 864 through 879 removed outlier: 4.283A pdb=" N ILE D 878 " --> pdb=" O ALA D 874 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY D 879 " --> pdb=" O MET D 875 " (cutoff:3.500A) Processing helix chain 'D' and resid 890 through 895 removed outlier: 3.518A pdb=" N ARG D 893 " --> pdb=" O ASP D 890 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ARG D 895 " --> pdb=" O ALA D 892 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 924 removed outlier: 4.227A pdb=" N GLN D 924 " --> pdb=" O TYR D 921 " (cutoff:3.500A) Processing helix chain 'D' and resid 950 through 958 Processing helix chain 'D' and resid 976 through 991 Processing helix chain 'D' and resid 1005 through 1015 removed outlier: 4.370A pdb=" N ILE D1009 " --> pdb=" O GLY D1005 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS D1015 " --> pdb=" O ALA D1011 " (cutoff:3.500A) Processing helix chain 'D' and resid 1034 through 1040 Processing helix chain 'D' and resid 1044 through 1059 removed outlier: 4.214A pdb=" N GLY D1048 " --> pdb=" O PRO D1044 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN D1054 " --> pdb=" O SER D1050 " (cutoff:3.500A) Processing helix chain 'D' and resid 1061 through 1065 removed outlier: 3.526A pdb=" N VAL D1065 " --> pdb=" O ARG D1062 " (cutoff:3.500A) Processing helix chain 'D' and resid 1075 through 1086 Processing helix chain 'D' and resid 1093 through 1101 Processing helix chain 'D' and resid 1107 through 1111 removed outlier: 3.531A pdb=" N ASN D1111 " --> pdb=" O CYS D1108 " (cutoff:3.500A) Processing helix chain 'D' and resid 1121 through 1126 removed outlier: 3.963A pdb=" N GLN D1126 " --> pdb=" O ASP D1122 " (cutoff:3.500A) Processing helix chain 'D' and resid 1131 through 1154 removed outlier: 3.998A pdb=" N VAL D1135 " --> pdb=" O THR D1131 " (cutoff:3.500A) Processing helix chain 'D' and resid 1157 through 1161 Processing helix chain 'D' and resid 1164 through 1166 No H-bonds generated for 'chain 'D' and resid 1164 through 1166' Processing helix chain 'D' and resid 1183 through 1188 Processing helix chain 'D' and resid 1211 through 1219 removed outlier: 3.558A pdb=" N ASP D1218 " --> pdb=" O ARG D1214 " (cutoff:3.500A) Processing helix chain 'D' and resid 1244 through 1254 Processing helix chain 'D' and resid 1316 through 1320 Processing helix chain 'D' and resid 1400 through 1405 Processing helix chain 'D' and resid 1417 through 1436 Processing helix chain 'D' and resid 1437 through 1446 Processing helix chain 'D' and resid 1450 through 1452 No H-bonds generated for 'chain 'D' and resid 1450 through 1452' Processing helix chain 'E' and resid 7 through 11 Processing helix chain 'E' and resid 22 through 26 Processing helix chain 'E' and resid 37 through 45 Processing helix chain 'E' and resid 65 through 74 removed outlier: 3.637A pdb=" N TRP E 69 " --> pdb=" O ASN E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 87 Processing helix chain 'E' and resid 91 through 99 removed outlier: 3.590A pdb=" N CYS E 95 " --> pdb=" O PHE E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 114 removed outlier: 3.595A pdb=" N SER E 114 " --> pdb=" O VAL E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'E' and resid 157 through 171 Processing helix chain 'E' and resid 184 through 188 removed outlier: 3.508A pdb=" N VAL E 188 " --> pdb=" O GLY E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 211 removed outlier: 3.842A pdb=" N VAL E 201 " --> pdb=" O GLU E 197 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA E 211 " --> pdb=" O LEU E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 234 removed outlier: 3.797A pdb=" N LEU E 230 " --> pdb=" O SER E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 275 Processing helix chain 'E' and resid 278 through 283 removed outlier: 3.995A pdb=" N GLU E 282 " --> pdb=" O VAL E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 312 removed outlier: 4.068A pdb=" N ALA E 302 " --> pdb=" O GLY E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 328 Processing helix chain 'E' and resid 331 through 342 removed outlier: 3.866A pdb=" N VAL E 335 " --> pdb=" O SER E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 411 removed outlier: 3.611A pdb=" N ALA E 410 " --> pdb=" O ASP E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 447 removed outlier: 4.425A pdb=" N ARG E 446 " --> pdb=" O GLY E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 450 through 475 Processing helix chain 'F' and resid 7 through 11 Processing helix chain 'F' and resid 22 through 27 removed outlier: 4.202A pdb=" N GLN F 27 " --> pdb=" O GLU F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 45 Processing helix chain 'F' and resid 54 through 59 removed outlier: 3.710A pdb=" N VAL F 58 " --> pdb=" O PRO F 54 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N HIS F 59 " --> pdb=" O PHE F 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 54 through 59' Processing helix chain 'F' and resid 65 through 76 removed outlier: 3.667A pdb=" N TRP F 69 " --> pdb=" O ASN F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 87 Processing helix chain 'F' and resid 91 through 99 Processing helix chain 'F' and resid 109 through 114 removed outlier: 3.643A pdb=" N SER F 114 " --> pdb=" O VAL F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 132 removed outlier: 3.592A pdb=" N ALA F 132 " --> pdb=" O ILE F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 171 Processing helix chain 'F' and resid 184 through 188 removed outlier: 3.781A pdb=" N VAL F 188 " --> pdb=" O GLY F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 211 removed outlier: 3.978A pdb=" N VAL F 201 " --> pdb=" O GLU F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 234 Processing helix chain 'F' and resid 262 through 275 Processing helix chain 'F' and resid 278 through 283 removed outlier: 3.936A pdb=" N GLU F 282 " --> pdb=" O VAL F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 312 Processing helix chain 'F' and resid 324 through 328 Processing helix chain 'F' and resid 332 through 342 removed outlier: 3.808A pdb=" N ALA F 336 " --> pdb=" O GLN F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 412 Processing helix chain 'F' and resid 450 through 475 Processing helix chain 'G' and resid 22 through 26 Processing helix chain 'G' and resid 37 through 45 Processing helix chain 'G' and resid 65 through 75 removed outlier: 3.531A pdb=" N TRP G 69 " --> pdb=" O ASN G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.886A pdb=" N ALA G 81 " --> pdb=" O ARG G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 99 Processing helix chain 'G' and resid 111 through 115 Processing helix chain 'G' and resid 120 through 131 Processing helix chain 'G' and resid 132 through 134 No H-bonds generated for 'chain 'G' and resid 132 through 134' Processing helix chain 'G' and resid 157 through 171 Processing helix chain 'G' and resid 185 through 190 removed outlier: 3.956A pdb=" N TYR G 189 " --> pdb=" O GLY G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 211 removed outlier: 4.097A pdb=" N VAL G 201 " --> pdb=" O GLU G 197 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA G 211 " --> pdb=" O LEU G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 220 through 225 Processing helix chain 'G' and resid 226 through 234 Processing helix chain 'G' and resid 262 through 275 Processing helix chain 'G' and resid 278 through 283 removed outlier: 4.429A pdb=" N GLU G 282 " --> pdb=" O VAL G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 299 through 312 Processing helix chain 'G' and resid 324 through 328 removed outlier: 3.527A pdb=" N ASN G 327 " --> pdb=" O ASP G 324 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET G 328 " --> pdb=" O ARG G 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 324 through 328' Processing helix chain 'G' and resid 332 through 342 removed outlier: 3.751A pdb=" N ALA G 336 " --> pdb=" O GLN G 332 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 411 Processing helix chain 'G' and resid 442 through 447 removed outlier: 4.104A pdb=" N ARG G 446 " --> pdb=" O GLY G 442 " (cutoff:3.500A) Processing helix chain 'G' and resid 450 through 475 Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 181 removed outlier: 4.040A pdb=" N ALA A 49 " --> pdb=" O PHE A 204 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N PHE A 204 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU A 362 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ILE A 357 " --> pdb=" O ILE A 380 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 109 removed outlier: 5.319A pdb=" N ILE A 104 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLY A 134 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY A 106 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N VAL A 73 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LEU A 172 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLN A 75 " --> pdb=" O CYS A 170 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 332 through 336 Processing sheet with id=AA4, first strand: chain 'A' and resid 476 through 477 Processing sheet with id=AA5, first strand: chain 'A' and resid 499 through 501 Processing sheet with id=AA6, first strand: chain 'A' and resid 524 through 526 Processing