Starting phenix.real_space_refine on Mon Mar 25 09:41:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cnb_7530/03_2024/6cnb_7530.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cnb_7530/03_2024/6cnb_7530.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/6cnb_7530/03_2024/6cnb_7530.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cnb_7530/03_2024/6cnb_7530.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cnb_7530/03_2024/6cnb_7530.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cnb_7530/03_2024/6cnb_7530.pdb" } 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= 0.001 sd= 0.007 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 Zn 7 6.06 5 P 110 5.49 5 S 242 5.16 5 C 29975 2.51 5 N 8269 2.21 5 O 9234 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 184": "NH1" <-> "NH2" Residue "P ARG 262": "NH1" <-> "NH2" Residue "R ARG 14": "NH1" <-> "NH2" Residue "R ARG 294": "NH1" <-> "NH2" Residue "S ARG 413": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 47837 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 11159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1428, 11159 Classifications: {'peptide': 1428} Link IDs: {'PCIS': 1, 'PTRANS': 65, 'TRANS': 1361} Chain breaks: 2 Chain: "B" Number of atoms: 8788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1114, 8788 Classifications: {'peptide': 1114} Link IDs: {'PTRANS': 43, 'TRANS': 1070} Chain: "C" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2655 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 20, 'TRANS': 314} Chain: "D" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 977 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain breaks: 2 Chain: "E" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1759 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 671 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1484 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 12, 'TRANS': 171} Chain breaks: 2 Chain: "H" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1120 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 135} Chain breaks: 1 Chain: "I" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 321 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 3, 'TRANS': 38} Chain: "J" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 549 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 792 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "L" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 363 Classifications: {'peptide': 46} Link IDs: {'TRANS': 45} Chain: "M" Number of atoms: 1338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1338 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 8, 'TRANS': 155} Chain breaks: 1 Chain: "N" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 845 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain breaks: 1 Chain: "O" Number of atoms: 4329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4329 Classifications: {'peptide': 539} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 520} Chain breaks: 2 Chain: "P" Number of atoms: 2242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2242 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 7, 'TRANS': 269} Chain breaks: 2 Chain: "Q" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 368 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 5, 'TRANS': 48} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "R" Number of atoms: 4131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4131 Classifications: {'peptide': 522} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 502} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1649 Classifications: {'peptide': 217} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 42} Link IDs: {'PTRANS': 7, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 43} Unresolved non-hydrogen planarities: 43 Chain: "X" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1036 Classifications: {'DNA': 51} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 50} Chain breaks: 1 Chain: "Y" Number of atoms: 1254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1254 Classifications: {'DNA': 61} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 60} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 492 SG CYS A 67 87.892 70.818 82.655 1.00 0.00 S ATOM 510 SG CYS A 70 90.376 72.991 79.270 1.00 0.00 S ATOM 557 SG CYS A 77 90.063 72.348 82.559 1.00 0.00 S ATOM 795 SG CYS A 107 72.458 115.688 90.316 1.00 0.00 S ATOM 818 SG CYS A 110 70.017 116.718 87.878 1.00 0.00 S ATOM 1184 SG CYS A 154 72.602 118.862 89.642 1.00 0.00 S ATOM 1208 SG CYS A 157 69.606 119.012 90.784 1.00 0.00 S ATOM 19520 SG CYS B1095 92.163 87.229 71.607 1.00 0.00 S ATOM 19543 SG CYS B1098 89.182 90.179 73.623 1.00 0.00 S ATOM 19609 SG CYS B1107 89.999 85.887 74.166 1.00 0.00 S ATOM 19629 SG CYS B1110 88.210 87.606 71.818 1.00 0.00 S ATOM 28652 SG CYS I 5 79.034 122.486 156.301 1.00 0.00 S ATOM 28671 SG CYS I 8 75.409 122.494 157.182 1.00 0.00 S ATOM 28799 SG CYS I 26 78.460 123.015 153.420 1.00 0.00 S ATOM 28822 SG CYS I 29 75.856 121.003 154.253 1.00 0.00 S ATOM 28988 SG CYS J 7 140.119 50.483 126.161 1.00 0.00 S ATOM 29011 SG CYS J 10 143.941 51.514 126.858 1.00 0.00 S ATOM 29291 SG CYS J 45 142.060 53.867 127.667 1.00 0.00 S ATOM 29297 SG CYS J 46 142.768 49.687 128.697 1.00 0.00 S ATOM 30330 SG CYS L 31 98.206 34.620 125.951 1.00 0.00 S ATOM 30350 SG CYS L 34 97.599 33.834 129.743 1.00 0.00 S ATOM 30454 SG CYS L 48 94.875 35.188 126.730 1.00 0.00 S ATOM 30477 SG CYS L 51 95.909 36.003 128.834 1.00 0.00 S ATOM 39788 SG CYS R 4 104.134 53.468 76.632 1.00 0.00 S ATOM 39811 SG CYS R 7 104.530 50.365 77.114 1.00 0.00 S ATOM 39952 SG CYS R 25 106.441 51.600 79.757 1.00 0.00 S ATOM 39972 SG CYS R 28 107.310 52.216 76.562 1.00 0.00 S Time building chain proxies: 24.73, per 1000 atoms: 0.52 Number of scatterers: 47837 At special positions: 0 Unit cell: (199.42, 169.92, 202.96, 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) Zn 7 29.99 S 242 16.00 P 110 15.00 O 9234 8.00 N 8269 7.00 C 29975 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.75 Conformation dependent library (CDL) restraints added in 8.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1501 " pdb="ZN ZN A1501 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 70 " pdb=" ZN A1502 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 154 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 157 " pdb=" ZN B2000 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1107 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1095 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1098 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1110 " pdb=" ZN I2000 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 26 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 5 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 8 " pdb="ZN ZN I2000 " - pdb=" SG CYS I 29 " pdb=" ZN J2000 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 46 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 10 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 45 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 7 " pdb=" ZN L2000 " pdb="ZN ZN L2000 " - pdb=" SG CYS L 34 " pdb="ZN ZN L2000 " - pdb=" SG CYS L 51 " pdb="ZN ZN L2000 " - pdb=" SG CYS L 48 " pdb="ZN ZN L2000 " - pdb=" SG CYS L 31 " pdb=" ZN R1001 " pdb="ZN ZN R1001 " - pdb=" SG CYS R 4 " pdb="ZN ZN R1001 " - pdb=" SG CYS R 7 " pdb="ZN