Starting phenix.real_space_refine on Sun Mar 24 13:21:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2z_14468/03_2024/7z2z_14468_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2z_14468/03_2024/7z2z_14468.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2z_14468/03_2024/7z2z_14468.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2z_14468/03_2024/7z2z_14468.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2z_14468/03_2024/7z2z_14468_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2z_14468/03_2024/7z2z_14468_updated.pdb" } resolution = 3.07 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= 0.006 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: 7 Type Number sf(0) Gaussians Zn 7 6.06 5 P 44 5.49 5 Mg 2 5.21 5 S 217 5.16 5 C 26270 2.51 5 N 7189 2.21 5 O 7941 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 516": "OE1" <-> "OE2" Residue "A GLU 530": "OE1" <-> "OE2" Residue "A GLU 751": "OE1" <-> "OE2" Residue "A ARG 937": "NH1" <-> "NH2" Residue "C PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 27": "OE1" <-> "OE2" Residue "I GLU 92": "OE1" <-> "OE2" Residue "K ASP 129": "OD1" <-> "OD2" Residue "M GLU 72": "OE1" <-> "OE2" Residue "M GLU 253": "OE1" <-> "OE2" Residue "N GLU 213": "OE1" <-> "OE2" Residue "O TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 223": "OE1" <-> "OE2" Residue "P GLU 266": "OE1" <-> "OE2" Residue "Q GLU 35": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 41670 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 11192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1431, 11192 Classifications: {'peptide': 1431} Link IDs: {'PCIS': 2, 'PTRANS': 63, 'TRANS': 1365} Chain breaks: 3 Chain: "B" Number of atoms: 8715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1104, 8715 Classifications: {'peptide': 1104} Link IDs: {'PTRANS': 41, 'TRANS': 1062} Chain breaks: 1 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: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1140 Classifications: {'peptide': 145} Incomplete info: {'backbone_only': 11} Link IDs: {'PTRANS': 3, 'TRANS': 141} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 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: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1544 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 12, 'TRANS': 178} Chain breaks: 2 Chain: "H" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1103 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain breaks: 1 Chain: "I" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 864 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} 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: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 381 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 49} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'UNK:plan-1': 6} Unresolved non-hydrogen planarities: 6 Chain: "M" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1492 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 8, 'TRANS': 174} Chain breaks: 1 Chain: "N" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1171 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 142} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'UNK:plan-1': 5} Unresolved non-hydrogen planarities: 5 Chain: "O" Number of atoms: 4558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4558 Classifications: {'peptide': 568} Link IDs: {'PTRANS': 20, 'TRANS': 547} Chain breaks: 1 Chain: "P" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1126 Classifications: {'peptide': 136} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 829 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 8, 'TRANS': 95} Chain breaks: 1 Chain: "R" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 68 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "S" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 383 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "T" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 453 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "W" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 134 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 2, 'TRANS': 13} Chain: "X" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 55 Classifications: {'peptide': 11} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'TRANS': 10} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'UNK:plan-1': 11} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' MG': 1, ' ZN': 2, '4QM': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 492 SG CYS A 67 76.415 61.958 78.255 1.00 41.35 S ATOM 510 SG CYS A 70 78.336 64.311 75.997 1.00 56.56 S ATOM 557 SG CYS A 77 79.050 62.947 79.720 1.00 31.80 S ATOM 795 SG CYS A 107 59.605 105.876 95.974 1.00 25.56 S ATOM 818 SG CYS A 110 58.747 106.454 92.247 1.00 35.40 S ATOM 1184 SG CYS A 154 60.308 109.069 93.893 1.00 51.01 S ATOM 1208 SG CYS A 157 56.688 108.163 95.099 1.00 41.49 S ATOM 19480 SG CYS B1095 79.669 79.903 71.477 1.00 35.95 S ATOM 19503 SG CYS B1098 78.246 80.998 74.865 1.00 27.81 S ATOM 19569 SG CYS B1107 77.189 77.924 72.352 1.00 42.19 S ATOM 19589 SG CYS B1110 75.965 80.282 71.514 1.00 34.73 S ATOM 28818 SG CYS I 5 71.647 105.371 160.873 1.00 30.74 S ATOM 28837 SG CYS I 8 71.085 102.814 159.589 1.00 46.17 S ATOM 28965 SG CYS I 26 69.689 106.006 157.689 1.00 46.65 S ATOM 28988 SG CYS I 29 68.471 105.037 161.313 1.00 56.95 S ATOM 29315 SG CYS I 69 132.678 94.447 113.243 1.00 76.37 S ATOM 29363 SG CYS I 75 134.380 97.761 114.437 1.00 75.13 S ATOM 29565 SG CYS I 100 132.752 95.661 117.179 1.00 76.08 S ATOM 29586 SG CYS I 103 131.003 97.682 115.013 1.00 73.09 S ATOM 29697 SG CYS J 7 133.965 40.077 117.911 1.00 19.79 S ATOM 29720 SG CYS J 10 138.021 40.542 117.382 1.00 39.72 S ATOM 30000 SG CYS J 45 136.879 42.291 119.183 1.00 31.23 S ATOM 30006 SG CYS J 46 136.947 38.563 119.833 1.00 24.26 S ATOM 31057 SG CYS L 31 93.400 22.883 120.435 1.00 47.09 S ATOM 31077 SG CYS L 34 94.056 19.964 122.052 1.00 56.56 S ATOM 31181 SG CYS L 48 91.572 20.286 119.520 1.00 54.77 S ATOM 31204 SG CYS L 51 91.554 21.807 123.409 1.00 74.53 S Time building chain proxies: 21.40, per 1000 atoms: 0.51 Number of scatterers: 41670 At special positions: 0 Unit cell: (190.96, 157.325, 203.