sheet with id=AA7, first strand: chain 'A' and resid 566 through 569 removed outlier: 6.236A pdb=" N ALA A 567 " --> pdb=" O ILE A 605 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N THR A 607 " --> pdb=" O ALA A 567 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ILE A 569 " --> pdb=" O THR A 607 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N VAL A 604 " --> pdb=" O ASN A 643 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ARG A 645 " --> pdb=" O VAL A 604 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU A 606 " --> pdb=" O ARG A 645 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR A 646 " --> pdb=" O ASN A 667 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 572 through 574 Processing sheet with id=AA9, first strand: chain 'A' and resid 829 through 831 Processing sheet with id=AB1, first strand: chain 'A' and resid 853 through 854 removed outlier: 3.771A pdb=" N GLU A1089 " --> pdb=" O LEU A1067 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ILE A1021 " --> pdb=" O ARG A1068 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ASP A1070 " --> pdb=" O ILE A1021 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE A1023 " --> pdb=" O ASP A1070 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER A1024 " --> pdb=" O LEU A1000 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 943 through 944 Processing sheet with id=AB3, first strand: chain 'A' and resid 1229 through 1231 removed outlier: 6.497A pdb=" N MET A1229 " --> pdb=" O THR A1265 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N ARG A1267 " --> pdb=" O MET A1229 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU A1231 " --> pdb=" O ARG A1267 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ARG A1269 " --> pdb=" O LEU A1231 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ILE A1284 " --> pdb=" O THR A1304 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL A1306 " --> pdb=" O ILE A1284 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU A1286 " --> pdb=" O VAL A1306 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ARG A1308 " --> pdb=" O LEU A1286 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N VAL A1288 " --> pdb=" O ARG A1308 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N LYS A1335 " --> pdb=" O GLY A1302 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N THR A1304 " --> pdb=" O LYS A1335 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N PHE A1337 " --> pdb=" O THR A1304 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL A1306 " --> pdb=" O PHE A1337 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLY A1334 " --> pdb=" O THR A1354 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N VAL A1356 " --> pdb=" O GLY A1334 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU A1336 " --> pdb=" O VAL A1356 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET A1391 " --> pdb=" O GLY A1371 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA A1373 " --> pdb=" O MET A1391 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 176 through 181 removed outlier: 4.140A pdb=" N ALA B 49 " --> pdb=" O PHE B 204 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N PHE B 204 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LEU B 362 " --> pdb=" O THR B 358 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TYR B 355 " --> pdb=" O LYS B 382 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LYS B 382 " --> pdb=" O TYR B 355 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE B 357 " --> pdb=" O ILE B 380 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 104 through 108 removed outlier: 7.178A pdb=" N VAL B 73 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LEU B 172 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLN B 75 " --> pdb=" O CYS B 170 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 333 through 336 Processing sheet with id=AB7, first strand: chain 'B' and resid 499 through 501 Processing sheet with id=AB8, first strand: chain 'B' and resid 524 through 526 Processing sheet with id=AB9, first strand: chain 'B' and resid 566 through 570 removed outlier: 5.577A pdb=" N ALA B 567 " --> pdb=" O ILE B 605 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR B 607 " --> pdb=" O ALA B 567 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ILE B 569 " --> pdb=" O THR B 607 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N VAL B 604 " --> pdb=" O ASN B 643 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ARG B 645 " --> pdb=" O VAL B 604 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU B 606 " --> pdb=" O ARG B 645 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR B 665 " --> pdb=" O LEU B 642 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 572 through 574 Processing sheet with id=AC2, first strand: chain 'B' and resid 829 through 831 Processing sheet with id=AC3, first strand: chain 'B' and resid 853 through 854 removed outlier: 3.757A pdb=" N GLU B1089 " --> pdb=" O LEU B1067 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG B1068 " --> pdb=" O ILE B1021 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP B1070 " --> pdb=" O ILE B1023 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL B 996 " --> pdb=" O ILE B1020 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N LEU B1022 " --> pdb=" O VAL B 996 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL B 998 " --> pdb=" O LEU B1022 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N SER B1024 " --> pdb=" O VAL B 998 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU B1000 " --> pdb=" O SER B1024 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS B 999 " --> pdb=" O ILE B 930 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 1229 through 1234 removed outlier: 6.281A pdb=" N MET B1229 " --> pdb=" O THR B1265 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ARG B1267 " --> pdb=" O MET B1229 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU B1231 " --> pdb=" O ARG B1267 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N ARG B1269 " --> pdb=" O LEU B1231 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TYR B1233 " --> pdb=" O ARG B1269 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE B1284 " --> pdb=" O GLY B1302 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ALA B1333 " --> pdb=" O SER B1301 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLY B1303 " --> pdb=" O ALA B1333 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS B1335 " --> pdb=" O GLY B1303 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLY B1334 " --> pdb=" O THR B1354 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N VAL B1356 " --> pdb=" O GLY B1334 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU B1336 " --> pdb=" O VAL B1356 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 176 through 181 removed outlier: 4.275A pdb=" N ALA C 49 " --> pdb=" O PHE C 204 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N PHE C 204 " --> pdb=" O ALA C 49 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU C 362 " --> pdb=" O THR C 358 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N TYR C 355 " --> pdb=" O LYS C 382 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N LYS C 382 " --> pdb=" O TYR C 355 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE C 357 " --> pdb=" O ILE C 380 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 103 through 109 removed outlier: 5.137A pdb=" N ILE C 104 " --> pdb=" O GLY C 134 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLY C 134 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL C 73 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU C 172 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLN C 75 " --> pdb=" O CYS C 170 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 332 through 335 Processing sheet with id=AC8, first strand: chain 'C' and resid 424 through 425 removed outlier: 6.759A pdb=" N THR C 424 " --> pdb=" O GLN C 544 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 476 through 477 removed outlier: 3.789A pdb=" N SER C1033 " --> pdb=" O GLY C 477 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 499 through 501 Processing sheet with id=AD2, first strand: chain 'C' and resid 566 through 570 removed outlier: 3.663A pdb=" N ILE C 605 " --> pdb=" O ALA C 567 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL C 604 " --> pdb=" O ASN C 643 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 572 through 574 Processing sheet with id=AD4, first strand: chain 'C' and resid 829 through 831 Processing sheet with id=AD5, first strand: chain 'C' and resid 853 through 854 removed outlier: 7.005A pdb=" N LEU C1067 " --> pdb=" O GLU C1089 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N GLY C1091 " --> pdb=" O LEU C1067 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N THR C1069 " --> pdb=" O GLY C1091 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ILE C1021 " --> pdb=" O ARG C1068 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N ASP C1070 " --> pdb=" O ILE C1021 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ILE C1023 " --> pdb=" O ASP C1070 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 943 through 944 Processing sheet with id=AD7, first strand: chain 