ZN R1001 " - pdb=" SG CYS R 25 " pdb="ZN ZN R1001 " - pdb=" SG CYS R 28 " Number of angles added : 39 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10898 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 53 sheets defined 41.2% alpha, 10.7% beta 40 base pairs and 81 stacking pairs defined. Time for finding SS restraints: 17.73 Creating SS restraints... Processing helix chain 'A' and resid 22 through 28 removed outlier: 4.097A pdb=" N ILE A 26 " --> pdb=" O SER A 22 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 42 removed outlier: 4.276A pdb=" N ASP A 41 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU A 42 " --> pdb=" O LEU A 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 38 through 42' Processing helix chain 'A' and resid 72 through 77 removed outlier: 3.705A pdb=" N CYS A 77 " --> pdb=" O ASN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 103 removed outlier: 3.540A pdb=" N GLN A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 128 removed outlier: 3.750A pdb=" N ARG A 121 " --> pdb=" O GLU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 150 removed outlier: 3.957A pdb=" N ASP A 146 " --> pdb=" O LYS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 206 removed outlier: 4.163A pdb=" N GLU A 203 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 removed outlier: 3.943A pdb=" N LEU A 228 " --> pdb=" O PRO A 224 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 284 through 302 removed outlier: 3.581A pdb=" N LEU A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR A 290 " --> pdb=" O THR A 286 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TRP A 294 " --> pdb=" O THR A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 328 removed outlier: 3.671A pdb=" N MET A 313 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU A 314 " --> pdb=" O ASN A 310 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N HIS A 315 " --> pdb=" O ASN A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 400 Processing helix chain 'A' and resid 412 through 423 removed outlier: 4.475A pdb=" N GLU A 418 " --> pdb=" O HIS A 414 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL A 421 " --> pdb=" O GLN A 417 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN A 422 " --> pdb=" O GLU A 418 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 506 removed outlier: 4.132A pdb=" N THR A 506 " --> pdb=" O CYS A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 536 removed outlier: 3.544A pdb=" N ARG A 528 " --> pdb=" O THR A 524 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA A 529 " --> pdb=" O GLU A 525 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 541 removed outlier: 3.563A pdb=" N LEU A 541 " --> pdb=" O LYS A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 566 Processing helix chain 'A' and resid 572 through 583 Processing helix chain 'A' and resid 605 through 615 removed outlier: 3.925A pdb=" N LEU A 613 " --> pdb=" O VAL A 609 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE A 614 " --> pdb=" O PHE A 610 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS A 615 " --> pdb=" O SER A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 670 Processing helix chain 'A' and resid 676 through 686 removed outlier: 4.019A pdb=" N LEU A 682 " --> pdb=" O PHE A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 709 removed outlier: 3.593A pdb=" N ALA A 690 " --> pdb=" O GLY A 686 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ARG A 703 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY A 706 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASN A 707 " --> pdb=" O ARG A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 718 removed outlier: 3.925A pdb=" N VAL A 717 " --> pdb=" O GLY A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 747 removed outlier: 4.079A pdb=" N ALA A 734 " --> pdb=" O LEU A 730 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS A 736 " --> pdb=" O GLU A 732 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LYS A 747 " --> pdb=" O THR A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 784 removed outlier: 3.501A pdb=" N GLU A 784 " --> pdb=" O VAL A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 794 Processing helix chain 'A' and resid 802 through 811 Processing helix chain 'A' and resid 857 through 894 removed outlier: 3.565A pdb=" N ILE A 866 " --> pdb=" O LEU A 862 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER A 867 " --> pdb=" O PHE A 863 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLY A 868 " --> pdb=" O HIS A 864 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ARG A 869 " --> pdb=" O ALA A 865 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS A 878 " --> pdb=" O ASP A 874 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU A 881 " --> pdb=" O VAL A 877 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR A 884 " --> pdb=" O ALA A 880 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS A 891 " --> pdb=" O ARG A 887 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER A 892 " --> pdb=" O ARG A 888 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 893 " --> pdb=" O LEU A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 931 removed outlier: 3.541A pdb=" N GLN A 931 " --> pdb=" O GLY A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 947 removed outlier: 3.696A pdb=" N ASP A 940 " --> pdb=" O ASN A 936 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE A 945 " --> pdb=" O HIS A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 975 Proline residue: A 969 - end of helix removed outlier: 3.557A pdb=" N GLU A 972 " --> pdb=" O GLY A 968 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ARG A 973 " --> pdb=" O PRO A 969 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A 975 " --> pdb=" O GLU A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1026 removed outlier: 3.722A pdb=" N ALA A1018 " --> pdb=" O GLY A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1051 through 1060 Processing helix chain 'A' and resid 1064 through 1081 Processing helix chain 'A' and resid 1088 through 1099 removed outlier: 3.624A pdb=" N ILE A1092 " --> pdb=" O ALA A1088 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLU A1099 " --> pdb=" O GLN A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1132 removed outlier: 3.864A pdb=" N ILE A1126 " --> pdb=" O GLY A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1161 removed outlier: 3.905A pdb=" N LYS A1158 " --> pdb=" O ALA A1154 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1170 Processing helix chain 'A' and resid 1189 through 1196 removed outlier: 4.011A pdb=" N ILE A1193 " --> pdb=" O ASP A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1213 removed outlier: 3.700A pdb=" N THR A1210 " --> pdb=" O ALA A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1214 through 1216 No H-bonds generated for 'chain 'A' and resid 1214 through 1216' Processing helix chain 'A' and resid 1254 through 1267 Processing helix chain 'A' and resid 1301 through 1306 Processing helix chain 'A' and resid 1318 through 1324 removed outlier: 3.809A pdb=" N VAL A1322 " --> pdb=" O HIS A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1328 through 1346 removed outlier: 3.600A pdb=" N ARG A1337 " --> pdb=" O TYR A1333 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN A1340 " --> pdb=" O ILE A1336 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N HIS A1346 " --> pdb=" O