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 7 29.99 S 217 16.00 P 44 15.00 Mg 2 11.99 O 7941 8.00 N 7189 7.00 C 26270 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: 15.23 Conformation dependent library (CDL) restraints added in 7.4 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 70 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 67 " pdb=" ZN A1502 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 157 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 154 " pdb=" ZN B2000 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1110 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1098 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1107 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1095 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 8 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 26 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 5 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 29 " pdb=" ZN I 203 " pdb="ZN ZN I 203 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 203 " - pdb=" SG CYS I 100 " pdb="ZN ZN I 203 " - pdb=" SG CYS I 69 " pdb="ZN ZN I 203 " - pdb=" SG CYS I 75 " pdb=" ZN J2000 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 10 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 46 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 7 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 45 " pdb=" ZN L2001 " pdb="ZN ZN L2001 " - pdb=" SG CYS L 48 " pdb="ZN ZN L2001 " - pdb=" SG CYS L 51 " pdb="ZN ZN L2001 " - pdb=" SG CYS L 34 " pdb="ZN ZN L2001 " - pdb=" SG CYS L 31 " Number of angles added : 39 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9668 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 181 helices and 44 sheets defined 33.9% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.83 Creating SS restraints... Processing helix chain 'A' and resid 25 through 28 No H-bonds generated for 'chain 'A' and resid 25 through 28' Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 93 through 105 removed outlier: 3.574A pdb=" N PHE A 96 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LYS A 97 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN A 104 " --> pdb=" O GLN A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 127 Processing helix chain 'A' and resid 134 through 150 Processing helix chain 'A' and resid 182 through 184 No H-bonds generated for 'chain 'A' and resid 182 through 184' Processing helix chain 'A' and resid 192 through 207 removed outlier: 3.921A pdb=" N GLU A 203 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 205 " --> pdb=" O TRP A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 224 through 233 removed outlier: 4.073A pdb=" N GLN A 233 " --> pdb=" O ASN A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 242 No H-bonds generated for 'chain 'A' and resid 240 through 242' Processing helix chain 'A' and resid 253 through 256 removed outlier: 3.554A pdb=" N TYR A 256 " --> pdb=" O PRO A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 253 through 256' Processing helix chain 'A' and resid 284 through 305 removed outlier: 3.947A pdb=" N ASP A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 327 removed outlier: 3.532A pdb=" N GLU A 314 " --> pdb=" O ASN A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 363 through 366 No H-bonds generated for 'chain 'A' and resid 363 through 366' Processing helix chain 'A' and resid 396 through 399 No H-bonds generated for 'chain 'A' and resid 396 through 399' Processing helix chain 'A' and resid 413 through 422 Processing helix chain 'A' and resid 449 through 455 Processing helix chain 'A' and resid 482 through 484 No H-bonds generated for 'chain 'A' and resid 482 through 484' Processing helix chain 'A' and resid 502 through 508 removed outlier: 3.984A pdb=" N THR A 506 " --> pdb=" O CYS A 503 " (cutoff:3.500A) Proline residue: A 507 - end of helix Processing helix chain 'A' and resid 525 through 535 Processing helix chain 'A' and resid 537 through 540 Processing helix chain 'A' and resid 555 through 565 removed outlier: 3.980A pdb=" N SER A 561 " --> pdb=" O PHE A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 583 Processing helix chain 'A' and resid 606 through 614 Processing helix chain 'A' and resid 643 through 645 No H-bonds generated for 'chain 'A' and resid 643 through 645' Processing helix chain 'A' and resid 666 through 669 No H-bonds generated for 'chain 'A' and resid 666 through 669' Processing helix chain 'A' and resid 677 through 685 Processing helix chain 'A' and resid 687 through 708 removed outlier: 3.636A pdb=" N ARG A 703 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A 705 " --> pdb=" O CYS A 701 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLY A 706 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN A 707 " --> pdb=" O ARG A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 717 No H-bonds generated for 'chain 'A' and resid 714 through 717' Processing helix chain 'A' and resid 721 through 747 removed outlier: 3.750A pdb=" N GLN A 725 " --> pdb=" O ASP A 721 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU A 728 " --> pdb=" O LYS A 724 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 734 " --> pdb=" O LEU A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 784 removed outlier: 3.681A pdb=" N LEU A 762 " --> pdb=" O GLU A 758 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU A 763 " --> pdb=" O GLU A 759 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLY A 768 " --> pdb=" O ALA A 764 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER A 771 " --> pdb=" O GLY A 767 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL A 773 " --> pdb=" O LEU A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 797 Processing helix chain 'A' and resid 803 through 810 Processing helix chain 'A' and resid 858 through 893 removed outlier: 4.162A pdb=" N GLY A 871 " --> pdb=" O SER A 867 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 872 " --> pdb=" O GLY A 868 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA A 876 " --> pdb=" O LEU A 872 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL A 877 " --> pdb=" O VAL A 873 