'C' and resid 1229 through 1234 removed outlier: 6.749A pdb=" N MET C1229 " --> pdb=" O THR C1265 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N ARG C1267 " --> pdb=" O MET C1229 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU C1231 " --> pdb=" O ARG C1267 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ARG C1269 " --> pdb=" O LEU C1231 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TYR C1233 " --> pdb=" O ARG C1269 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE C1284 " --> pdb=" O THR C1304 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N VAL C1306 " --> pdb=" O ILE C1284 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU C1286 " --> pdb=" O VAL C1306 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ARG C1308 " --> pdb=" O LEU C1286 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL C1288 " --> pdb=" O ARG C1308 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LYS C1335 " --> pdb=" O GLY C1302 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR C1304 " --> pdb=" O LYS C1335 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N PHE C1337 " --> pdb=" O THR C1304 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL C1306 " --> pdb=" O PHE C1337 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLY C1334 " --> pdb=" O THR C1354 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N VAL C1356 " --> pdb=" O GLY C1334 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU C1336 " --> pdb=" O VAL C1356 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLY C1371 " --> pdb=" O MET C1391 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N TYR C1393 " --> pdb=" O GLY C1371 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA C1373 " --> pdb=" O TYR C1393 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 176 through 181 removed outlier: 4.310A pdb=" N ALA D 49 " --> pdb=" O PHE D 204 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N PHE D 204 " --> pdb=" O ALA D 49 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU D 362 " --> pdb=" O THR D 358 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N TYR D 355 " --> pdb=" O LYS D 382 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LYS D 382 " --> pdb=" O TYR D 355 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE D 357 " --> pdb=" O ILE D 380 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 103 through 108 removed outlier: 3.921A pdb=" N TYR D 103 " --> pdb=" O GLY D 134 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE D 132 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TRP D 107 " --> pdb=" O GLN D 130 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLN D 130 " --> pdb=" O TRP D 107 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N VAL D 73 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LEU D 172 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLN D 75 " --> pdb=" O CYS D 170 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 332 through 336 Processing sheet with id=AE2, first strand: chain 'D' and resid 499 through 501 Processing sheet with id=AE3, first strand: chain 'D' and resid 524 through 526 Processing sheet with id=AE4, first strand: chain 'D' and resid 549 through 550 removed outlier: 4.330A pdb=" N ALA D 668 " --> pdb=" O LEU D 550 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR D 665 " --> pdb=" O LEU D 642 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL D 604 " --> pdb=" O ASN D 643 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ARG D 645 " --> pdb=" O VAL D 604 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU D 606 " --> pdb=" O ARG D 645 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ALA D 567 " --> pdb=" O ILE D 605 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR D 607 " --> pdb=" O ALA D 567 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ILE D 569 " --> pdb=" O THR D 607 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 572 through 574 Processing sheet with id=AE6, first strand: chain 'D' and resid 829 through 831 Processing sheet with id=AE7, first strand: chain 'D' and resid 853 through 854 Processing sheet with id=AE8, first strand: chain 'D' and resid 927 through 930 removed outlier: 6.832A pdb=" N VAL D 996 " --> pdb=" O ILE D1020 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N LEU D1022 " --> pdb=" O VAL D 996 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL D 998 " --> pdb=" O LEU D1022 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N SER D1024 " --> pdb=" O VAL D 998 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU D1000 " --> pdb=" O SER D1024 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE D1021 " --> pdb=" O ARG D1068 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 1229 through 1234 removed outlier: 3.752A pdb=" N THR D1265 " --> pdb=" O MET D1229 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE D1284 " --> pdb=" O THR D1304 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N VAL D1306 " --> pdb=" O ILE D1284 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU D1286 " --> pdb=" O VAL D1306 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ARG D1308 " --> pdb=" O LEU D1286 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL D1288 " --> pdb=" O ARG D1308 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LYS D1335 " --> pdb=" O GLY D1302 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N THR D1304 " --> pdb=" O LYS D1335 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N PHE D1337 " --> pdb=" O THR D1304 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL D1306 " --> pdb=" O PHE D1337 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N GLY D1334 " --> pdb=" O THR D1354 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N VAL D1356 " --> pdb=" O GLY D1334 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU D1336 " --> pdb=" O VAL D1356 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ALA D1353 " --> pdb=" O THR D1372 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N VAL D1374 " --> pdb=" O ALA D1353 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL D1355 " --> pdb=" O VAL D1374 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N LEU D1376 " --> pdb=" O VAL D1355 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL D1357 " --> pdb=" O LEU D1376 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLY D1371 " --> pdb=" O MET D1391 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N TYR D1393 " --> pdb=" O GLY D1371 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ALA D1373 " --> pdb=" O TYR D1393 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N TYR D1395 " --> pdb=" O ALA D1373 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ILE D1375 " --> pdb=" O TYR D1395 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 174 through 175 Processing sheet with id=AF2, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.949A pdb=" N VAL E 260 " --> pdb=" O LYS E 398 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS E 318 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU E 320 " --> pdb=" O VAL E 295 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL E 317 " --> pdb=" O GLU E 344 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ILE E 346 " --> pdb=" O VAL E 317 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N CYS E 319 " --> pdb=" O ILE E 346 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 349 through 356 removed outlier: 5.786A pdb=" N ALA E 349 " --> pdb=" O ILE E 368 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE E 368 " --> pdb=" O ALA E 349 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL E 366 " --> pdb=" O PRO E 351 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 349 through 356 removed outlier: 5.786A pdb=" N ALA E 349 " --> pdb=" O ILE E 368 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE E 368 " --> pdb=" O ALA E 349 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL E 366 " --> pdb=" O PRO E 351 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 214 through 216 removed outlier: 3.758A pdb=" N ILE F 214 " --> pdb=" O VAL F 174 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL F 176 " --> pdb=" O ILE F 214 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 245 through 246 Processing sheet with id=AF7, first strand: chain 'F' and resid 260 through 261 removed outlier: 6.603A pdb=" N VAL F 260 " --> pdb=" O LYS F 398 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL F 293 " --> pdb=" O LYS F 318 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N LEU F 320 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL F 295 " --> pdb=" O LEU F 320 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL F 317 " --> pdb=" O GLU F 344 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ILE F 346 " --> pdb=" O VAL F 317 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N CYS F 319 " --> pdb=" O ILE F 346 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 349 through 356 removed outlier: 6.019A pdb=" N ALA F 349 " --> pdb=" O ILE F 368 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE F 368 " --> pdb=" O ALA F 349 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N VAL F 366 " --> pdb=" O PRO F 351 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 349 through 356 removed outlier: 6.019A pdb=" N ALA F 349 " --> pdb=" O ILE F 368 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE F 368 " --> pdb=" O ALA F 349 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N VAL F 366 " --> pdb=" O PRO F 351 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 173 through 177 Processing sheet with id=AG2, first strand: chain 'G' and resid 245 through 246 removed outlier: 3.774A pdb=" N LYS G 245 " --> pdb=" O GLU G 403 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 259 through 261 removed outlier: 3.563A pdb=" N VAL G 260 " --> pdb=" O VAL G 396 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS G 318 " --> pdb=" O VAL G 293 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU G 320 " --> pdb=" O VAL G 295 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ILE G 346 " --> pdb=" O VAL G 317 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N CYS G 319 " --> pdb=" O ILE G 346 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 350 through 355 removed outlier: 6.745A pdb=" N ARG G 364 " --> pdb=" O GLU G 352 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N PHE G 354 " --> pdb=" O GLY G 362 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLY G 362 " --> pdb=" O PHE G 354 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 368 through 370 2161 hydrogen bonds defined for protein. 