THR A1342 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1364 removed outlier: 4.700A pdb=" N HIS A1354 " --> pdb=" O VAL A1350 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE A1355 " --> pdb=" O ASP A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1403 removed outlier: 3.537A pdb=" N TYR A1402 " --> pdb=" O ASP A1398 " (cutoff:3.500A) Processing helix chain 'A' and resid 1413 through 1418 removed outlier: 3.861A pdb=" N LEU A1417 " --> pdb=" O GLU A1413 " (cutoff:3.500A) Processing helix chain 'A' and resid 1423 through 1428 removed outlier: 4.161A pdb=" N PHE A1428 " --> pdb=" O THR A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1437 through 1441 removed outlier: 3.533A pdb=" N ASP A1440 " --> pdb=" O SER A1437 " (cutoff:3.500A) Processing helix chain 'A' and resid 1447 through 1454 removed outlier: 3.927A pdb=" N LEU A1451 " --> pdb=" O LEU A1447 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER A1452 " --> pdb=" O PHE A1448 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU A1454 " --> pdb=" O SER A1450 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 45 Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.558A pdb=" N ALA B 50 " --> pdb=" O HIS B 46 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 71 removed outlier: 3.504A pdb=" N PHE B 65 " --> pdb=" O HIS B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 80 removed outlier: 3.795A pdb=" N LYS B 78 " --> pdb=" O LYS B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 121 removed outlier: 3.729A pdb=" N ARG B 121 " --> pdb=" O GLU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 252 through 260 Processing helix chain 'B' and resid 266 through 273 Processing helix chain 'B' and resid 279 through 292 removed outlier: 4.240A pdb=" N ASN B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU B 289 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER B 290 " --> pdb=" O ASN B 286 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 309 removed outlier: 4.078A pdb=" N ILE B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 320 Processing helix chain 'B' and resid 325 through 331 removed outlier: 3.827A pdb=" N THR B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 362 removed outlier: 3.737A pdb=" N ARG B 355 " --> pdb=" O MET B 351 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL B 356 " --> pdb=" O MET B 352 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN B 362 " --> pdb=" O MET B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 379 through 409 removed outlier: 3.910A pdb=" N LEU B 383 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER B 385 " --> pdb=" O GLY B 381 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS B 405 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL B 406 " --> pdb=" O SER B 402 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B 407 " --> pdb=" O ILE B 403 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LYS B 409 " --> pdb=" O LYS B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 425 removed outlier: 4.113A pdb=" N VAL B 424 " --> pdb=" O LEU B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 440 Processing helix chain 'B' and resid 462 through 470 removed outlier: 3.904A pdb=" N LEU B 467 " --> pdb=" O TYR B 463 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N MET B 470 " --> pdb=" O ALA B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 494 Processing helix chain 'B' and resid 526 through 536 Processing helix chain 'B' and resid 540 through 544 Processing helix chain 'B' and resid 567 through 580 Processing helix chain 'B' and resid 627 through 632 Processing helix chain 'B' and resid 639 through 644 Processing helix chain 'B' and resid 651 through 657 Processing helix chain 'B' and resid 676 through 680 removed outlier: 3.677A pdb=" N THR B 679 " --> pdb=" O GLU B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 688 Processing helix chain 'B' and resid 690 through 694 Processing helix chain 'B' and resid 695 through 704 removed outlier: 4.092A pdb=" N ASN B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 709 Processing helix chain 'B' and resid 741 through 749 removed outlier: 6.343A pdb=" N TYR B 746 " --> pdb=" O LEU B 743 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ASP B 747 " --> pdb=" O ILE B 744 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 749 " --> pdb=" O TYR B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 781 removed outlier: 3.698A pdb=" N GLY B 781 " --> pdb=" O ILE B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 947 through 953 removed outlier: 3.948A pdb=" N SER B 951 " --> pdb=" O HIS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 971 removed outlier: 4.231A pdb=" N ILE B 962 " --> pdb=" O MET B 958 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN B 970 " --> pdb=" O ALA B 966 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 993 removed outlier: 3.891A pdb=" N MET B 987 " --> pdb=" O LYS B 983 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER B 988 " --> pdb=" O LEU B 984 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LYS B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP B 993 " --> pdb=" O LYS B 989 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1035 removed outlier: 3.735A pdb=" N LYS B1034 " --> pdb=" O MET B1030 " (cutoff:3.500A) Processing helix chain 'B' and resid 1063 through 1074 removed outlier: 3.509A pdb=" N ASP B1068 " --> pdb=" O GLU B1064 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N CYS B1069 " --> pdb=" O MET B1065 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL B1070 " --> pdb=" O GLU B1066 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE B1071 " --> pdb=" O ARG B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1083 Processing helix chain 'B' and resid 1122 through 1135 Processing helix chain 'C' and resid 60 through 74 removed outlier: 4.226A pdb=" N ALA C 64 " --> pdb=" O ASP C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 104 Processing helix chain 'C' and resid 121 through 125 Processing helix chain 'C' and resid 127 through 131 Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 174 through 180 removed outlier: 3.588A pdb=" N THR C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE C 179 " --> pdb=" O GLN C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 220 removed outlier: 5.813A pdb=" N ALA C 217 " --> pdb=" O GLY C 214 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LYS C 218 " --> pdb=" O ASP C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 251 removed outlier: 3.888A pdb=" N ARG C 245 " --> pdb=" O GLY C 241 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS C 249 " --> pdb=" O ARG C 245 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE C 251 " --> pdb=" O PHE C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 287 No H-bonds generated for 'chain 'C' and resid 285 through 287' Processing helix chain 'C' and resid 309 through 330 removed outlier: 3.513A pdb=" N LEU C 321 " --> pdb=" O SER C 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 27 removed outlier: 4.293A pdb=" N LYS D 18 " --> pdb=" O TYR D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 72 removed outlier: 3.701A pdb=" N THR D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN D 61 " --> pdb=" O GLY D 57 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ASN D 69 " --> pdb=" O TYR D 65 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LYS