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLU A 881 " --> pdb=" O VAL A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 918 No H-bonds generated for 'chain 'A' and resid 916 through 918' Processing helix chain 'A' and resid 935 through 945 Processing helix chain 'A' and resid 956 through 966 removed outlier: 3.919A pdb=" N MET A 960 " --> pdb=" O PRO A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 972 No H-bonds generated for 'chain 'A' and resid 969 through 972' Processing helix chain 'A' and resid 999 through 1024 Processing helix chain 'A' and resid 1052 through 1059 Processing helix chain 'A' and resid 1064 through 1080 Processing helix chain 'A' and resid 1089 through 1102 Proline residue: A1100 - end of helix Processing helix chain 'A' and resid 1123 through 1131 Processing helix chain 'A' and resid 1155 through 1158 No H-bonds generated for 'chain 'A' and resid 1155 through 1158' Processing helix chain 'A' and resid 1166 through 1170 Processing helix chain 'A' and resid 1191 through 1195 Processing helix chain 'A' and resid 1203 through 1216 Processing helix chain 'A' and resid 1255 through 1266 Processing helix chain 'A' and resid 1300 through 1305 Processing helix chain 'A' and resid 1319 through 1325 Processing helix chain 'A' and resid 1328 through 1344 Processing helix chain 'A' and resid 1352 through 1362 Processing helix chain 'A' and resid 1373 through 1376 No H-bonds generated for 'chain 'A' and resid 1373 through 1376' Processing helix chain 'A' and resid 1383 through 1389 Processing helix chain 'A' and resid 1392 through 1401 Processing helix chain 'A' and resid 1411 through 1416 Processing helix chain 'A' and resid 1424 through 1426 No H-bonds generated for 'chain 'A' and resid 1424 through 1426' Processing helix chain 'A' and resid 1439 through 1441 No H-bonds generated for 'chain 'A' and resid 1439 through 1441' Processing helix chain 'A' and resid 1453 through 1456 removed outlier: 3.850A pdb=" N ALA A1456 " --> pdb=" O ASN A1453 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1453 through 1456' Processing helix chain 'B' and resid 40 through 54 removed outlier: 5.633A pdb=" N TRP B 45 " --> pdb=" O ALA B 41 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N HIS B 46 " --> pdb=" O GLN B 42 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N LEU B 47 " --> pdb=" O ASP B 43 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N LEU B 48 " --> pdb=" O LYS B 44 " (cutoff:3.500A) Proline residue: B 49 - end of helix removed outlier: 3.795A pdb=" N VAL B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 79 removed outlier: 5.480A pdb=" N LEU B 73 " --> pdb=" O VAL B 69 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LYS B 74 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 121 Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 253 through 259 Processing helix chain 'B' and resid 267 through 272 Processing helix chain 'B' and resid 277 through 283 removed outlier: 3.980A pdb=" N ILE B 282 " --> pdb=" O SER B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 292 No H-bonds generated for 'chain 'B' and resid 289 through 292' Processing helix chain 'B' and resid 298 through 306 Processing helix chain 'B' and resid 317 through 319 No H-bonds generated for 'chain 'B' and resid 317 through 319' Processing helix chain 'B' and resid 322 through 328 Processing helix chain 'B' and resid 330 through 332 No H-bonds generated for 'chain 'B' and resid 330 through 332' Processing helix chain 'B' and resid 343 through 361 Processing helix chain 'B' and resid 372 through 374 No H-bonds generated for 'chain 'B' and resid 372 through 374' Processing helix chain 'B' and resid 380 through 408 removed outlier: 3.560A pdb=" N LEU B 386 " --> pdb=" O GLN B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 439 removed outlier: 3.591A pdb=" N ILE B 422 " --> pdb=" O ALA B 418 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ASN B 427 " --> pdb=" O ASN B 423 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ASN B 428 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ILE B 429 " --> pdb=" O HIS B 425 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THR B 430 " --> pdb=" O SER B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 469 removed outlier: 3.690A pdb=" N LEU B 467 " --> pdb=" O TYR B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 487 No H-bonds generated for 'chain 'B' and resid 485 through 487' Processing helix chain 'B' and resid 491 through 493 No H-bonds generated for 'chain 'B' and resid 491 through 493' Processing helix chain 'B' and resid 528 through 536 removed outlier: 3.814A pdb=" N LEU B 532 " --> pdb=" O PRO B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 580 Processing helix chain 'B' and resid 625 through 632 Processing helix chain 'B' and resid 638 through 642 Processing helix chain 'B' and resid 651 through 656 removed outlier: 3.668A pdb=" N ASN B 655 " --> pdb=" O VAL B 651 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP B 656 " --> pdb=" O ASN B 652 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 651 through 656' Processing helix chain 'B' and resid 663 through 665 No H-bonds generated for 'chain 'B' and resid 663 through 665' Processing helix chain 'B' and resid 684 through 687 removed outlier: 3.690A pdb=" N LEU B 687 " --> pdb=" O VAL B 684 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 684 through 687' Processing helix chain 'B' and resid 691 through 693 No H-bonds generated for 'chain 'B' and resid 691 through 693' Processing helix chain 'B' and resid 696 through 707 removed outlier: 4.738A pdb=" N LYS B 707 " --> pdb=" O CYS B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 743 removed outlier: 3.763A pdb=" N LEU B 743 " --> pdb=" O LYS B 739 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 739 through 743' Processing helix chain 'B' and resid 819 through 821 No H-bonds generated for 'chain 'B' and resid 819 through 821' Processing helix chain 'B' and resid 928 through 930 No H-bonds generated for 'chain 'B' and resid 928 through 930' Processing helix chain 'B' and resid 946 through 948 No H-bonds generated for 'chain 'B' and resid 946 through 948' Processing helix chain 'B' and resid 956 