5976 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: 29.76 Time building geometry restraints manager: 13.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.77: 57026 1.77 - 2.32: 596 2.32 - 2.87: 0 2.87 - 3.42: 0 3.42 - 3.97: 12 Bond restraints: 57634 Sorted by residual: bond pdb=" S4 F3S A1502 " pdb="FE1 F3S A1502 " ideal model delta sigma weight residual 2.233 3.956 -1.723 2.00e-02 2.50e+03 7.42e+03 bond pdb=" S4 F3S D1502 " pdb="FE1 F3S D1502 " ideal model delta sigma weight residual 2.233 3.954 -1.721 2.00e-02 2.50e+03 7.40e+03 bond pdb=" S4 F3S B1502 " pdb="FE1 F3S B1502 " ideal model delta sigma weight residual 2.233 3.939 -1.706 2.00e-02 2.50e+03 7.27e+03 bond pdb=" S4 F3S C1502 " pdb="FE1 F3S C1502 " ideal model delta sigma weight residual 2.233 3.938 -1.705 2.00e-02 2.50e+03 7.27e+03 bond pdb=" S2 F3S B1502 " pdb="FE3 F3S B1502 " ideal model delta sigma weight residual 2.300 3.967 -1.667 2.00e-02 2.50e+03 6.95e+03 ... (remaining 57629 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.09: 78041 10.09 - 20.17: 0 20.17 - 30.26: 10 30.26 - 40.35: 22 40.35 - 50.44: 8 Bond angle restraints: 78081 Sorted by residual: angle pdb=" S1 F3S D1502 " pdb="FE4 F3S D1502 " pdb=" S3 F3S D1502 " ideal model delta sigma weight residual 114.75 64.31 50.44 3.00e+00 1.11e-01 2.83e+02 angle pdb=" S3 F3S A1502 " pdb="FE1 F3S A1502 " pdb=" S4 F3S A1502 " ideal model delta sigma weight residual 112.59 62.99 49.60 3.00e+00 1.11e-01 2.73e+02 angle pdb=" S1 F3S A1502 " pdb="FE4 F3S A1502 " pdb=" S3 F3S A1502 " ideal model delta sigma weight residual 114.75 65.21 49.54 3.00e+00 1.11e-01 2.73e+02 angle pdb=" S1 F3S B1502 " pdb="FE4 F3S B1502 " pdb=" S3 F3S B1502 " ideal model delta sigma weight residual 114.75 65.45 49.30 3.00e+00 1.11e-01 2.70e+02 angle pdb=" S1 F3S C1502 " pdb="FE4 F3S C1502 " pdb=" S3 F3S C1502 " ideal model delta sigma weight residual 114.75 65.53 49.22 3.00e+00 1.11e-01 2.69e+02 ... (remaining 78076 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.62: 33998 32.62 - 65.24: 591 65.24 - 97.86: 59 97.86 - 130.48: 1 130.48 - 163.10: 2 Dihedral angle restraints: 34651 sinusoidal: 14013 harmonic: 20638 Sorted by residual: dihedral pdb=" O5' FAD E 503 " pdb=" O3P FAD E 503 " pdb=" P FAD E 503 " pdb=" PA FAD E 503 " ideal model delta sinusoidal sigma weight residual -61.77 101.33 -163.10 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" CA PHE G 36 " pdb=" C PHE G 36 " pdb=" N SER G 37 " pdb=" CA SER G 37 " ideal model delta harmonic sigma weight residual 180.00 158.07 21.93 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" O5' FAD G 503 " pdb=" O3P FAD G 503 " pdb=" P FAD G 503 " pdb=" PA FAD G 503 " ideal model delta sinusoidal sigma weight residual -61.77 77.68 -139.45 1 3.00e+01 1.11e-03 1.88e+01 ... (remaining 34648 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.722: 8689 0.722 - 1.444: 0 1.444 - 2.167: 0 2.167 - 2.889: 0 2.889 - 3.611: 4 Chirality restraints: 8693 Sorted by residual: chirality pdb=" S2 F3S B1502 " pdb="FE1 F3S B1502 " pdb="FE3 F3S B1502 " pdb="FE4 F3S B1502 " both_signs ideal model delta sigma weight residual False 10.77 7.16 3.61 2.00e-01 2.50e+01 3.26e+02 chirality pdb=" S2 F3S C1502 " pdb="FE1 F3S C1502 " pdb="FE3 F3S C1502 " pdb="FE4 F3S C1502 " both_signs ideal model delta sigma weight residual False 10.77 7.49 3.28 2.00e-01 2.50e+01 2.69e+02 chirality pdb=" S2 F3S D1502 " pdb="FE1 F3S D1502 " pdb="FE3 F3S D1502 " pdb="FE4 F3S D1502 " both_signs ideal model delta sigma weight residual False 10.77 7.67 3.10 2.00e-01 2.50e+01 2.40e+02 ... (remaining 8690 not shown) Planarity restraints: 10217 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B1184 " 0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO B1185 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO B1185 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B1185 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 191 " -0.026 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO E 192 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO E 192 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 192 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 968 " 0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO D 969 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO D 969 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 969 " 0.022 5.00e-02 4.00e+02 ... (remaining 10214 not shown) Histogram of nonbonded interaction distances: 1.16 - 1.91: 3 1.91 - 2.66: 955 2.66 - 3.41: 77598 3.41 - 4.15: 124660 4.15 - 4.90: 228519 Nonbonded interactions: 431735 Sorted by model distance: nonbonded pdb=" SG CYS A1113 " pdb=" S1 F3S A1502 " model vdw 1.163 3.760 nonbonded pdb=" SG CYS A1102 " pdb=" S3 F3S A1502 " model vdw 1.244 3.760 nonbonded pdb=" SG CYS D1102 " pdb=" S3 F3S D1502 " model vdw 1.547 3.760 nonbonded pdb=" OE1 GLU G 125 " pdb="FE3 SF4 G 502 " model vdw 2.119 3.000 nonbonded pdb=" OG SER D 864 " pdb=" OE1 GLU D 866 " model vdw 2.168 3.040 ... (remaining 431730 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 1.850 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: 0.100 Extract box with map and model: 1.820 Check model and map are aligned: 0.350 Set scattering table: 0.420 Process input model: 122.820 Find NCS groups from input model: 2.110 Set up NCS constraints: 0.340 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: 0.030 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 132.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 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 : 0.024 1.723 57634 Z= 1.654 Angle : 0.981 50.437 78081 Z= 0.412 Chirality : 0.081 3.611 8693 Planarity : 0.003 0.041 10217 Dihedral : 13.048 163.099 21485 Min Nonbonded Distance : 1.163 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.02 % Allowed : 6.13 % Favored : 93.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.08), residues: 7290 helix: -0.97 (0.09), residues: 2451 sheet: -2.33 (0.15), residues: 910 loop : -2.92 (0.08), residues: 3929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 69 HIS 0.005 0.001 HIS A 796 PHE 0.019 0.001 PHE G 36 TYR 0.020 0.001 TYR D1367 ARG 0.006 0.000 ARG A1186 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 5923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 779 time to evaluate : 5.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7586 (mm-30) REVERT: A 371 MET cc_start: 0.7923 (mtm) cc_final: 0.7718 (mtm) REVERT: A 458 MET cc_start: 0.8278 (ppp) cc_final: 0.8019 (ppp) REVERT: A 693 MET cc_start: 0.8692 (mmm) cc_final: 0.8457 (mmm) REVERT: A 1368 MET cc_start: 0.8876 (ttt) cc_final: 0.8560 (ttm) REVERT: A 1387 MET cc_start: 0.8680 (ttt) cc_final: 0.7629 (ttt) REVERT: B 86 GLN cc_start: 0.8051 (mt0) cc_final: 0.7754 (mt0) REVERT: B 251 MET cc_start: 0.8314 (ptt) cc_final: 0.8109 (ptm) REVERT: B 461 MET cc_start: 0.8100 (mmt) cc_final: 0.7723 (mmt) REVERT: B 562 MET cc_start: 0.8718 (mtm) cc_final: 0.8457 (mtm) REVERT: B 895 ARG cc_start: 0.4994 (mmt90) cc_final: 0.4301 (ptp90) REVERT: B 1017 ASN cc_start: 0.8585 (m-40) cc_final: 0.8029 (m-40) REVERT: B 1137 ASN cc_start: 0.6737 (m-40) cc_final: 0.6403 (p0) REVERT: C 235 ASN cc_start: 0.8205 (m-40) cc_final: 0.7917 (m-40) REVERT: C 244 MET cc_start: 0.8663 (tpp) cc_final: 0.8388 (tpp) REVERT: C 350 LEU cc_start: 0.9019 (mt) cc_final: 0.8684 (mp) REVERT: C 458 MET cc_start: 0.8497 (ppp) cc_final: 0.8253 (tmm) REVERT: C 708 MET cc_start: 0.8863 (ttp) cc_final: 0.8651 (ttp) REVERT: C 953 ILE cc_start: 0.8509 (tp) cc_final: 0.7882 (tp) REVERT: C 1249 MET cc_start: 0.8313 (mmm) cc_final: 0.8041 (tpp) REVERT: C 1368 MET cc_start: 0.8566 (ttt) cc_final: 0.8028 (ttp) REVERT: C 1387 MET cc_start: 0.9019 (ttt) cc_final: 0.8784 (ttm) REVERT: D 416 TRP cc_start: 0.7065 (m100) cc_final: 0.6854 (m100) REVERT: D 427 ASP cc_start: 0.8174 (p0) cc_final: 0.7876 (p0) REVERT: D 448 ARG cc_start: 0.8213 (mtt-85) cc_final: 0.7935 (mtp85) REVERT: D 591 GLN cc_start: 0.8008 (tt0) cc_final: 0.7742 (tm-30) REVERT: D 767 ASN cc_start: 0.8033 (t0) cc_final: 0.7830 (t0) REVERT: D 929 GLU cc_start: 0.7724 (tt0) cc_final: 0.7523 (tt0) REVERT: D 1009 ILE cc_start: 0.9124 (mp) cc_final: 0.8789 (mt) REVERT: D 1100 MET cc_start: 0.8748 (mmm) cc_final: 0.8459 (mmp) REVERT: E 183 MET cc_start: 0.7570 (mtp) cc_final: 0.7200 (mtt) REVERT: E 270 ASN cc_start: 0.8102 (t0) cc_final: 0.7568 (t0) REVERT: F 6 MET cc_start: 0.6930 (ptp) cc_final: 0.6438 (ptp) REVERT: F 27 GLN cc_start: 0.7455 (mp10) cc_final: 0.7248 (mt0) REVERT: G 149 LEU cc_start: 0.6615 (tp) cc_final: 0.6359 (tp) REVERT: G 435 MET cc_start: 0.6818 (ptm) cc_final: 0.6185 (ptm) outliers start: 1 outliers final: 0 residues processed: 780 average time/residue: 0.6031 time to fit residues: 767.3835 Evaluate side-chains 484 residues out of total 5923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 484 time to evaluate : 4.