D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 111 removed outlier: 3.617A pdb=" N MET D 107 " --> pdb=" O PHE D 103 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N THR D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N LYS D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 123 removed outlier: 3.608A pdb=" N LEU D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 136 removed outlier: 3.623A pdb=" N LEU D 134 " --> pdb=" O ASN D 130 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR D 135 " --> pdb=" O MET D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 159 removed outlier: 4.006A pdb=" N MET D 153 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU D 154 " --> pdb=" O ILE D 150 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU D 155 " --> pdb=" O GLU D 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 25 removed outlier: 3.722A pdb=" N GLU E 6 " --> pdb=" O ASP E 2 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS E 24 " --> pdb=" O LYS E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 47 Processing helix chain 'E' and resid 54 through 59 removed outlier: 3.850A pdb=" N MET E 58 " --> pdb=" O GLN E 54 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER E 59 " --> pdb=" O ARG E 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 54 through 59' Processing helix chain 'E' and resid 66 through 72 Processing helix chain 'E' and resid 89 through 103 removed outlier: 3.533A pdb=" N PHE E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 123 removed outlier: 3.849A pdb=" N LEU E 123 " --> pdb=" O SER E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 169 removed outlier: 4.074A pdb=" N ARG E 162 " --> pdb=" O SER E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 86 through 103 removed outlier: 4.130A pdb=" N ARG F 90 " --> pdb=" O THR F 86 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA F 91 " --> pdb=" O LYS F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 126 removed outlier: 3.819A pdb=" N ILE F 120 " --> pdb=" O ASP F 116 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA F 121 " --> pdb=" O PRO F 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 20 removed outlier: 3.617A pdb=" N GLN G 17 " --> pdb=" O PRO G 14 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N HIS G 19 " --> pdb=" O ASP G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 34 Processing helix chain 'G' and resid 162 through 166 Processing helix chain 'G' and resid 207 through 211 Processing helix chain 'H' and resid 130 through 134 removed outlier: 4.485A pdb=" N ASN H 133 " --> pdb=" O ARG H 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 27 removed outlier: 4.248A pdb=" N SER J 20 " --> pdb=" O ASP J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 52 removed outlier: 4.361A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 62 removed outlier: 3.610A pdb=" N ARG J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 82 removed outlier: 3.815A pdb=" N GLY K 73 " --> pdb=" O ASP K 69 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N TYR K 78 " --> pdb=" O ASN K 74 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS K 82 " --> pdb=" O TYR K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 142 removed outlier: 3.644A pdb=" N ASP K 126 " --> pdb=" O LYS K 122 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS K 128 " --> pdb=" O LEU K 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 139 removed outlier: 3.543A pdb=" N ALA M 136 " --> pdb=" O ASN M 132 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU M 139 " --> pdb=" O LYS M 135 " (cutoff:3.500A) Processing helix chain 'M' and resid 184 through 195 removed outlier: 4.337A pdb=" N GLN M 195 " --> pdb=" O VAL M 191 " (cutoff:3.500A) Processing helix chain 'M' and resid 229 through 240 removed outlier: 3.546A pdb=" N VAL M 236 " --> pdb=" O LEU M 232 " (cutoff:3.500A) Processing helix chain 'M' and resid 252 through 261 removed outlier: 3.585A pdb=" N LYS M 256 " --> pdb=" O PHE M 252 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N THR M 258 " --> pdb=" O GLN M 254 " (cutoff:3.500A) Processing helix chain 'N' and resid 275 through 296 removed outlier: 3.504A pdb=" N LEU N 283 " --> pdb=" O GLU N 279 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASN N 284 " --> pdb=" O LEU N 280 " (cutoff:3.500A) Processing helix chain 'N' and resid 297 through 299 No H-bonds generated for 'chain 'N' and resid 297 through 299' Processing helix chain 'O' and resid 46 through 57 removed outlier: 3.682A pdb=" N GLU O 51 " --> pdb=" O PHE O 47 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS O 54 " --> pdb=" O LYS O 50 " (cutoff:3.500A) Processing helix chain 'O' and resid 58 through 72 removed outlier: 3.536A pdb=" N VAL O 64 " --> pdb=" O ARG O 60 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE O 65 " --> pdb=" O ALA O 61 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY O 66 " --> pdb=" O ALA O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 84 removed outlier: 4.055A pdb=" N VAL O 80 " --> pdb=" O VAL O 76 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU O 81 " --> pdb=" O ARG O 77 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS O 82 " --> pdb=" O GLU O 78 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASP O 84 " --> pdb=" O VAL O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 101 Processing helix chain 'O' and resid 126 through 133 removed outlier: 4.093A pdb=" N LEU O 130 " --> pdb=" O GLY O 126 " (cutoff:3.500A) Processing helix chain 'O' and resid 133 through 139 Processing helix chain 'O' and resid 139 through 144 removed outlier: 4.043A pdb=" N GLN O 143 " --> pdb=" O GLU O 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 150 through 167 Processing helix chain 'O' and resid 170 through 178 Processing helix chain 'O' and resid 183 through 188 Processing helix chain 'O' and resid 204 through 208 Processing helix chain 'O' and resid 210 through 219 Processing helix chain 'O' and resid 233 through 258 removed outlier: 3.717A pdb=" N LYS O 237 " --> pdb=" O SER O 233 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN O 240 " --> pdb=" O LYS O 236 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA O 241 " --> pdb=" O LYS O 237 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS O 251 " --> pdb=" O THR O 247 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE O 252 " --> pdb=" O ASP O 248 " (cutoff:3.500A) Proline residue: O 256 - end of helix Processing helix chain 'O' and resid 259 through 264 Processing helix chain 'O' and resid 284 through 304 removed outlier: 3.572A pdb=" N ARG O 303 " --> pdb=" O LEU O 299 " (cutoff:3.500A) Processing helix chain 'O' and resid 305 through 320 removed outlier: 3.964A pdb=" N ARG O 317 " --> pdb=" O LYS O 313 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU O 318 " --> pdb=" O ILE O 314 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR O 319 " --> pdb=" O ALA O 315 " (cutoff:3.500A) Processing helix chain 'O' and resid 329 through 333 Processing helix chain 'O' and resid 340 through 352 removed outlier: 3.567A pdb=" N SER O 344 " --> pdb=" O GLU O 340 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU O 348 " --> pdb=" O SER O 344 " (cutoff:3.500A) Processing helix chain 'O' and resid 355 through 361 removed outlier: 3.883A pdb=" N THR O 360 " --> pdb=" O THR O 356 " (cutoff:3.500A) Processing helix chain 'O' and