through 970 Processing helix chain 'B' and resid 984 through 992 Processing helix chain 'B' and resid 1031 through 1033 No H-bonds generated for 'chain 'B' and resid 1031 through 1033' Processing helix chain 'B' and resid 1064 through 1072 Processing helix chain 'B' and resid 1076 through 1083 Processing helix chain 'B' and resid 1123 through 1134 Processing helix chain 'C' and resid 36 through 39 No H-bonds generated for 'chain 'C' and resid 36 through 39' Processing helix chain 'C' and resid 61 through 73 removed outlier: 3.998A pdb=" N ALA C 66 " --> pdb=" O SER C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 103 Processing helix chain 'C' and resid 122 through 125 No H-bonds generated for 'chain 'C' and resid 122 through 125' Processing helix chain 'C' and resid 173 through 178 removed outlier: 3.602A pdb=" N SER C 176 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR C 178 " --> pdb=" O GLN C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 242 through 250 removed outlier: 3.874A pdb=" N ARG C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 281 No H-bonds generated for 'chain 'C' and resid 279 through 281' Processing helix chain 'C' and resid 310 through 330 Processing helix chain 'D' and resid 15 through 26 removed outlier: 4.234A pdb=" N LEU D 20 " --> pdb=" O VAL D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 35 No H-bonds generated for 'chain 'D' and resid 33 through 35' Processing helix chain 'D' and resid 53 through 67 Processing helix chain 'D' and resid 100 through 105 Processing helix chain 'D' and resid 107 through 112 Processing helix chain 'D' and resid 120 through 123 No H-bonds generated for 'chain 'D' and resid 120 through 123' Processing helix chain 'D' and resid 131 through 137 Processing helix chain 'D' and resid 141 through 144 No H-bonds generated for 'chain 'D' and resid 141 through 144' Processing helix chain 'D' and resid 151 through 157 Processing helix chain 'E' and resid 2 through 27 removed outlier: 3.730A pdb=" N GLY E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 35 No H-bonds generated for 'chain 'E' and resid 32 through 35' Processing helix chain 'E' and resid 39 through 46 Processing helix chain 'E' and resid 55 through 57 No H-bonds generated for 'chain 'E' and resid 55 through 57' Processing helix chain 'E' and resid 66 through 71 Processing helix chain 'E' and resid 90 through 103 Processing helix chain 'E' and resid 120 through 124 Processing helix chain 'E' and resid 144 through 146 No H-bonds generated for 'chain 'E' and resid 144 through 146' Processing helix chain 'E' and resid 158 through 168 Processing helix chain 'E' and resid 183 through 187 removed outlier: 3.502A pdb=" N TYR E 187 " --> pdb=" O PRO E 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 183 through 187' Processing helix chain 'F' and resid 87 through 102 Processing helix chain 'F' and resid 117 through 127 Processing helix chain 'G' and resid 15 through 19 removed outlier: 4.321A pdb=" N HIS G 19 " --> pdb=" O ASP G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 33 removed outlier: 3.732A pdb=" N HIS G 28 " --> pdb=" O SER G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 163 through 172 Processing helix chain 'G' and resid 208 through 210 No H-bonds generated for 'chain 'G' and resid 208 through 210' Processing helix chain 'J' and resid 18 through 26 Processing helix chain 'J' and resid 32 through 38 Processing helix chain 'J' and resid 44 through 51 removed outlier: 3.710A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 63 removed outlier: 4.098A pdb=" N ARG J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N TYR J 63 " --> pdb=" O LYS J 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 82 removed outlier: 3.990A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS K 82 " --> pdb=" O TYR K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 141 Processing helix chain 'M' and resid 133 through 139 Processing helix chain 'M' and resid 184 through 193 Processing helix chain 'M' and resid 230 through 239 Processing helix chain 'M' and resid 256 through 263 Processing helix chain 'M' and resid 274 through 280 removed outlier: 3.673A pdb=" N ILE M 278 " --> pdb=" O GLN M 274 " (cutoff:3.500A) Processing helix chain 'N' and resid 212 through 222 removed outlier: 3.994A pdb=" N ARG N 217 " --> pdb=" O GLU N 213 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU N 218 " --> pdb=" O THR N 214 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN N 220 " --> pdb=" O LYS N 216 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N GLU N 221 " --> pdb=" O ARG N 217 " (cutoff:3.500A) Processing helix chain 'N' and resid 275 through 296 removed outlier: 3.755A pdb=" N GLU N 279 " --> pdb=" O GLU N 275 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 34 removed outlier: 3.696A pdb=" N THR O 33 " --> pdb=" O GLU O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 56 Processing helix chain 'O' and resid 59 through 71 Processing helix chain 'O' and resid 76 through 82 Processing helix chain 'O' and resid 88 through 100 Processing helix chain 'O' and resid 124 through 131 removed outlier: 3.647A pdb=" N ILE O 129 " --> pdb=" O GLU O 125 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU O 130 " --> pdb=" O GLY O 126 " (cutoff:3.500A) Processing helix chain 'O' and resid 133 through 143 Processing helix chain 'O' and resid 150 through 166 Processing helix chain 'O' and resid 171 through 176 Processing helix chain 'O' and resid 189 through 197 Processing helix chain 'O' and resid 211 through 219 Processing helix chain 'O' and resid 234 through 257 removed outlier: 4.214A pdb=" N THR O 247 " --> pdb=" O MET O 243 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASP O 248 " --> pdb=" O ASN O 244 " (cutoff:3.500A) Proline residue: O 256 - end of helix Processing helix chain 'O' and resid 261 through 264 No H-bonds generated for 'chain 'O' and resid 261 through 264' Processing helix chain 'O' and resid 284 through 302 removed outlier: 4.178A pdb=" N THR O 302 " --> pdb=" O ASN O 298 " (cutoff:3.500A) Processing helix chain 'O' and resid 306 through 318 removed outlier: 3.639A pdb=" N ILE O 314 " --> pdb=" O GLN O 310 