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 729 random chunks: chunk 615 optimal weight: 20.0000 chunk 552 optimal weight: 6.9990 chunk 306 optimal weight: 10.0000 chunk 188 optimal weight: 2.9990 chunk 372 optimal weight: 0.0570 chunk 295 optimal weight: 0.0470 chunk 571 optimal weight: 3.9990 chunk 221 optimal weight: 5.9990 chunk 347 optimal weight: 6.9990 chunk 425 optimal weight: 8.9990 chunk 662 optimal weight: 3.9990 overall best weight: 2.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 165 ASN A 235 ASN A 653 HIS A1054 GLN A1205 ASN ** A1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1282 GLN A1341 GLN A1419 HIS A1471 HIS B 52 GLN B 58 HIS B 64 HIS B 135 ASN B 143 GLN B 235 ASN B 653 HIS B 796 HIS B 800 GLN B 818 ASN ** B 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1126 GLN ** B1274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1341 GLN B1363 ASN ** B1471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN C 135 ASN C 321 ASN C 409 HIS C 643 ASN C 724 ASN C 738 HIS C 767 ASN C1234 ASN C1325 ASN C1419 HIS C1471 HIS ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN D 422 ASN D 539 GLN D 653 HIS D 943 GLN D 971 HIS ** D 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1120 GLN D1137 ASN D1177 HIS ** D1274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1325 ASN D1419 HIS D1431 HIS E 89 ASN E 129 ASN E 312 GLN E 379 GLN F 11 HIS F 50 GLN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 175 HIS F 270 ASN F 379 GLN F 434 ASN ** G 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 258 ASN G 379 GLN Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.171 57634 Z= 0.224 Angle : 0.891 76.931 78081 Z= 0.364 Chirality : 0.046 1.418 8693 Planarity : 0.004 0.068 10217 Dihedral : 5.750 161.765 8145 Min Nonbonded Distance : 1.523 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.07 % Allowed : 3.72 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: -2.23 (0.09), residues: 7290 helix: 0.00 (0.10), residues: 2524 sheet: -1.79 (0.16), residues: 866 loop : -2.51 (0.09), residues: 3900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 219 HIS 0.007 0.001 HIS C1109 PHE 0.017 0.001 PHE G 36 TYR 0.012 0.001 TYR F 215 ARG 0.011 0.000 ARG C1186 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 5923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 651 time to evaluate : 5.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLN cc_start: 0.8275 (mp10) cc_final: 0.7969 (tm-30) REVERT: A 233 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7513 (mm-30) REVERT: A 293 MET cc_start: 0.8155 (mmm) cc_final: 0.7690 (tpp) REVERT: A 1368 MET cc_start: 0.8842 (ttt) cc_final: 0.8511 (ttm) REVERT: A 1387 MET cc_start: 0.8694 (ttt) cc_final: 0.7594 (ttt) REVERT: B 86 GLN cc_start: 0.8003 (mt0) cc_final: 0.7762 (mt0) REVERT: B 458 MET cc_start: 0.7000 (tmm) cc_final: 0.6693 (tmm) REVERT: B 461 MET cc_start: 0.7737 (mmt) cc_final: 0.7313 (mmm) REVERT: B 687 MET cc_start: 0.7079 (ppp) cc_final: 0.6076 (mpp) REVERT: B 895 ARG cc_start: 0.4818 (mmt90) cc_final: 0.4376 (ptp90) REVERT: B 1017 ASN cc_start: 0.8667 (m-40) cc_final: 0.8215 (m-40) REVERT: B 1047 MET cc_start: 0.8404 (ptp) cc_final: 0.7576 (mtm) REVERT: B 1079 ILE cc_start: 0.8660 (mt) cc_final: 0.8459 (mt) REVERT: B 1104 MET cc_start: 0.7312 (mmm) cc_final: 0.6729 (mmm) REVERT: B 1131 THR cc_start: 0.8809 (OUTLIER) cc_final: 0.8333 (m) REVERT: B 1137 ASN cc_start: 0.7114 (m-40) cc_final: 0.6773 (p0) REVERT: B 1295 TYR cc_start: 0.8926 (m-80) cc_final: 0.8576 (m-80) REVERT: B 1387 MET cc_start: 0.8237 (ttt) cc_final: 0.7983 (ttm) REVERT: C 131 ILE cc_start: 0.8173 (pt) cc_final: 0.7967 (pt) REVERT: C 235 ASN cc_start: 0.8206 (m-40) cc_final: 0.6384 (m-40) REVERT: C 244 MET cc_start: 0.8626 (tpp) cc_final: 0.8368 (tpp) REVERT: C 260 MET cc_start: 0.8134 (tpp) cc_final: 0.7622 (tpp) REVERT: C 350 LEU cc_start: 0.8943 (mt) cc_final: 0.8574 (mp) REVERT: C 520 MET cc_start: 0.8261 (ptp) cc_final: 0.7964 (ptm) REVERT: C 711 MET cc_start: 0.8277 (ttm) cc_final: 0.8016 (ttm) REVERT: C 978 GLU cc_start: 0.8440 (pm20) cc_final: 0.8116 (mp0) REVERT: C 1249 MET cc_start: 0.8337 (mmm) cc_final: 0.8061 (tpp) REVERT: D 227 MET cc_start: 0.7927 (tmm) cc_final: 0.7714 (tmm) REVERT: D 416 TRP cc_start: 0.7012 (m100) cc_final: 0.6705 (m100) REVERT: D 448 ARG cc_start: 0.8303 (mtt-85) cc_final: 0.7999 (mtp85) REVERT: D 591 GLN cc_start: 0.8019 (tt0) cc_final: 0.7728 (tm-30) REVERT: D 767 ASN cc_start: 0.7967 (t0) cc_final: 0.7746 (t0) REVERT: D 980 LEU cc_start: 0.9158 (tp) cc_final: 0.8904 (tp) REVERT: D 1100 MET cc_start: 0.8457 (mmm) cc_final: 0.8116 (mmp) REVERT: E 183 MET cc_start: 0.7561 (mtp) cc_final: 0.7263 (mtm) REVERT: F 6 MET cc_start: 0.7241 (ptp) cc_final: 0.6607 (ptp) REVERT: G 303 MET cc_start: 0.5998 (tpp) cc_final: 0.5784 (tpp) REVERT: G 328 MET cc_start: 0.5008 (ptm) cc_final: 0.4644 (ptm) REVERT: G 332 GLN cc_start: 0.7145 (pp30) cc_final: 0.6114 (mp10) REVERT: G 435 MET cc_start: 0.6285 (ptm) cc_final: 0.5754 (ptm) outliers start: 4 outliers final: 1 residues processed: 655 average time/residue: 0.5384 time to fit residues: 603.3202 Evaluate side-chains 462 residues out of total 5923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 460 time to evaluate : 4.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 729 random chunks: chunk 367 optimal weight: 3.9990 chunk 205 optimal weight: 4.9990 chunk 550 optimal weight: 7.9990 chunk 450 optimal weight: 6.9990 chunk 182 optimal weight: 6.9990 chunk 663 optimal weight: 0.7980 chunk 716 optimal weight: 9.9990 chunk 590 optimal weight: 20.0000 chunk 657 optimal weight: 9.9990 chunk 226 optimal weight: 5.9990 chunk 532 optimal weight: 9.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 788 HIS B 30 HIS B 818 ASN ** B 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1120 GLN B1205 ASN ** B1325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 GLN ** C 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1431 HIS ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 628 HIS ** D 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 270 ASN E 392 GLN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 ASN F 337 HIS G 50 GLN ** G 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 258 ASN G 379 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.184 57634 Z= 0.309 Angle : 0.817 94.090 78081 Z= 0.355 Chirality : 0.056 2.387 8693 Planarity : 0.004 0.056 10217 Dihedral : 5.752 160.693 8145 Min Nonbonded Distance : 1.668 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.03 % Allowed : 4.39 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: -1.97 (0.09), residues: 7290 helix: 0.16 (0.10), residues: 2551 sheet: -1.57 (0.17), residues: 866 loop : -2.35 (0.09), residues: 3873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 69 HIS 0.018 0.001 HIS D 603 PHE 0.016 0.001 PHE G 36 TYR 0.015 0.001 TYR D1367 ARG 0.007 0.000 ARG C 832 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 5923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 599 time to evaluate : 5.