resid 453 through 458 Processing helix chain 'O' and resid 459 through 463 Processing helix chain 'O' and resid 482 through 489 removed outlier: 3.862A pdb=" N SER O 489 " --> pdb=" O PRO O 485 " (cutoff:3.500A) Processing helix chain 'O' and resid 501 through 514 removed outlier: 4.203A pdb=" N MET O 505 " --> pdb=" O GLY O 501 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG O 506 " --> pdb=" O PRO O 502 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU O 507 " --> pdb=" O SER O 503 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP O 513 " --> pdb=" O ARG O 509 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN O 514 " --> pdb=" O CYS O 510 " (cutoff:3.500A) Processing helix chain 'O' and resid 518 through 526 Processing helix chain 'O' and resid 529 through 543 removed outlier: 3.537A pdb=" N ILE O 533 " --> pdb=" O LYS O 529 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER O 535 " --> pdb=" O LYS O 531 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU O 540 " --> pdb=" O THR O 536 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TYR O 543 " --> pdb=" O SER O 539 " (cutoff:3.500A) Processing helix chain 'O' and resid 569 through 576 removed outlier: 3.828A pdb=" N SER O 573 " --> pdb=" O LYS O 569 " (cutoff:3.500A) Processing helix chain 'O' and resid 578 through 585 removed outlier: 3.649A pdb=" N GLU O 582 " --> pdb=" O ARG O 578 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN O 584 " --> pdb=" O ASN O 580 " (cutoff:3.500A) Processing helix chain 'O' and resid 586 through 610 removed outlier: 3.845A pdb=" N LEU O 595 " --> pdb=" O LYS O 591 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN O 597 " --> pdb=" O GLU O 593 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLU O 598 " --> pdb=" O LYS O 594 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN O 599 " --> pdb=" O LEU O 595 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N THR O 601 " --> pdb=" O GLN O 597 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N LEU O 602 " --> pdb=" O GLU O 598 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS O 604 " --> pdb=" O SER O 600 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS O 605 " --> pdb=" O THR O 601 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP O 610 " --> pdb=" O ALA O 606 " (cutoff:3.500A) Processing helix chain 'O' and resid 620 through 653 removed outlier: 3.508A pdb=" N LEU O 624 " --> pdb=" O LEU O 620 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N VAL O 650 " --> pdb=" O SER O 646 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N PHE O 651 " --> pdb=" O LEU O 647 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN O 652 " --> pdb=" O TRP O 648 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N MET O 653 " --> pdb=" O GLU O 649 " (cutoff:3.500A) Processing helix chain 'P' and resid 11 through 25 removed outlier: 3.503A pdb=" N GLN P 21 " --> pdb=" O THR P 17 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET P 22 " --> pdb=" O LEU P 18 " (cutoff:3.500A) Processing helix chain 'P' and resid 32 through 40 Processing helix chain 'P' and resid 44 through 58 Processing helix chain 'P' and resid 77 through 86 Processing helix chain 'P' and resid 87 through 99 removed outlier: 3.784A pdb=" N LEU P 92 " --> pdb=" O ALA P 88 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER P 95 " --> pdb=" O ALA P 91 " (cutoff:3.500A) Processing helix chain 'P' and resid 100 through 104 removed outlier: 4.093A pdb=" N GLU P 103 " --> pdb=" O SER P 100 " (cutoff:3.500A) Processing helix chain 'P' and resid 108 through 115 removed outlier: 4.159A pdb=" N ALA P 112 " --> pdb=" O LYS P 108 " (cutoff:3.500A) Processing helix chain 'P' and resid 118 through 132 removed outlier: 3.920A pdb=" N LYS P 123 " --> pdb=" O HIS P 119 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N CYS P 124 " --> pdb=" O VAL P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 175 through 191 removed outlier: 3.548A pdb=" N ILE P 181 " --> pdb=" O SER P 177 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N PHE P 191 " --> pdb=" O SER P 187 " (cutoff:3.500A) Processing helix chain 'P' and resid 219 through 226 removed outlier: 4.189A pdb=" N GLU P 223 " --> pdb=" O GLN P 219 " (cutoff:3.500A) Processing helix chain 'P' and resid 236 through 250 removed outlier: 3.786A pdb=" N VAL P 246 " --> pdb=" O SER P 242 " (cutoff:3.500A) Processing helix chain 'P' and resid 266 through 271 Processing helix chain 'Q' and resid 48 through 68 removed outlier: 3.897A pdb=" N PHE Q 61 " --> pdb=" O LYS Q 57 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY Q 62 " --> pdb=" O TYR Q 58 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP Q 67 " --> pdb=" O LYS Q 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1084 through 1088 Processing helix chain 'R' and resid 74 through 94 removed outlier: 3.543A pdb=" N ALA R 78 " --> pdb=" O GLU R 74 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR R 92 " --> pdb=" O ARG R 88 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA R 93 " --> pdb=" O ALA R 89 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU R 94 " --> pdb=" O VAL R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 114 removed outlier: 3.845A pdb=" N THR R 101 " --> pdb=" O PRO R 97 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP R 102 " --> pdb=" O GLU R 98 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA R 103 " --> pdb=" O TYR R 99 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN R 114 " --> pdb=" O LEU R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 121 through 137 removed outlier: 3.799A pdb=" N ALA R 133 " --> pdb=" O CYS R 129 " (cutoff:3.500A) Processing helix chain 'R' and resid 142 through 148 Processing helix chain 'R' and resid 155 through 168 removed outlier: 3.840A pdb=" N LYS R 166 " --> pdb=" O LEU R 162 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS R 167 " --> pdb=" O LYS R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 189 removed outlier: 4.166A pdb=" N PHE R 181 " --> pdb=" O ASP R 177 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLN R 183 " --> pdb=" O SER R 179 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N HIS R 184 " --> pdb=" O LEU R 180 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS R 188 " --> pdb=" O HIS R 184 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 212 removed outlier: 4.265A pdb=" N LYS R 197 " --> pdb=" O ASP R 193 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS R 204 " --> pdb=" O LYS R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 219 through 235 removed outlier: 3.685A pdb=" N ILE R 223 " --> pdb=" O ARG R 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 241 through 249 removed outlier: 3.887A pdb=" N VAL R 247 " --> pdb=" O GLU R 243 " (cutoff:3.500A) Processing helix chain 'R' and resid 251 through 264 removed outlier: 3.757A pdb=" N ARG R 258 " --> pdb=" O THR R 254 " (cutoff:3.500A) Processing helix chain 'R' and resid 289 through 297 removed outlier: 3.702A pdb=" N ASN R 293 " --> pdb=" O SER R 289 " (cutoff:3.500A) Processing helix chain 'R' and resid 407 through 412 Processing helix chain 'R' and resid 455 through 472 removed outlier: 3.632A pdb=" N ALA R 466 " --> pdb=" O SER R 462 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE R 468 " --> pdb=" O LYS R 464 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE R 469 " --> pdb=" O TYR R 465 " (cutoff:3.500A) Processing helix chain 'R' and resid 497 through 506 removed outlier: 3.734A pdb=" N LEU R 501 " --> pdb=" O ARG R 497 " (cutoff:3.500A) Processing helix chain 'R' and resid 545 through 561 removed outlier: 3.517A pdb=" N TYR R 550 " --> pdb=" O ARG R 546 " (cutoff:3.500A) Proline residue: R 558 - end of helix Processing helix chain 'R' and resid 587 through 594 removed outlier: 3.696A pdb=" N TYR R 591 " --> pdb=" O THR R 587 " (cutoff:3.500A) Processing helix chain 'R' and resid 608 through 614 removed outlier: 3.711A pdb=" N ALA R 612 " --> pdb=" O GLU R 608 " (cutoff:3.500A) Processing helix chain 'R' and resid 616 through 648 removed outlier: 5.546A pdb=" N ASP R 633 " --> pdb=" O GLY R 629 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N PHE R 634 " --> pdb=" O LEU R 630 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU R 646 " --> pdb=" O ARG R 642 " (cutoff:3.500A) Processing helix chain 'S' and resid 292 through 317 removed outlier: 3.508A pdb=" N UNK S 296 " --> pdb=" O UNK S 292 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N UNK S 299 " --> pdb=" O UNK S 295 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N UNK S 317 " --> pdb=" O UNK S 313 " (cutoff:3.500A) Processing helix chain 'S' and resid 383 through 393 removed outlier: 3.945A pdb=" N ALA S 387 " --> pdb=" O ARG S 383 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N TYR S 393 " --> pdb=" O ILE S 389 " (cutoff:3.500A) Processing helix chain 'S' and resid 421 through 435 removed outlier: 3.673A pdb=" N LYS S 427 " --> pdb=" O GLU S 423 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE S 428 " --> pdb=" O GLU S 424 " (cutoff:3.500A) Processing helix chain 'S' and resid 438 through 446 removed outlier: 4.120A pdb=" N ILE S 442 " --> pdb=" O ASP S 438 " (cutoff:3.500A) Processing helix chain 'S' and resid 450 through 465 Processing helix chain 'S' and resid 465 through 475 removed outlier: 3.750A pdb=" N ILE S 469 " --> pdb=" O ARG S 465 " (cutoff:3.500A) Processing helix chain 'S' and resid 480 through 486 Processing helix chain 'S' and resid 494 through 531 removed outlier: 3.561A pdb=" N GLN S 528 " --> pdb=" O LYS S 524 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 17 removed outlier: 5.315A pdb=" N ILE A 13 " --> pdb=" O GLU B1144 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLU B1144 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLY A 15 " --> pdb=" O ARG B1142 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG B1142 " --> pdb=" O GLY A 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 84 Processing sheet with id=AA3, first strand: chain 'A' and resid 377 through 378 Processing sheet with id=AA4, first strand: chain 'A' and resid 391 through 395 Processing sheet with id=AA5, first strand: chain 'A' and resid 404 through 407 removed outlier: 4.517A pdb=" N TYR A 432 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 597 through 598 removed outlier: 3.992A pdb=" N ILE A 597 " --> pdb=" O LEU A 603 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 603 " --> pdb=" O ILE A 597 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 625 through 626 removed outlier: 6.778A pdb=" N ILE A 653 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 897 through 898 Processing sheet with id=AA9, first strand: chain 'A' and resid 1278 through 1283 removed outlier: 4.022A pdb=" N ARG A1280 " --> pdb=" O GLU A1296 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU A1293 " --> pdb=" O ALA A1143 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A1143 " --> pdb=" O LEU A1293 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1173 through 1178 removed outlier: 3.825A pdb=" N VAL A1176 " --> pdb=" O PHE A1183 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 145 through 147 removed outlier: 3.774A pdb=" N LYS A1432 " --> pdb=" O GLY G 57 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLY G 57 " --> pdb=" O LYS A1432 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.521A pdb=" N LEU B 93 " --> pdb=" O ILE B 83 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 98 through 100 Processing sheet with id=AB5, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AB6, first strand: chain 'B' and resid 375 through 378 removed outlier: 6.442A pdb=" N VAL B 196 " --> pdb=" O SER B 474 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 510 " --> pdb=" O SER B 475 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 205 through 207 removed outlier: 4.618A pdb=" N TYR B 232 " --> pdb=" O LYS B 243 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LYS B 243 " --> pdb=" O TYR B 232 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ILE B 234 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N TYR B 241 " --> pdb=" O ILE B 234 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 442 through 444 removed outlier: 3.662A pdb=" N ARG B 451 " --> pdb=" O TRP B 442 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU B 444 " --> pdb=" O MET B 449 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 555 through 557 Processing sheet with id=AC1, first strand: chain 'B' and resid 646 through 650 removed outlier: 3.620A pdb=" N LEU B 612 " --> pdb=" O GLU B 647 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG B 610 " --> pdb=" O LEU B 649 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 724 through 728 removed outlier: 3.736A pdb=" N LEU B 727 " --> pdb=" O GLU B 786 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLN B 883 " --> pdb=" O LEU B 899 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ARG B 901 " --> pdb=" O ILE B 881 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ILE B 881 " --> pdb=" O ARG B 901 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 724 through 728 removed outlier: 3.736A pdb=" N LEU B 727 " --> pdb=" O GLU B 786 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLN B 883 " --> pdb=" O LEU B 899 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ARG B 901 " --> pdb=" O ILE B 881 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ILE B 881 " --> pdb=" O ARG B 901 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 943 through 944 removed outlier: 8.180A pdb=" N MET B 944 " --> pdb=" O THR B 756 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA B 758 " --> pdb=" O MET B 944 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY B1020 " --> pdb=" O VAL B 757 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 797 through 798 Processing sheet with id=AC6, first strand: chain 'B' and resid 846 through 848 Processing sheet with id=AC7, first strand: chain 'B' and resid 911 through 913 Processing sheet with id=AC8, first strand: chain 'B' and resid 976 through 977 removed outlier: 4.141A pdb=" N THR B 977 " --> pdb=" O GLY B 980 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD1, first strand: chain 'B' and resid 1101 through 1102 removed outlier: 3.668A pdb=" N ASP B1093 " --> pdb=" O GLY B1102 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 12 through 13 removed outlier: 3.768A pdb=" N ARG C 293 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE C 7 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU C 291 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASN C 53 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU C 41 " --> pdb=" O ILE C 57 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 12 through 13 removed outlier: 3.768A pdb=" N ARG C 293 