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG O 317 " --> pdb=" O LYS O 313 " (cutoff:3.500A) Processing helix chain 'O' and resid 341 through 355 removed outlier: 4.696A pdb=" N ASP O 347 " --> pdb=" O SER O 344 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU O 354 " --> pdb=" O LEU O 351 " (cutoff:3.500A) Processing helix chain 'O' and resid 365 through 368 No H-bonds generated for 'chain 'O' and resid 365 through 368' Processing helix chain 'O' and resid 450 through 462 removed outlier: 3.674A pdb=" N SER O 455 " --> pdb=" O SER O 451 " (cutoff:3.500A) Processing helix chain 'O' and resid 480 through 499 Proline residue: O 485 - end of helix Processing helix chain 'O' and resid 502 through 513 Processing helix chain 'O' and resid 519 through 526 Processing helix chain 'O' and resid 530 through 541 Processing helix chain 'O' and resid 570 through 608 removed outlier: 5.442A pdb=" N THR O 601 " --> pdb=" O GLN O 597 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU O 602 " --> pdb=" O GLU O 598 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU O 603 " --> pdb=" O ASN O 599 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS O 605 " --> pdb=" O THR O 601 " (cutoff:3.500A) Processing helix chain 'O' and resid 611 through 614 No H-bonds generated for 'chain 'O' and resid 611 through 614' Processing helix chain 'O' and resid 621 through 652 removed outlier: 4.573A pdb=" N VAL O 650 " --> pdb=" O SER O 646 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N PHE O 651 " --> pdb=" O LEU O 647 " (cutoff:3.500A) Processing helix chain 'P' and resid 173 through 190 removed outlier: 3.751A pdb=" N ILE P 181 " --> pdb=" O SER P 177 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG P 184 " --> pdb=" O THR P 180 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE P 186 " --> pdb=" O VAL P 182 " (cutoff:3.500A) Processing helix chain 'P' and resid 196 through 200 removed outlier: 4.011A pdb=" N ASN P 200 " --> pdb=" O ASN P 197 " (cutoff:3.500A) Processing helix chain 'P' and resid 218 through 228 Processing helix chain 'P' and resid 237 through 248 Processing helix chain 'P' and resid 266 through 270 Processing helix chain 'P' and resid 296 through 298 No H-bonds generated for 'chain 'P' and resid 296 through 298' Processing helix chain 'Q' and resid 49 through 60 Processing helix chain 'Q' and resid 129 through 131 No H-bonds generated for 'chain 'Q' and resid 129 through 131' Processing helix chain 'Q' and resid 134 through 137 Processing helix chain 'W' and resid 613 through 616 No H-bonds generated for 'chain 'W' and resid 613 through 616' Processing sheet with id= A, first strand: chain 'A' and resid 82 through 85 Processing sheet with id= B, first strand: chain 'A' and resid 178 through 180 removed outlier: 4.482A pdb=" N ILE A 178 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 376 through 380 removed outlier: 3.537A pdb=" N THR A 379 " --> pdb=" O MET A 517 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 381 through 383 removed outlier: 5.954A pdb=" N PHE A 498 " --> pdb=" O SER A 382 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 404 through 407 removed outlier: 3.742A pdb=" N TYR A 432 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 626 through 629 removed outlier: 3.609A pdb=" N SER A 661 " --> pdb=" O ILE A 653 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ARG A 655 " --> pdb=" O ILE A 659 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ILE A 659 " --> pdb=" O ARG A 655 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1309 through 1316 removed outlier: 4.755A pdb=" N VAL A1144 " --> pdb=" O ILE A1310 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N SER A1312 " --> pdb=" O ASN A1142 " (cutoff:3.500A) removed outlier: 11.052A pdb=" N ASN A1142 " --> pdb=" O SER A1312 " (cutoff:3.500A) removed outlier: 10.138A pdb=" N THR A1314 " --> pdb=" O ILE A1140 " (cutoff:3.500A) removed outlier: 11.272A pdb=" N ILE A1140 " --> pdb=" O THR A1314 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA A1143 " --> pdb=" O LEU A1293 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU A1293 " --> pdb=" O ALA A1143 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LEU A1145 " --> pdb=" O ARG A1291 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N ARG A1291 " --> pdb=" O LEU A1145 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL A1282 " --> pdb=" O LEU A1294 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG A1280 " --> pdb=" O GLU A1296 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1173 through 1177 Processing sheet with id= I, first strand: chain 'B' and resid 98 through 100 Processing sheet with id= J, first strand: chain 'B' and resid 126 through 128 Processing sheet with id= K, first strand: chain 'B' and resid 185 through 187 Processing sheet with id= L, first strand: chain 'B' and resid 197 through 200 Processing sheet with id= M, first strand: chain 'B' and resid 206 through 210 removed outlier: 3.630A pdb=" N GLU B 208 " --> pdb=" O VAL B 216 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 220 through 222 Processing sheet with id= O, first strand: chain 'B' and resid 554 through 557 Processing sheet with id= P, first strand: chain 'B' and resid 646 through 648 Processing sheet with id= Q, first strand: chain 'B' and resid 724 through 728 removed outlier: 6.326A pdb=" N ARG B 901 " --> pdb=" O ILE B 881 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ILE B 881 " --> pdb=" O ARG B 901 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 1018 through 1024 removed outlier: 4.295A pdb=" N PHE B1018 " --> pdb=" O VAL B 759 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ILE B 942 " --> pdb=" O ALA B 758 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 1089 through 1095 Processing sheet with id= T, first strand: chain 'B' and resid 770 through 774 removed outlier: 6.791A pdb=" N VAL B 921 " --> pdb=" O LEU B 771 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N LEU B 773 " --> pdb=" O VAL B 921 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N GLY B 923 " --> pdb=" O LEU B 773 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'C' and resid 4 through 6 removed outlier: 3.577A pdb=" N ASN C 234 