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLN cc_start: 0.8341 (mp10) cc_final: 0.8016 (tm-30) REVERT: A 293 MET cc_start: 0.8140 (mmm) cc_final: 0.7702 (tpt) REVERT: A 296 MET cc_start: 0.8645 (mmt) cc_final: 0.8302 (mmt) REVERT: A 1366 GLU cc_start: 0.8085 (tt0) cc_final: 0.7836 (tt0) REVERT: A 1368 MET cc_start: 0.8845 (ttt) cc_final: 0.8550 (ttm) REVERT: A 1387 MET cc_start: 0.8692 (ttt) cc_final: 0.7610 (ttt) REVERT: B 335 MET cc_start: 0.8152 (pmm) cc_final: 0.7832 (pmm) REVERT: B 442 MET cc_start: 0.7408 (pmm) cc_final: 0.7179 (pmm) REVERT: B 461 MET cc_start: 0.7776 (mmt) cc_final: 0.7386 (mmm) REVERT: B 520 MET cc_start: 0.8099 (mmt) cc_final: 0.7798 (mmp) REVERT: B 562 MET cc_start: 0.8731 (mtm) cc_final: 0.8455 (mtm) REVERT: B 895 ARG cc_start: 0.4970 (mmt90) cc_final: 0.4331 (ptp90) REVERT: B 1017 ASN cc_start: 0.8800 (m-40) cc_final: 0.8390 (m-40) REVERT: B 1137 ASN cc_start: 0.7234 (m-40) cc_final: 0.6849 (p0) REVERT: B 1289 MET cc_start: 0.8167 (mmm) cc_final: 0.7332 (mtm) REVERT: C 83 LEU cc_start: 0.8841 (mt) cc_final: 0.8524 (tt) REVERT: C 207 TYR cc_start: 0.9234 (p90) cc_final: 0.9025 (p90) REVERT: C 244 MET cc_start: 0.8682 (tpp) cc_final: 0.8367 (tpp) REVERT: C 320 CYS cc_start: 0.9158 (m) cc_final: 0.8660 (m) REVERT: C 345 MET cc_start: 0.8368 (tpp) cc_final: 0.7516 (ttt) REVERT: C 520 MET cc_start: 0.8322 (ptp) cc_final: 0.7949 (ptm) REVERT: C 745 ARG cc_start: 0.7638 (mtp-110) cc_final: 0.7325 (mtm180) REVERT: C 875 MET cc_start: 0.8457 (tpp) cc_final: 0.8167 (tpp) REVERT: C 978 GLU cc_start: 0.8405 (pm20) cc_final: 0.8084 (mp0) REVERT: C 1249 MET cc_start: 0.8373 (mmm) cc_final: 0.8152 (tpp) REVERT: C 1366 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7778 (tm-30) REVERT: D 416 TRP cc_start: 0.7041 (m100) cc_final: 0.6787 (m100) REVERT: D 448 ARG cc_start: 0.8232 (mtt-85) cc_final: 0.7995 (mtp85) REVERT: D 454 PHE cc_start: 0.8368 (m-10) cc_final: 0.8064 (m-10) REVERT: D 479 MET cc_start: 0.8430 (tpp) cc_final: 0.8214 (tpp) REVERT: D 591 GLN cc_start: 0.8152 (tt0) cc_final: 0.7828 (tm-30) REVERT: D 651 ASP cc_start: 0.8333 (t0) cc_final: 0.8053 (t0) REVERT: D 767 ASN cc_start: 0.7960 (t0) cc_final: 0.7713 (t0) REVERT: D 1100 MET cc_start: 0.8561 (mmm) cc_final: 0.8262 (mmp) REVERT: E 392 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8470 (tm-30) REVERT: F 6 MET cc_start: 0.7606 (ptp) cc_final: 0.6970 (ptp) REVERT: F 31 GLU cc_start: 0.7720 (mt-10) cc_final: 0.6798 (tp30) REVERT: G 332 GLN cc_start: 0.7080 (pp30) cc_final: 0.6092 (mp10) REVERT: G 435 MET cc_start: 0.6160 (ptm) cc_final: 0.5692 (ptm) outliers start: 2 outliers final: 1 residues processed: 601 average time/residue: 0.5395 time to fit residues: 555.9423 Evaluate side-chains 439 residues out of total 5923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 437 time to evaluate : 5.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 729 random chunks: chunk 655 optimal weight: 5.9990 chunk 498 optimal weight: 0.0270 chunk 344 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 316 optimal weight: 4.9990 chunk 445 optimal weight: 7.9990 chunk 665 optimal weight: 7.9990 chunk 704 optimal weight: 6.9990 chunk 347 optimal weight: 7.9990 chunk 630 optimal weight: 0.0870 chunk 189 optimal weight: 6.9990 overall best weight: 3.6222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 ASN A1054 GLN ** A1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 796 HIS B1120 GLN ** B1325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 HIS C 767 ASN C 818 ASN C 971 HIS ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 724 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 270 ASN E 312 GLN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 ASN ** G 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 379 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 57634 Z= 0.252 Angle : 0.795 85.122 78081 Z= 0.341 Chirality : 0.051 1.582 8693 Planarity : 0.004 0.054 10217 Dihedral : 5.623 160.687 8145 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.02 % Allowed : 3.14 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: -1.72 (0.09), residues: 7290 helix: 0.33 (0.10), residues: 2579 sheet: -1.43 (0.17), residues: 874 loop : -2.19 (0.09), residues: 3837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP C 416 HIS 0.020 0.001 HIS D 868 PHE 0.015 0.001 PHE G 36 TYR 0.033 0.001 TYR C 319 ARG 0.014 0.000 ARG C1186 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 5923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 603 time to evaluate : 5.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.8089 (mmm) cc_final: 0.7629 (tpt) REVERT: A 296 MET cc_start: 0.8657 (mmt) cc_final: 0.8371 (mmt) REVERT: A 463 LEU cc_start: 0.8285 (tp) cc_final: 0.8047 (tp) REVERT: A 1047 MET cc_start: 0.7609 (mtt) cc_final: 0.7352 (mtt) REVERT: A 1366 GLU cc_start: 0.8231 (tt0) cc_final: 0.7872 (tt0) REVERT: A 1368 MET cc_start: 0.8821 (ttt) cc_final: 0.8552 (ttm) REVERT: A 1387 MET cc_start: 0.8645 (ttt) cc_final: 0.7628 (ttt) REVERT: B 112 ILE cc_start: 0.9199 (pt) cc_final: 0.8895 (mt) REVERT: B 345 MET cc_start: 0.8950 (mmm) cc_final: 0.8703 (mmm) REVERT: B 442 MET cc_start: 0.7621 (pmm) cc_final: 0.7387 (pmm) REVERT: B 458 MET cc_start: 0.7087 (tmm) cc_final: 0.6398 (tmm) REVERT: B 461 MET cc_start: 0.7884 (mmt) cc_final: 0.7613 (mmm) REVERT: B 520 MET cc_start: 0.8132 (mmt) cc_final: 0.7756 (mmp) REVERT: B 550 LEU cc_start: 0.9072 (mt) cc_final: 0.8849 (mt) REVERT: B 562 MET cc_start: 0.8727 (mtm) cc_final: 0.8475 (mtm) REVERT: B 860 MET cc_start: 0.7642 (tpp) cc_final: 0.7251 (tpp) REVERT: B 895 ARG cc_start: 0.4980 (mmt90) cc_final: 0.4341 (ptp90) REVERT: B 964 MET cc_start: 0.8094 (ppp) cc_final: 0.7638 (ppp) REVERT: B 1017 ASN cc_start: 0.8787 (m-40) cc_final: 0.8387 (m-40) REVERT: B 1047 MET cc_start: 0.8185 (ptp) cc_final: 0.7724 (mtm) REVERT: B 1137 ASN cc_start: 0.7232 (m-40) cc_final: 0.6843 (p0) REVERT: C 244 MET cc_start: 0.8637 (tpp) cc_final: 0.8394 (tpp) REVERT: C 260 MET cc_start: 0.8220 (tpp) cc_final: 0.7631 (tpp) REVERT: C 320 CYS cc_start: 0.9102 (m) cc_final: 0.8747 (m) REVERT: C 345 MET cc_start: 0.8079 (tpp) cc_final: 0.7147 (ttt) REVERT: C 353 MET cc_start: 0.8636 (tpp) cc_final: 0.8429 (tpp) REVERT: C 860 MET cc_start: 0.8749 (mmm) cc_final: 0.8211 (tpp) REVERT: C 978 GLU cc_start: 0.8405 (pm20) cc_final: 0.8005 (mp0) REVERT: C 1249 MET cc_start: 0.8355 (mmm) cc_final: 0.8130 (tpp) REVERT: C 1366 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7866 (tm-30) REVERT: D 416 TRP cc_start: 0.7037 (m100) cc_final: 0.6777 (m100) REVERT: D 448 ARG cc_start: 0.8359 (mtt-85) cc_final: 0.8102 (mtp85) REVERT: D 454 PHE cc_start: 0.8515 (m-10) cc_final: 0.8223 (m-10) REVERT: D 479 MET cc_start: 0.8341 (tpp) cc_final: 0.8079 (tpp) REVERT: D 591 GLN cc_start: 0.8140 (tt0) cc_final: 0.7829 (tm-30) REVERT: D 767 ASN cc_start: 0.8081 (t0) cc_final: 0.7764 (t0) REVERT: D 980 LEU cc_start: 0.9231 (tp) cc_final: 0.9011 (tp) REVERT: D 1100 MET cc_start: 0.8450 (mmm) cc_final: 0.8156 (mmp) REVERT: F 6 MET cc_start: 0.7758 (ptp) cc_final: 0.7479 (ptp) REVERT: F 31 GLU cc_start: 0.7676 (mt-10) cc_final: 0.6775 (tp30) REVERT: F 304 ASP cc_start: 0.7341 (m-30) cc_final: 0.6962 (m-30) REVERT: G 332 GLN cc_start: 0.7062 (pp30) cc_final: 0.6079 (mp10) REVERT: G 435 MET cc_start: 0.6084 (ptm) cc_final: 0.5804 (ptm) outliers start: 1 outliers final: 0 residues processed: 604 average time/residue: 0.5307 time to fit residues: 555.4202 Evaluate side-chains 433 residues out of total 5923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 433 time to evaluate : 4.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 729 random chunks: chunk 586 optimal weight: 8.9990 chunk 400 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 524 optimal weight: 6.9990 chunk 290 optimal weight: 2.9990 chunk 601 optimal weight: 9.9990 chunk 487 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 359 optimal weight: 6.9990 chunk 632 optimal weight: 7.9990 chunk 177 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 971 HIS B 544 GLN B 796 HIS B 982 GLN B1120 GLN ** B1325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 HIS C 767 ASN C 971 HIS D 544 GLN D 724 ASN D1293 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 270 ASN ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 ASN ** G 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 379 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 57634 Z= 0.260 Angle : 0.800 83.094 78081 Z= 0.345 Chirality : 0.052 1.567 8693 Planarity : 0.004 0.055 10217 Dihedral : 5.624 159.751 8145 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.03 % Allowed : 2.57 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: -1.60 (0.09), residues: 7290 helix: 0.41 (0.10), residues: 2587 sheet: -1.41 (0.17), residues: 898 loop : -2.08 (0.09), residues: 3805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 69 HIS 0.016 0.001 HIS D 603 PHE 0.018 0.001 PHE B 810 TYR 0.015 0.001 TYR B1295 ARG 0.005 0.000 ARG C1186 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 5923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 578 time to evaluate : 5.