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE C 7 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU C 291 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN C 234 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LEU C 230 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 9.352A pdb=" N ASN C 296 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 10.419A pdb=" N ARG C 228 " --> pdb=" O ASN C 296 " (cutoff:3.500A) removed outlier: 9.636A pdb=" N PHE C 298 " --> pdb=" O SER C 226 " (cutoff:3.500A) removed outlier: 10.250A pdb=" N SER C 226 " --> pdb=" O PHE C 298 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 168 through 169 removed outlier: 3.568A pdb=" N SER C 135 " --> pdb=" O LYS C 168 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER C 203 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLY C 211 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL C 78 " --> pdb=" O GLY C 211 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL L 65 " --> pdb=" O PHE C 85 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 161 through 163 removed outlier: 4.106A pdb=" N ALA C 194 " --> pdb=" O VAL C 162 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 257 through 258 Processing sheet with id=AD7, first strand: chain 'D' and resid 3 through 9 removed outlier: 12.068A pdb=" N VAL D 3 " --> pdb=" O LEU G 10 " (cutoff:3.500A) removed outlier: 12.067A pdb=" N LEU G 10 " --> pdb=" O VAL D 3 " (cutoff:3.500A) removed outlier: 9.475A pdb=" N GLU D 5 " --> pdb=" O ALA G 8 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N ALA G 8 " --> pdb=" O GLU D 5 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ARG D 7 " --> pdb=" O LYS G 6 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LYS G 6 " --> pdb=" O ARG D 7 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ARG G 73 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ILE G 48 " --> pdb=" O ARG G 73 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL G 75 " --> pdb=" O ILE G 46 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.200A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.751A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 88 through 89 Processing sheet with id=AE2, first strand: chain 'G' and resid 152 through 155 Processing sheet with id=AE3, first strand: chain 'H' and resid 100 through 107 removed outlier: 5.795A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG H 25 " --> pdb=" O ASP H 16 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP H 16 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 47 through 49 Processing sheet with id=AE5, first strand: chain 'L' and resid 29 through 30 Processing sheet with id=AE6, first strand: chain 'N' and resid 305 through 308 removed outlier: 7.738A pdb=" N LEU M 170 " --> pdb=" O PRO M 75 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LYS M 77 " --> pdb=" O LEU M 170 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 121 through 123 Processing sheet with id=AE8, first strand: chain 'M' and resid 121 through 123 removed outlier: 3.715A pdb=" N ALA M 177 " --> pdb=" O VAL M 87 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN M 89 " --> pdb=" O ALA M 177 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TYR M 90 " --> pdb=" O ASP N 393 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASP N 393 " --> pdb=" O TYR M 90 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ALA M 248 " --> pdb=" O LEU N 408 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 104 through 109 Processing sheet with id=AF1, first strand: chain 'O' and resid 200 through 202 Processing sheet with id=AF2, first strand: chain 'O' and resid 549 through 551 removed outlier: 3.695A pdb=" N VAL O 563 " --> pdb=" O VAL O 551 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'P' and resid 63 through 64 Processing sheet with id=AF4, first strand: chain 'P' and resid 134 through 137 removed outlier: 3.744A pdb=" N MET P 149 " --> pdb=" O LYS P 135 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'P' and resid 253 through 255 Processing sheet with id=AF6, first strand: chain 'R' and resid 12 through 14 Processing sheet with id=AF7, first strand: chain 'R' and resid 446 through 452 removed outlier: 5.186A pdb=" N VAL R 448 " --> pdb=" O VAL R 400 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N VAL R 400 " --> pdb=" O VAL R 448 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N THR R 450 " --> pdb=" O ALA R 398 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ALA R 398 " --> pdb=" O THR R 450 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU R 393 " --> pdb=" O VAL R 487 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL R 487 " --> pdb=" O LEU R 393 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ASN R 395 " --> pdb=" O ASN R 485 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ASN R 485 " --> pdb=" O ASN R 395 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL R 397 " --> pdb=" O ILE R 483 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ILE R 483 " --> pdb=" O VAL R 397 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR R 399 " --> pdb=" O PHE R 481 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE R 481 " --> pdb=" O THR R 399 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE R 486 " --> pdb=" O GLY R 542 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY R 542 " --> pdb=" O ILE R 486 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'R' and resid 420 through 421 removed outlier: 4.257A pdb=" N ASN R 421 " --> pdb=" O PHE R 425 " (cutoff:3.500A) 1615 hydrogen bonds defined for protein. 4509 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 90 hydrogen bonds 168 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 81 stacking parallelities Total time for adding SS restraints: 19.99 Time building geometry restraints manager: 20.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 14708 1.34 - 1.46: 9446 1.46 - 1.58: 24146 1.58 - 1.70: 220 1.70 - 1.82: 393 Bond restraints: 48913 Sorted by residual: bond pdb=" CA GLN R 151 " pdb=" C GLN R 151 " ideal model delta sigma weight residual 1.522 1.622 -0.100 1.39e-02 5.18e+03 5.22e+01 bond pdb=" CA MET B 517 " pdb=" CB MET B 517 " ideal model delta sigma weight residual 1.528 1.450 0.078 1.39e-02 5.18e+03 3.12e+01 bond pdb=" CA GLU M 103 " pdb=" C GLU M 103 " ideal model delta sigma weight residual 1.523 1.590 -0.067 1.34e-02 5.57e+03 2.50e+01 bond pdb=" N PRO B 946 " pdb=" CD PRO B 946 " ideal model delta sigma weight residual 1.473 1.405 0.068 1.40e-02 5.10e+03 2.37e+01 bond pdb=" CA ASP A 283 " pdb=" C ASP A 283 " ideal model delta sigma weight residual 1.526 1.574 -0.047 1.03e-02 9.43e+03 2.12e+01 ... (remaining 48908 not shown) Histogram of bond angle deviations from ideal: 95.51 - 104.03: 1118 104.03 - 112.56: 25824 112.56 - 121.08: 26244 121.08 - 129.61: 13055 129.61 - 138.13: 277 Bond angle restraints: 66518 Sorted by residual: angle pdb=" N LYS M 184 " pdb=" CA LYS M 184 " pdb=" C LYS M 184 " ideal model delta sigma weight residual 113.18 100.52 12.66 1.21e+00 6.83e-01 1.09e+02 angle pdb=" N VAL C 96 " pdb=" CA VAL C 96 " pdb=" C VAL C 96 " ideal model delta sigma weight residual 110.23 120.39 -10.16 1.04e+00 9.25e-01 9.54e+01 angle pdb=" N LEU B 335 " pdb=" CA LEU B 335 " pdb=" C LEU B 335 " ideal model delta sigma weight residual 112.88 100.71 12.17 1.29e+00 6.01e-01 8.91e+01 angle pdb=" N ASN B 428 " pdb=" CA ASN B 428 " pdb=" C ASN