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU C 230 " --> pdb=" O VAL C 294 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 41 through 48 removed outlier: 6.954A pdb=" N ASN C 53 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N LEU C 47 " --> pdb=" O GLU C 51 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLU C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR C 224 " --> pdb=" O GLU C 303 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 132 through 140 removed outlier: 4.018A pdb=" N GLN C 200 " --> pdb=" O CYS C 140 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR C 82 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLY C 211 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N VAL C 78 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 60 through 62 removed outlier: 3.589A pdb=" N ALA E 62 " --> pdb=" O LEU E 78 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU E 78 " --> pdb=" O ALA E 62 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 107 through 111 removed outlier: 6.767A pdb=" N THR E 131 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N PHE E 110 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLU E 133 " --> pdb=" O PHE E 110 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.866A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 133 through 137 Processing sheet with id= AB, first strand: chain 'G' and resid 7 through 13 removed outlier: 7.027A pdb=" N ARG G 73 " --> pdb=" O LEU G 51 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LEU G 51 " --> pdb=" O ARG G 73 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'G' and resid 145 through 148 removed outlier: 3.563A pdb=" N PHE G 148 " --> pdb=" O VAL G 85 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL G 85 " --> pdb=" O PHE G 148 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TRP G 88 " --> pdb=" O SER G 100 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N SER G 90 " --> pdb=" O LYS G 98 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N LYS G 98 " --> pdb=" O SER G 90 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N CYS G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N GLY G 96 " --> pdb=" O CYS G 92 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'G' and resid 152 through 155 Processing sheet with id= AE, first strand: chain 'G' and resid 44 through 48 removed outlier: 3.614A pdb=" N LEU G 44 " --> pdb=" O PHE G 77 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL G 75 " --> pdb=" O ILE G 46 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'H' and resid 100 through 105 removed outlier: 6.961A pdb=" N TYR H 115 " --> pdb=" O TYR H 102 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N PHE H 104 " --> pdb=" O ALA H 113 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA H 113 " --> pdb=" O PHE H 104 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG H 25 " --> pdb=" O ASP H 16 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP H 16 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'I' and resid 80 through 83 removed outlier: 3.917A pdb=" N THR I 96 " --> pdb=" O GLU I 109 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'K' and resid 47 through 50 removed outlier: 4.620A pdb=" N SER K 62 " --> pdb=" O LEU K 50 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'L' and resid 29 through 31 Processing sheet with id= AJ, first strand: chain 'M' and resid 86 through 90 removed outlier: 7.265A pdb=" N ARG M 175 " --> pdb=" O VAL M 87 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N GLN M 89 " --> pdb=" O ARG M 175 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ALA M 177 " --> pdb=" O GLN M 89 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ Processing sheet with id= AK, first strand: chain 'M' and resid 121 through 124 removed outlier: 4.262A pdb=" N THR M 147 " --> pdb=" O PHE M 182 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'M' and resid 159 through 163 Processing sheet with id= AM, first strand: chain 'N' and resid 306 through 308 Processing sheet with id= AN, first strand: chain 'N' and resid 362 through 365 Processing sheet with id= AO, first strand: chain 'N' and resid 393 through 397 removed outlier: 3.514A pdb=" N VAL N 394 " --> pdb=" O GLY N 410 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLY N 410 " --> pdb=" O VAL N 394 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ALA N 396 " --> pdb=" O LEU N 408 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU N 408 " --> pdb=" O ALA N 396 " (cutoff:3.500A) No H-bonds generated for sheet with id= AO Processing sheet with id= AP, first strand: chain 'O' and resid 104 through 110 removed outlier: 3.667A pdb=" N GLU O 109 " --> pdb=" O THR O 117 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'O' and resid 547 through 551 Processing sheet with id= AR, first strand: chain 'P' and resid 254 through 256 1226 hydrogen bonds defined for protein. 3489 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: 16.04 Time building geometry restraints manager: 16.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11426 1.33 - 1.45: 7410 1.45 - 1.58: 23236 1.58 - 1.70: 87 1.70 - 1.82: 352 Bond restraints: 42511 Sorted by residual: bond pdb=" N ASP A 511 " pdb=" CA ASP A 511 " ideal model delta sigma weight residual 1.459 1.491 -0.031 9.10e-03 1.21e+04 1.20e+01 bond pdb=" N HIS A 427 " pdb=" CA HIS A 427 " ideal model delta sigma weight residual 1.462 1.491 -0.029 8.50e-03 1.38e+04 1.20e+01 bond pdb=" N VAL A 426 " pdb=" CA VAL A 426 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.12e-02 7.97e+03 1.11e+01 bond pdb=" N VAL A 90 " pdb=" CA VAL A 90 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.11e-02 8.12e+03 1.08e+01 bond pdb=" C TYR P 208 " pdb=" N ALA P 209 " ideal model delta sigma weight residual 1.331 1.398 -0.067 2.07e-02 2.33e+03 1.05e+01 ... (remaining 42506 not shown) Histogram of bond angle deviations from ideal: 96.04 - 103.70: 662 103.70 - 111.35: 17924 111.35 - 119.01: 16841 119.01 - 126.67: 21597 126.67 - 134.33: 565 Bond angle restraints: 57589 Sorted by residual: angle pdb=" CA PRO P 301 " pdb=" N PRO P 301 " pdb=" CD PRO P 301 " ideal model delta sigma weight residual 112.00 104.59 7.41 1.40e+00 