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 MET cc_start: 0.8087 (mmm) cc_final: 0.7634 (tpt) REVERT: A 296 MET cc_start: 0.8605 (mmt) cc_final: 0.8301 (mmt) REVERT: A 463 LEU cc_start: 0.8323 (tp) cc_final: 0.8062 (tp) REVERT: A 523 LYS cc_start: 0.8699 (mmtt) cc_final: 0.8452 (mmtp) REVERT: A 711 MET cc_start: 0.7491 (mtt) cc_final: 0.7245 (mtp) REVERT: A 1047 MET cc_start: 0.7656 (mtt) cc_final: 0.7440 (mtt) REVERT: A 1366 GLU cc_start: 0.8153 (tt0) cc_final: 0.7843 (tt0) REVERT: A 1368 MET cc_start: 0.8834 (ttt) cc_final: 0.8530 (ttm) REVERT: A 1387 MET cc_start: 0.8669 (ttt) cc_final: 0.7610 (ttt) REVERT: B 112 ILE cc_start: 0.9192 (pt) cc_final: 0.8905 (mt) REVERT: B 264 LYS cc_start: 0.6961 (mmtt) cc_final: 0.6709 (tppt) REVERT: B 458 MET cc_start: 0.7083 (tmm) cc_final: 0.6368 (tmm) REVERT: B 520 MET cc_start: 0.8262 (mmt) cc_final: 0.7895 (mmp) REVERT: B 550 LEU cc_start: 0.9114 (mt) cc_final: 0.8894 (mt) REVERT: B 562 MET cc_start: 0.8753 (mtm) cc_final: 0.8503 (mtm) REVERT: B 860 MET cc_start: 0.7607 (tpp) cc_final: 0.7178 (tpp) REVERT: B 895 ARG cc_start: 0.4977 (mmt90) cc_final: 0.4343 (ptp90) REVERT: B 1017 ASN cc_start: 0.8806 (m-40) cc_final: 0.8426 (m-40) REVERT: B 1047 MET cc_start: 0.8250 (ptp) cc_final: 0.7885 (mtm) REVERT: B 1137 ASN cc_start: 0.7097 (m-40) cc_final: 0.6694 (p0) REVERT: C 207 TYR cc_start: 0.9200 (p90) cc_final: 0.8987 (p90) REVERT: C 244 MET cc_start: 0.8648 (tpp) cc_final: 0.8337 (tpp) REVERT: C 320 CYS cc_start: 0.8910 (m) cc_final: 0.8540 (m) REVERT: C 726 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7255 (mp0) REVERT: C 860 MET cc_start: 0.8825 (mmm) cc_final: 0.8268 (tpp) REVERT: C 978 GLU cc_start: 0.8476 (pm20) cc_final: 0.8147 (mp0) REVERT: C 985 TYR cc_start: 0.8613 (t80) cc_final: 0.8389 (t80) REVERT: C 1249 MET cc_start: 0.8373 (mmm) cc_final: 0.8168 (tpp) REVERT: C 1366 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7969 (tm-30) REVERT: D 251 MET cc_start: 0.7872 (ptt) cc_final: 0.7286 (ptm) REVERT: D 416 TRP cc_start: 0.7046 (m100) cc_final: 0.6798 (m100) REVERT: D 442 MET cc_start: 0.3310 (ptp) cc_final: 0.3043 (ptp) REVERT: D 448 ARG cc_start: 0.8360 (mtt-85) cc_final: 0.8113 (mtp85) REVERT: D 454 PHE cc_start: 0.8600 (m-10) cc_final: 0.8279 (m-10) REVERT: D 479 MET cc_start: 0.8388 (tpp) cc_final: 0.8128 (tpp) REVERT: D 591 GLN cc_start: 0.8150 (tt0) cc_final: 0.7832 (tm-30) REVERT: D 767 ASN cc_start: 0.8091 (t0) cc_final: 0.7739 (t0) REVERT: D 1100 MET cc_start: 0.8433 (mmm) cc_final: 0.8148 (mmp) REVERT: E 183 MET cc_start: 0.7364 (mtp) cc_final: 0.7155 (mtm) REVERT: E 303 MET cc_start: 0.8290 (mmm) cc_final: 0.7979 (mmp) REVERT: F 31 GLU cc_start: 0.7676 (mt-10) cc_final: 0.6643 (tp30) REVERT: G 332 GLN cc_start: 0.7052 (pp30) cc_final: 0.6045 (mp10) REVERT: G 435 MET cc_start: 0.6187 (ptm) cc_final: 0.5815 (ptm) outliers start: 2 outliers final: 1 residues processed: 580 average time/residue: 0.5405 time to fit residues: 542.1569 Evaluate side-chains 438 residues out of total 5923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 437 time to evaluate : 5.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 729 random chunks: chunk 237 optimal weight: 20.0000 chunk 634 optimal weight: 10.0000 chunk 139 optimal weight: 2.9990 chunk 413 optimal weight: 20.0000 chunk 173 optimal weight: 9.9990 chunk 705 optimal weight: 30.0000 chunk 585 optimal weight: 0.7980 chunk 326 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 233 optimal weight: 7.9990 chunk 370 optimal weight: 7.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 824 GLN ** B1325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 GLN C1205 ASN D 321 ASN ** D 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 724 ASN D 943 GLN ** D1274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1293 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 270 ASN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 ASN ** G 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 379 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 57634 Z= 0.308 Angle : 0.825 82.790 78081 Z= 0.360 Chirality : 0.053 1.557 8693 Planarity : 0.004 0.066 10217 Dihedral : 5.748 158.857 8145 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 0.03 % Allowed : 2.31 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: -1.57 (0.10), residues: 7290 helix: 0.42 (0.10), residues: 2583 sheet: -1.39 (0.17), residues: 906 loop : -2.05 (0.09), residues: 3801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 69 HIS 0.014 0.001 HIS A 971 PHE 0.020 0.001 PHE B 810 TYR 0.015 0.001 TYR E 82 ARG 0.009 0.000 ARG C 832 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 5923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 565 time to evaluate : 4.980 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: A 463 LEU cc_start: 0.8460 (tp) cc_final: 0.8232 (tp) REVERT: A 964 MET cc_start: 0.7933 (tmm) cc_final: 0.7723 (tmm) REVERT: A 1047 MET cc_start: 0.7870 (mtt) cc_final: 0.7594 (mtt) REVERT: A 1366 GLU cc_start: 0.8276 (tt0) cc_final: 0.7898 (tt0) REVERT: A 1368 MET cc_start: 0.8819 (ttt) cc_final: 0.8553 (ttm) REVERT: A 1387 MET cc_start: 0.8694 (ttt) cc_final: 0.7690 (ttt) REVERT: B 458 MET cc_start: 0.7088 (tmm) cc_final: 0.6272 (tmm) REVERT: B 461 MET cc_start: 0.8579 (mmp) cc_final: 0.8165 (mmm) REVERT: B 520 MET cc_start: 0.8327 (mmt) cc_final: 0.7993 (mmp) REVERT: B 550 LEU cc_start: 0.9128 (mt) cc_final: 0.8908 (mt) REVERT: B 562 MET cc_start: 0.8763 (mtm) cc_final: 0.8530 (mtm) REVERT: B 860 MET cc_start: 0.7462 (tpp) cc_final: 0.7007 (tpp) REVERT: B 895 ARG cc_start: 0.5001 (mmt90) cc_final: 0.4341 (ptp90) REVERT: B 1017 ASN cc_start: 0.8832 (m-40) cc_final: 0.8537 (m110) REVERT: B 1084 MET cc_start: 0.8786 (tpp) cc_final: 0.8479 (tpp) REVERT: B 1137 ASN cc_start: 0.7306 (m-40) cc_final: 0.6888 (p0) REVERT: B 1147 ARG cc_start: 0.7370 (mtp180) cc_final: 0.7144 (mtp85) REVERT: B 1256 MET cc_start: 0.7887 (ttm) cc_final: 0.7686 (ttm) REVERT: C 207 TYR cc_start: 0.9200 (p90) cc_final: 0.8992 (p90) REVERT: C 244 MET cc_start: 0.8667 (tpp) cc_final: 0.8348 (tpp) REVERT: C 260 MET cc_start: 0.8244 (tpp) cc_final: 0.7671 (tpp) REVERT: C 860 MET cc_start: 0.8904 (mmm) cc_final: 0.8550 (tpp) REVERT: C 978 GLU cc_start: 0.8311 (pm20) cc_final: 0.8023 (pm20) REVERT: C 1186 ARG cc_start: 0.7903 (mmp-170) cc_final: 0.7529 (tpp80) REVERT: C 1249 MET cc_start: 0.8413 (mmm) cc_final: 0.8137 (tpp) REVERT: C 1300 LEU cc_start: 0.8579 (tp) cc_final: 0.8376 (tp) REVERT: C 1366 GLU cc_start: 0.8399 (tm-30) cc_final: 0.7985 (tm-30) REVERT: D 442 MET cc_start: 0.3425 (ptp) cc_final: 0.3156 (ptp) REVERT: D 448 ARG cc_start: 0.8370 (mtt-85) cc_final: 0.8128 (mtp85) REVERT: D 454 PHE cc_start: 0.8589 (m-10) cc_final: 0.8261 (m-10) REVERT: D 479 MET cc_start: 0.8464 (tpp) cc_final: 0.8008 (tpp) REVERT: D 591 GLN cc_start: 0.8202 (tt0) cc_final: 0.7848 (tm-30) REVERT: D 651 ASP cc_start: 0.8497 (t0) cc_final: 0.8082 (t0) REVERT: D 767 ASN cc_start: 0.8088 (t0) cc_final: 0.7735 (t0) REVERT: D 980 LEU cc_start: 0.9282 (tp) cc_final: 0.8982 (tp) REVERT: D 1100 MET cc_start: 0.8449 (mmm) cc_final: 0.8191 (mmp) REVERT: E 183 MET cc_start: 0.7475 (mtp) cc_final: 0.7134 (mtm) REVERT: F 6 MET cc_start: 0.7777 (ptp) cc_final: 0.7307 (ptp) REVERT: F 304 ASP cc_start: 0.7544 (m-30) cc_final: 0.6939 (m-30) REVERT: G 332 GLN cc_start: 0.7061 (pp30) cc_final: 0.6123 (mp10) REVERT: G 435 MET cc_start: 0.6180 (ptm) cc_final: 0.5814 (ptm) outliers start: 2 outliers final: 0 residues processed: 567 average time/residue: 0.5299 time to fit residues: 519.6108 Evaluate side-chains 429 residues out of total 5923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 429 time to evaluate : 4.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 729 random chunks: chunk 680 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 401 optimal weight: 5.9990 chunk 515 optimal weight: 4.9990 chunk 399 optimal weight: 5.9990 chunk 593 optimal weight: 0.7980 chunk 393 optimal weight: 5.9990 chunk 702 optimal weight: 20.0000 chunk 439 optimal weight: 6.9990 chunk 428 optimal weight: 9.9990 chunk 324 optimal weight: 8.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN ** A 724 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 796 HIS B1120 GLN ** B1325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 GLN C 767 ASN C 971 HIS C1382 ASN D 544 GLN D 724 ASN ** D1293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN E 270 ASN F 4 GLN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 ASN ** G 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 57634 Z= 0.221 Angle : 0.793 82.759 78081 Z= 0.340 Chirality : 0.051 1.553 8693 Planarity : 0.004 0.093 10217 Dihedral : 5.599 158.362 8145 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.05 % Allowed : 1.05 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: -1.38 (0.10), residues: 7290 helix: 0.54 (0.10), residues: 2594 sheet: -1.26 (0.17), residues: 890 loop : -1.93 (0.09), residues: 3806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 69 HIS 0.007 0.001 HIS A 971 PHE 0.021 0.001 PHE B 810 TYR 0.024 0.001 TYR B1295 ARG 0.010 0.000 ARG B 347 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 5923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 574 time to evaluate : 5.