B 428 " ideal model delta sigma weight residual 112.38 101.09 11.29 1.22e+00 6.72e-01 8.57e+01 angle pdb=" N ASP O 556 " pdb=" CA ASP O 556 " pdb=" C ASP O 556 " ideal model delta sigma weight residual 111.40 100.25 11.15 1.22e+00 6.72e-01 8.36e+01 ... (remaining 66513 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 28940 35.82 - 71.64: 764 71.64 - 107.46: 50 107.46 - 143.27: 1 143.27 - 179.09: 2 Dihedral angle restraints: 29757 sinusoidal: 12945 harmonic: 16812 Sorted by residual: dihedral pdb=" CA ALA A 169 " pdb=" C ALA A 169 " pdb=" N GLY A 170 " pdb=" CA GLY A 170 " ideal model delta harmonic sigma weight residual 180.00 150.04 29.96 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA ASP A1269 " pdb=" C ASP A1269 " pdb=" N VAL A1270 " pdb=" CA VAL A1270 " ideal model delta harmonic sigma weight residual 180.00 -150.25 -29.75 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA GLY A 586 " pdb=" C GLY A 586 " pdb=" N ILE A 587 " pdb=" CA ILE A 587 " ideal model delta harmonic sigma weight residual 180.00 150.31 29.69 0 5.00e+00 4.00e-02 3.53e+01 ... (remaining 29754 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 6441 0.079 - 0.158: 964 0.158 - 0.237: 85 0.237 - 0.316: 31 0.316 - 0.395: 8 Chirality restraints: 7529 Sorted by residual: chirality pdb=" CA VAL R 152 " pdb=" N VAL R 152 " pdb=" C VAL R 152 " pdb=" CB VAL R 152 " both_signs ideal model delta sigma weight residual False 2.44 2.05 0.40 2.00e-01 2.50e+01 3.91e+00 chirality pdb=" CA LYS A 538 " pdb=" N LYS A 538 " pdb=" C LYS A 538 " pdb=" CB LYS A 538 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA THR A 227 " pdb=" N THR A 227 " pdb=" C THR A 227 " pdb=" CB THR A 227 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.38 2.00e-01 2.50e+01 3.69e+00 ... (remaining 7526 not shown) Planarity restraints: 8164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 416 " 0.021 2.00e-02 2.50e+03 4.40e-02 1.93e+01 pdb=" C TYR B 416 " -0.076 2.00e-02 2.50e+03 pdb=" O TYR B 416 " 0.030 2.00e-02 2.50e+03 pdb=" N ASP B 417 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 877 " -0.053 5.00e-02 4.00e+02 8.02e-02 1.03e+01 pdb=" N PRO B 878 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO B 878 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 878 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER O 36 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.61e+00 pdb=" C SER O 36 " 0.048 2.00e-02 2.50e+03 pdb=" O SER O 36 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU O 37 " -0.016 2.00e-02 2.50e+03 ... (remaining 8161 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 403 2.45 - 3.06: 37337 3.06 - 3.67: 73922 3.67 - 4.29: 107160 4.29 - 4.90: 164169 Nonbonded interactions: 382991 Sorted by model distance: nonbonded pdb=" O LEU M 85 " pdb=" O LEU N 397 " model vdw 1.836 3.040 nonbonded pdb=" O VAL O 495 " pdb=" CG1 ILE O 496 " model vdw 1.958 3.440 nonbonded pdb=" O ASN O 123 " pdb=" O GLU O 124 " model vdw 1.969 3.040 nonbonded pdb=" NZ LYS A 235 " pdb=" CB PRO O 44 " model vdw 2.039 3.520 nonbonded pdb=" O MET A 598 " pdb=" CG LYS A 599 " model vdw 2.050 3.440 ... (remaining 382986 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 8.330 Check model and map are aligned: 0.660 Set scattering table: 0.370 Process input model: 141.480 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 155.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 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 : 0.007 0.100 48913 Z= 0.465 Angle : 1.154 15.867 66518 Z= 0.695 Chirality : 0.059 0.395 7529 Planarity : 0.006 0.080 8164 Dihedral : 14.172 179.093 18859 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 32.34 Ramachandran Plot: Outliers : 1.40 % Allowed : 17.44 % Favored : 81.16 % Rotamer: Outliers : 0.60 % Allowed : 1.93 % Favored : 97.47 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.66 % 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: -5.08 (0.08), residues: 5625 helix: -3.93 (0.07), residues: 1813 sheet: -2.40 (0.18), residues: 585 loop : -3.33 (0.09), residues: 3227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP C 31 HIS 0.014 0.002 HIS O 207 PHE 0.042 0.003 PHE F 143 TYR 0.030 0.003 TYR B1023 ARG 0.013 0.001 ARG F 135 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1162 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1132 time to evaluate : 5.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.9352 (mp) cc_final: 0.9034 (mm) REVERT: A 124 LEU cc_start: 0.8355 (mt) cc_final: 0.8150 (mt) REVERT: A 392 VAL cc_start: 0.9351 (t) cc_final: 0.9068 (m) REVERT: A 800 LYS cc_start: 0.9016 (mmmt) cc_final: 0.8485 (tttt) REVERT: A 1304 MET cc_start: 0.6128 (ttm) cc_final: 0.5841 (mtp) REVERT: A 1320 LEU cc_start: 0.8782 (tp) cc_final: 0.8580 (tt) REVERT: A 1415 ILE cc_start: 0.9190 (pt) cc_final: 0.8653 (mt) REVERT: B 352 MET cc_start: 0.6309 (ttp) cc_final: 0.5853 (ttm) REVERT: B 437 ILE cc_start: 0.9351 (tp) cc_final: 0.9105 (tt) REVERT: B 510 LEU cc_start: 0.7742 (tp) cc_final: 0.7258 (mp) REVERT: B 945 ASN cc_start: 0.8331 (t0) cc_final: 0.7307 (t0) REVERT: B 1084 MET cc_start: 0.7929 (tpt) cc_final: 0.7466 (tpt) REVERT: K 62 SER cc_start: 0.8717 (m) cc_final: 0.8002 (p) REVERT: K 123 ASP cc_start: 0.8170 (m-30) cc_final: 0.7881 (m-30) REVERT: M 94 PRO cc_start: 0.8104 (Cg_exo) cc_final: 0.7860 (Cg_endo) REVERT: M 186 ILE cc_start: 0.7453 (mm) cc_final: 0.7247 (mm) REVERT: N 381 ASP cc_start: 0.4780 (t0) cc_final: 0.4305 (t0) REVERT: N 382 ILE cc_start: 0.6124 (pp) cc_final: 0.5884 (pp) REVERT: O 103 CYS cc_start: 0.7291 (m) cc_final: 0.6495 (m) REVERT: P 315 TRP cc_start: 0.7437 (t60) cc_final: 0.6509 (t-100) REVERT: Q 47 ILE cc_start: 0.8191 (tt) cc_final: 0.7938 (pt) outliers start: 30 outliers final: 3 residues processed: 1150 average time/residue: 0.6535 time to fit residues: 1210.6103 Evaluate side-chains 622 residues out of total 5024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 619 time to evaluate : 5.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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: 70.5523 > 50: distance: 11 - 14: 34.594 distance: 14 - 15: 3.123 distance: 15 - 16: 45.603 distance: 15 - 18: 25.177 distance: 16 - 17: 27.230 distance: 16 - 23: 26.031 distance: 18 - 19: 15.991 distance: 20 - 22: 40.173 distance: 24 - 25: 28.519 distance: 25 - 26: 36.553 distance: 25 - 30: 39.501 distance: 27 - 28: 40.435 distance: 27 - 29: 56.762 distance: 30 - 31: 15.829 distance: 31 - 32: 39.838 distance: 32 - 35: 40.102 distance: 36 - 37: 39.363 distance: 36 - 39: 56.750 distance: 37 - 43: 39.992 distance: 39 - 40: 40.878 distance: 40 - 41: 39.712 distance: 44 - 45: 56.392 distance: 44 - 47: 40.046 distance: 50 - 51: 3.844 distance: 51 - 52: 28.363 distance: 51 - 54: 54.357 distance: 52 - 53: 39.470 distance: 52 - 59: 52.429 distance: 56 - 57: 39.695 distance: 56 - 58: 56.035 distance: 59 - 60: 56.237 distance: 60 - 63: 40.819 distance: 61 - 67: 41.428 distance: 63 - 64: 31.334 distance: 64 - 65: 29.143 distance: 64 - 66: 41.358 distance: 67 - 68: 10.475 distance: 68 - 69: 50.130 distance: 68 - 71: 41.481 distance: 69 - 70: 39.172 distance: 70 - 95: 35.478 distance: 74 - 80: 40.731 distance: 76 - 81: 39.505 distance: 77 - 103: 31.397 distance: 79 - 80: 39.818 distance: 81 - 82: 11.456 distance: 82 - 83: 30.447 distance: 82 - 85: 49.618 distance: 83 - 84: 10.539 distance: 83 - 87: 30.427 distance: 84 - 109: 35.571 distance: 85 - 86: 40.072