5.10e-01 2.80e+01 angle pdb=" N ASP P 171 " pdb=" CA ASP P 171 " pdb=" C ASP P 171 " ideal model delta sigma weight residual 113.88 107.99 5.89 1.23e+00 6.61e-01 2.29e+01 angle pdb=" N PRO N 301 " pdb=" CD PRO N 301 " pdb=" CG PRO N 301 " ideal model delta sigma weight residual 103.20 96.04 7.16 1.50e+00 4.44e-01 2.28e+01 angle pdb=" CA GLY I 57 " pdb=" C GLY I 57 " pdb=" O GLY I 57 " ideal model delta sigma weight residual 121.77 118.01 3.76 8.60e-01 1.35e+00 1.91e+01 angle pdb=" N GLY A 514 " pdb=" CA GLY A 514 " pdb=" C GLY A 514 " ideal model delta sigma weight residual 114.95 109.12 5.83 1.41e+00 5.03e-01 1.71e+01 ... (remaining 57584 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.26: 24190 29.26 - 58.51: 1648 58.51 - 87.77: 134 87.77 - 117.03: 9 117.03 - 146.28: 3 Dihedral angle restraints: 25984 sinusoidal: 11033 harmonic: 14951 Sorted by residual: dihedral pdb=" CA GLU B 249 " pdb=" C GLU B 249 " pdb=" N GLU B 250 " pdb=" CA GLU B 250 " ideal model delta harmonic sigma weight residual 180.00 151.52 28.48 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA ASN M 242 " pdb=" C ASN M 242 " pdb=" N ILE M 243 " pdb=" CA ILE M 243 " ideal model delta harmonic sigma weight residual 180.00 153.78 26.22 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA PHE A1171 " pdb=" C PHE A1171 " pdb=" N TYR A1172 " pdb=" CA TYR A1172 " ideal model delta harmonic sigma weight residual 180.00 154.03 25.97 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 25981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 4390 0.042 - 0.083: 1504 0.083 - 0.125: 507 0.125 - 0.167: 72 0.167 - 0.209: 18 Chirality restraints: 6491 Sorted by residual: chirality pdb=" CA ILE B 841 " pdb=" N ILE B 841 " pdb=" C ILE B 841 " pdb=" CB ILE B 841 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA THR B1108 " pdb=" N THR B1108 " pdb=" C THR B1108 " pdb=" CB THR B1108 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA LEU I 55 " pdb=" N LEU I 55 " pdb=" C LEU I 55 " pdb=" CB LEU I 55 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.85e-01 ... (remaining 6488 not shown) Planarity restraints: 7261 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 127 " 0.080 5.00e-02 4.00e+02 1.21e-01 2.33e+01 pdb=" N PRO D 128 " -0.209 5.00e-02 4.00e+02 pdb=" CA PRO D 128 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO D 128 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS N 300 " -0.075 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO N 301 " 0.192 5.00e-02 4.00e+02 pdb=" CA PRO N 301 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO N 301 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE M 74 " 0.058 5.00e-02 4.00e+02 8.84e-02 1.25e+01 pdb=" N PRO M 75 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO M 75 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO M 75 " 0.049 5.00e-02 4.00e+02 ... (remaining 7258 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1678 2.71 - 3.26: 41121 3.26 - 3.80: 66441 3.80 - 4.35: 85926 4.35 - 4.90: 141578 Nonbonded interactions: 336744 Sorted by model distance: nonbonded pdb=" OG SER A 388 " pdb=" O ILE A 389 " model vdw 2.161 2.440 nonbonded pdb=" O THR A 409 " pdb=" OG1 THR A 409 " model vdw 2.192 2.440 nonbonded pdb=" OG SER A1025 " pdb=" NZ LYS H 109 " model vdw 2.196 2.520 nonbonded pdb=" OH TYR M 131 " pdb=" O VAL M 143 " model vdw 2.197 2.440 nonbonded pdb=" OD2 ASP I 91 " pdb="MG MG I 201 " model vdw 2.211 2.170 ... (remaining 336739 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.750 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: 8.540 Check model and map are aligned: 0.500 Set scattering table: 0.370 Process input model: 110.640 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 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 : 0.006 0.108 42511 Z= 0.359 Angle : 0.698 12.785 57589 Z= 0.391 Chirality : 0.047 0.209 6491 Planarity : 0.006 0.121 7261 Dihedral : 18.273 146.283 16316 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 1.29 % Allowed : 22.35 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % 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: -1.50 (0.12), residues: 5052 helix: 0.22 (0.12), residues: 1807 sheet: -0.81 (0.20), residues: 633 loop : -1.97 (0.12), residues: 2612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 119 HIS 0.010 0.001 HIS B 692 PHE 0.037 0.002 PHE N 390 TYR 0.023 0.002 TYR A1172 ARG 0.007 0.001 ARG M 93 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 4521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 495 time to evaluate : 4.409 Fit side-chains revert: symmetry clash REVERT: E 121 MET cc_start: 0.7937 (mmm) cc_final: 0.7598 (mmm) REVERT: P 208 TYR cc_start: 0.4695 (p90) cc_final: 0.4481 (p90) outliers start: 58 outliers final: 23 residues processed: 521 average time/residue: 0.5571 time to fit residues: 465.4719 Evaluate side-chains 493 residues out of total 4521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 470 time to evaluate : 4.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 1080 LYS Chi-restraints excluded: chain A residue 1183 PHE Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain A residue 1421 MET Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 804 ASP Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain G residue 121 TYR Chi-restraints excluded: chain G residue 126 SER Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain N residue 390 PHE Chi-restraints excluded: chain P residue 248 VAL Chi-restraints excluded: chain P residue 264 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 429 optimal weight: 4.9990 chunk 385 optimal weight: 7.9990 chunk 214 optimal weight: 0.9990 chunk 131 optimal weight: 10.0000 chunk 260 optimal weight: 2.9990 chunk 206 optimal weight: 0.9990 chunk 398 optimal weight: 10.0000 chunk 154 optimal weight: 5.9990 chunk 242 optimal weight: 6.9990 chunk 296 optimal weight: 9.9990 chunk 462 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN A 518 ASN A 647 GLN ** A 808 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 GLN A 941 HIS A1254 ASN A1346 HIS B 286 ASN B 490 GLN B 708 GLN B 918 GLN B 997 ASN B1036 HIS C 29 ASN C 159 ASN D 8 ASN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 ASN G 201 GLN ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN I 64 GLN ** I 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 86 GLN L 53 HIS M 86 HIS M 104 HIS M 146 GLN N 289 HIS N 298 ASN N 366 HIS N 421 GLN O 295 GLN O 298 ASN P 193 ASN P 205 ASN P 229 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.0494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 42511 Z= 0.273 Angle : 0.610 15.180 57589 Z= 0.318 Chirality : 0.044 0.192 6491 Planarity : 0.005 0.083 7261 Dihedral : 11.054 145.911 6161 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 3.73 % Allowed : 21.53 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % 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: -1.37 (0.12), residues: 5052 helix: 0.34 (0.12), residues: 1814 sheet: -0.85 (0.20), residues: 649 loop : -1.89 (0.12), residues: 2589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 31 HIS 0.008 0.001 HIS A 427 PHE 0.023 0.002 PHE I 83 TYR 0.021 0.002 TYR A1172 ARG 0.006 0.000 ARG D 144 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10104 Ramachandran restraints generated. 5052 Oldfield, 0 Emsley, 5052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 4521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 496 time to evaluate : 4.720 Fit side-chains revert: symmetry clash REVERT: A 88 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.6653 (mp) REVERT: A 212 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.6218 (mp0) REVERT: A 477 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.6057 (mp-120) REVERT: B 152 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.6675 (tpt) REVERT: B 332 ILE cc_start: 0.6321 (OUTLIER) cc_final: 0.5927 (tp) REVERT: B 624 ASP cc_start: 0.6319 (OUTLIER) cc_final: 0.5773 (p0) REVERT: N 391 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7727 (mt) REVERT: N 411 ARG cc_start: 0.6914 (ptt90) cc_final: 0.6562 (ptt90) REVERT: O 154 GLN cc_start: 0.6363 (OUTLIER) cc_final: 0.6120 (tt0) REVERT: O 206 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7745 (pt) outliers start: 168 outliers final: 112 residues processed: 620 average time/residue: 0.5404 time to fit residues: 551.0862 Evaluate side-chains 601 residues out of total 4521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 480 time to evaluate : 4.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 477 GLN Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 889 LEU Chi-restraints excluded: chain A residue 907 SER Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1176 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1346 HIS Chi-restraints excluded: chain A residue 1360 ASP Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain B residue 800 ASN Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 851 SER Chi-restraints excluded: chain B residue 918 GLN Chi-restraints excluded: chain B residue 955 VAL Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 977 THR Chi-restraints excluded: chain B residue 1051 THR Chi-restraints excluded: chain B residue 1076 SER Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 121 TYR Chi-restraints excluded: chain G residue 126 SER Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 115 ASP Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain M residue 138 SER Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 363 ILE Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain N residue 390 PHE Chi-restraints excluded: chain N residue 391 LEU Chi-restraints excluded: chain N residue 419 THR Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 87 ASP Chi-restraints excluded: chain O residue 154 GLN Chi-restraints excluded: chain O residue 155 LEU Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain O residue 263 LEU Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 303 ARG Chi-restraints excluded: chain O residue 326 ILE Chi-restraints excluded: chain O residue 360 THR Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 642 SER Chi-restraints excluded: chain P residue 205 ASN Chi-restraints excluded: chain P residue 235 LEU Chi-restraints excluded: chain P residue 248 VAL Chi-restraints excluded: chain P residue 256 VAL Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain Q residue 16 MET Chi-restraints excluded: chain Q residue 103 ASP Chi-restraints excluded: chain Q residue 105 ILE Chi-restraints excluded: chain Q residue 110 ASP Chi-restraints excluded: chain Q residue 138 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- 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: 56.4027 > 50: distance: 51 - 52: 4.159 distance: 53 - 54: 4.858 distance: 55 - 56: 4.259 distance: 56 - 59: 5.814 distance: 57 - 58: 4.242 distance: 57 - 63: 4.199 distance: 58 - 89: 16.581 distance: 63 - 64: 3.963 distance: 64 - 65: 8.796 distance: 64 - 67: 6.358 distance: 65 - 66: 11.900 distance: 65 - 74: 5.363 distance: 66 - 97: 13.009 distance: 67 - 68: 8.615 distance: 68 - 69: 4.311 distance: 69 - 70: 3.192 distance: 70 - 71: 3.883 distance: 71 - 72: 3.971 distance: 71 - 73: 3.229 distance: 74 - 75: 7.931 distance: 75 - 76: 4.974 distance: 75 - 78: 8.741 distance: 76 - 77: 7.880 distance: 76 - 82: 7.475 distance: 78 - 79: 14.916 distance: 79 - 80: 4.492 distance: 79 - 81: 10.088 distance: 82 - 83: 4.966 distance: 83 - 84: 7.175 distance: 83 - 86: 9.281 distance: 84 - 85: 9.251 distance: 86 - 87: 18.301 distance: 86 - 88: 20.944 distance: 89 - 90: 6.622 distance: 90 - 91: 4.210 distance: 90 - 93: 4.424 distance: 91 - 92: 20.850 distance: 91 - 97: 8.891 distance: 93 - 94: 12.552 distance: 94 - 95: 17.815 distance: 95 - 96: 14.157 distance: 97 - 98: 9.833 distance: 98 - 99: 26.515 distance: 98 - 101: 22.623 distance: 99 - 100: 14.167 distance: 99 - 103: 5.271 distance: 101 - 102: 18.026 distance: 103 - 104: 12.219 distance: 104 - 105: 12.882 distance: 104 - 107: 19.745 distance: 105 - 106: 7.661 distance: 105 - 110: 12.049 distance: 107 - 108: 13.736 distance: 107 - 109: 16.471 distance: 110 - 111: 10.598 distance: 111 - 114: 8.817 distance: 112 - 113: 14.245 distance: 112 - 118: 10.657 distance: 114 - 115: 14.343 distance: 115 - 116: 21.181 distance: 115 - 117: 12.460 distance: 118 - 119: 4.801 distance: 119 - 120: 20.647 distance: 120 - 121: 18.137 distance: 120 - 122: 4.645