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7619 (tm-30) REVERT: A 463 LEU cc_start: 0.8470 (tp) cc_final: 0.8225 (tp) REVERT: A 964 MET cc_start: 0.7966 (tmm) cc_final: 0.7736 (tmm) REVERT: A 1047 MET cc_start: 0.7666 (mtt) cc_final: 0.7398 (mtt) REVERT: A 1179 ASP cc_start: 0.6181 (p0) cc_final: 0.5426 (p0) REVERT: A 1229 MET cc_start: 0.7865 (mtp) cc_final: 0.7645 (mmm) REVERT: A 1366 GLU cc_start: 0.8187 (tt0) cc_final: 0.7830 (tt0) REVERT: A 1368 MET cc_start: 0.8825 (ttt) cc_final: 0.8519 (ttm) REVERT: A 1387 MET cc_start: 0.8672 (ttt) cc_final: 0.7604 (ttt) REVERT: B 112 ILE cc_start: 0.9182 (pt) cc_final: 0.8904 (mt) REVERT: B 458 MET cc_start: 0.7126 (tmm) cc_final: 0.6216 (tmm) REVERT: B 461 MET cc_start: 0.8476 (mmp) cc_final: 0.8110 (mmm) REVERT: B 520 MET cc_start: 0.8270 (mmt) cc_final: 0.7856 (mmp) REVERT: B 550 LEU cc_start: 0.9123 (mt) cc_final: 0.8903 (mt) REVERT: B 562 MET cc_start: 0.8725 (mtm) cc_final: 0.8477 (mtm) REVERT: B 860 MET cc_start: 0.7567 (tpp) cc_final: 0.7142 (tpp) REVERT: B 895 ARG cc_start: 0.4960 (mmt90) cc_final: 0.4261 (ptp90) REVERT: B 1017 ASN cc_start: 0.8816 (m-40) cc_final: 0.8443 (m-40) REVERT: B 1047 MET cc_start: 0.7952 (ptp) cc_final: 0.7517 (mtm) REVERT: B 1137 ASN cc_start: 0.7076 (m-40) cc_final: 0.6698 (p0) REVERT: C 244 MET cc_start: 0.8629 (tpp) cc_final: 0.8317 (tpp) REVERT: C 260 MET cc_start: 0.8246 (tpp) cc_final: 0.7676 (tpp) REVERT: C 320 CYS cc_start: 0.9151 (m) cc_final: 0.8777 (m) REVERT: C 345 MET cc_start: 0.8450 (tpp) cc_final: 0.8164 (tpp) REVERT: C 860 MET cc_start: 0.8886 (mmm) cc_final: 0.8533 (tpp) REVERT: C 978 GLU cc_start: 0.8244 (pm20) cc_final: 0.7903 (pm20) REVERT: C 1249 MET cc_start: 0.8420 (mmm) cc_final: 0.8164 (tpp) REVERT: C 1300 LEU cc_start: 0.8717 (tp) cc_final: 0.8500 (tp) REVERT: C 1366 GLU cc_start: 0.8339 (tm-30) cc_final: 0.7859 (tm-30) REVERT: D 442 MET cc_start: 0.3276 (ptp) cc_final: 0.3061 (ptp) REVERT: D 448 ARG cc_start: 0.8365 (mtt-85) cc_final: 0.8131 (mtp85) REVERT: D 454 PHE cc_start: 0.8556 (m-10) cc_final: 0.8261 (m-10) REVERT: D 479 MET cc_start: 0.8391 (tpp) cc_final: 0.7939 (tpp) REVERT: D 591 GLN cc_start: 0.8141 (tt0) cc_final: 0.7833 (tm-30) REVERT: D 651 ASP cc_start: 0.8446 (t0) cc_final: 0.8211 (t0) REVERT: D 767 ASN cc_start: 0.8078 (t0) cc_final: 0.7724 (t0) REVERT: D 980 LEU cc_start: 0.9196 (tp) cc_final: 0.8937 (tp) REVERT: D 1100 MET cc_start: 0.8417 (mmm) cc_final: 0.8151 (mmp) REVERT: E 183 MET cc_start: 0.7572 (mtp) cc_final: 0.7354 (mtt) REVERT: F 6 MET cc_start: 0.7948 (ptp) cc_final: 0.7555 (ptp) REVERT: F 31 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7010 (mm-30) REVERT: F 227 LEU cc_start: 0.6751 (tt) cc_final: 0.6381 (mt) REVERT: F 304 ASP cc_start: 0.7492 (m-30) cc_final: 0.6924 (m-30) REVERT: G 332 GLN cc_start: 0.7185 (pp30) cc_final: 0.6128 (mp10) REVERT: G 435 MET cc_start: 0.6208 (ptm) cc_final: 0.5978 (ptm) outliers start: 3 outliers final: 1 residues processed: 577 average time/residue: 0.5250 time to fit residues: 527.8613 Evaluate side-chains 435 residues out of total 5923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 433 time to evaluate : 5.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 729 random chunks: chunk 434 optimal weight: 0.5980 chunk 280 optimal weight: 9.9990 chunk 419 optimal weight: 0.3980 chunk 211 optimal weight: 8.9990 chunk 138 optimal weight: 8.9990 chunk 136 optimal weight: 6.9990 chunk 446 optimal weight: 2.9990 chunk 478 optimal weight: 3.9990 chunk 347 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 552 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 GLN ** A1177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 796 HIS ** B1325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 GLN C 788 HIS C1382 ASN D 508 ASN D 724 ASN D1293 ASN E 270 ASN E 312 GLN F 4 GLN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 ASN ** G 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 57634 Z= 0.186 Angle : 0.778 82.653 78081 Z= 0.329 Chirality : 0.051 1.540 8693 Planarity : 0.004 0.054 10217 Dihedral : 5.465 157.257 8145 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.05 % Allowed : 0.73 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: -1.21 (0.10), residues: 7290 helix: 0.67 (0.11), residues: 2598 sheet: -1.08 (0.17), residues: 919 loop : -1.85 (0.09), residues: 3773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 69 HIS 0.005 0.001 HIS B 47 PHE 0.025 0.001 PHE C1439 TYR 0.019 0.001 TYR C 813 ARG 0.009 0.000 ARG A1173 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14580 Ramachandran restraints generated. 7290 Oldfield, 0 Emsley, 7290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 5923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 583 time to evaluate : 5.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 LEU cc_start: 0.8442 (tp) cc_final: 0.8221 (tp) REVERT: A 1047 MET cc_start: 0.7586 (mtt) cc_final: 0.7266 (mtt) REVERT: A 1054 GLN cc_start: 0.8478 (mt0) cc_final: 0.8221 (mt0) REVERT: A 1229 MET cc_start: 0.7803 (mtp) cc_final: 0.7599 (mmm) REVERT: A 1366 GLU cc_start: 0.8210 (tt0) cc_final: 0.7794 (tt0) REVERT: A 1368 MET cc_start: 0.8807 (ttt) cc_final: 0.8469 (ttm) REVERT: A 1387 MET cc_start: 0.8645 (ttt) cc_final: 0.7504 (ttt) REVERT: A 1462 MET cc_start: 0.8187 (mmm) cc_final: 0.7763 (mmp) REVERT: B 112 ILE cc_start: 0.9175 (pt) cc_final: 0.8917 (mt) REVERT: B 458 MET cc_start: 0.7165 (tmm) cc_final: 0.6248 (tmm) REVERT: B 461 MET cc_start: 0.8440 (mmp) cc_final: 0.8094 (mmm) REVERT: B 520 MET cc_start: 0.8239 (mmt) cc_final: 0.7891 (mmp) REVERT: B 860 MET cc_start: 0.7355 (tpp) cc_final: 0.6904 (tpp) REVERT: B 895 ARG cc_start: 0.4963 (mmt90) cc_final: 0.4233 (ptp90) REVERT: B 1017 ASN cc_start: 0.8783 (m-40) cc_final: 0.8342 (m-40) REVERT: B 1047 MET cc_start: 0.7909 (ptp) cc_final: 0.7383 (mtm) REVERT: B 1084 MET cc_start: 0.8548 (tpp) cc_final: 0.8289 (tpp) REVERT: B 1137 ASN cc_start: 0.7043 (m-40) cc_final: 0.6699 (p0) REVERT: C 207 TYR cc_start: 0.9123 (p90) cc_final: 0.8911 (p90) REVERT: C 244 MET cc_start: 0.8557 (tpp) cc_final: 0.8241 (tpp) REVERT: C 260 MET cc_start: 0.8250 (tpp) cc_final: 0.7679 (tpp) REVERT: C 320 CYS cc_start: 0.9206 (m) cc_final: 0.8805 (m) REVERT: C 345 MET cc_start: 0.8458 (tpp) cc_final: 0.8044 (tpp) REVERT: C 805 ASP cc_start: 0.8202 (t70) cc_final: 0.7929 (t70) REVERT: C 860 MET cc_start: 0.8890 (mmm) cc_final: 0.8511 (tpp) REVERT: C 978 GLU cc_start: 0.8177 (pm20) cc_final: 0.7875 (pm20) REVERT: C 1249 MET cc_start: 0.8385 (mmm) cc_final: 0.8139 (tpp) REVERT: C 1300 LEU cc_start: 0.8908 (tp) cc_final: 0.8673 (tp) REVERT: C 1366 GLU cc_start: 0.8388 (tm-30) cc_final: 0.7844 (tm-30) REVERT: D 448 ARG cc_start: 0.8357 (mtt-85) cc_final: 0.8126 (mtp85) REVERT: D 454 PHE cc_start: 0.8593 (m-10) cc_final: 0.8300 (m-10) REVERT: D 461 MET cc_start: 0.8391 (mmt) cc_final: 0.8074 (mpp) REVERT: D 479 MET cc_start: 0.8422 (tpp) cc_final: 0.8091 (tpp) REVERT: D 591 GLN cc_start: 0.8060 (tt0) cc_final: 0.7757 (tm-30) REVERT: D 651 ASP cc_start: 0.8436 (t0) cc_final: 0.8182 (t0) REVERT: D 767 ASN cc_start: 0.8091 (t0) cc_final: 0.7715 (t0) REVERT: D 860 MET cc_start: 0.8511 (mmp) cc_final: 0.8304 (mmp) REVERT: D 980 LEU cc_start: 0.9252 (tp) cc_final: 0.8913 (tp) REVERT: D 1100 MET cc_start: 0.8425 (mmm) cc_final: 0.8147 (mmp) REVERT: D 1328 LEU cc_start: 0.9045 (tt) cc_final: 0.8713 (tt) REVERT: E 183 MET cc_start: 0.7527 (mtp) cc_final: 0.7178 (mtm) REVERT: E 303 MET cc_start: 0.8265 (mmm) cc_final: 0.7920 (mmp) REVERT: F 6 MET cc_start: 0.8173 (ptp) cc_final: 0.7690 (ptp) REVERT: F 31 GLU cc_start: 0.7754 (mt-10) cc_final: 0.6886 (tp30) REVERT: F 227 LEU cc_start: 0.6862 (tt) cc_final: 0.6536 (mt) REVERT: F 304 ASP cc_start: 0.7445 (m-30) cc_final: 0.6828 (m-30) REVERT: G 332 GLN cc_start: 0.7194 (pp30) cc_final: 0.6094 (mp10) REVERT: G 435 MET cc_start: 0.6140 (ptm) cc_final: 0.5886 (ptm) outliers start: 3 outliers final: 0 residues processed: 586 average time/residue: 0.5199 time to fit residues: 535.9997 Evaluate side-chains 438 residues out of total 5923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 438 time to evaluate : 5.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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: 60.9568 > 50: distance: 68 - 70: 8.053 distance: 71 - 72: 15.949 distance: 71 - 74: 16.326 distance: 72 - 73: 16.817 distance: 72 - 78: 28.190 distance: 74 - 75: 25.491 distance: 75 - 76: 8.671 distance: 75 - 77: 7.714 distance: 78 - 79: 4.464 distance: 79 - 80: 26.545 distance: 79 - 82: 11.599 distance: 80 - 81: 14.668 distance: 80 - 84: 5.188 distance: 81 - 108: 23.971 distance: 84 - 85: 15.247 distance: 85 - 86: 21.865 distance: 85 - 88: 27.987 distance: 86 - 87: 5.668 distance: 86 - 95: 24.331 distance: 87 - 115: 45.869 distance: 88 - 89: 12.745 distance: 89 - 90: 27.806 distance: 90 - 91: 18.076 distance: 91 - 92: 25.591 distance: 92 - 93: 24.091 distance: 92 - 94: 20.638 distance: 95 - 96: 11.363 distance: 96 - 97: 11.011 distance: 96 - 99: 15.488 distance: 97 - 98: 44.416 distance: 97 - 100: 5.165 distance: 98 - 120: 40.053 distance: 100 - 101: 25.303 distance: 101 - 102: 10.948 distance: 101 - 104: 15.006 distance: 102 - 103: 4.423 distance: 102 - 108: 40.957 distance: 103 - 129: 6.436 distance: 104 - 105: 11.270 distance: 105 - 106: 39.096 distance: 105 - 107: 40.093 distance: 108 - 109: 20.994 distance: 109 - 110: 7.396 distance: 109 - 112: 31.422 distance: 110 - 111: 13.081 distance: 110 - 115: 24.053 distance: 111 - 139: 46.419 distance: 112 - 113: 41.159 distance: 112 - 114: 17.338 distance: 115 - 116: 18.910 distance: 116 - 117: 20.940 distance: 116 - 119: 13.294 distance: 117 - 118: 9.561 distance: 117 - 120: 18.112 distance: 120 - 121: 10.030 distance: 121 - 122: 37.785 distance: 121 - 124: 36.038 distance: 122 - 123: 19.340 distance: 122 - 129: 26.304 distance: 124 - 125: 19.975 distance: 125 - 126: 25.773 distance: 126 - 128: 15.643 distance: 129 - 130: 33.720 distance: 130 - 131: 16.608 distance: 130 - 133: 27.650 distance: 131 - 132: 7.260 distance: 131 - 139: 56.927 distance: 133 - 134: 11.856 distance: 134 - 135: 12.503 distance: 134 - 136: 11.364 distance: 135 - 137: 12.161 distance: 137 - 138: 10.822 distance: 139 - 140: 42.380 distance: 140 - 141: 21.359 distance: 140 - 143: 46.149 distance: 141 - 142: 16.515 distance: 141 - 150: 20.630 distance: 143 - 144: 35.566 distance: 144 - 145: 6.763 distance: 144 - 146: 53.444 distance: 146 - 148: 6.463 distance: 147 - 149: 13.013 distance: 148 - 149: 50.880