Starting phenix.real_space_refine (version: 1.21rc1) on Sat May 13 23:06:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eu0_31305/05_2023/7eu0_31305.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eu0_31305/05_2023/7eu0_31305.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eu0_31305/05_2023/7eu0_31305.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eu0_31305/05_2023/7eu0_31305.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eu0_31305/05_2023/7eu0_31305.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eu0_31305/05_2023/7eu0_31305.pdb" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 80 5.49 5 Mg 2 5.21 5 S 195 5.16 5 C 20549 2.51 5 N 5716 2.21 5 O 6136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 46": "NH1" <-> "NH2" Residue "A GLU 265": "OE1" <-> "OE2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A ARG 278": "NH1" <-> "NH2" Residue "A ARG 426": "NH1" <-> "NH2" Residue "A ARG 445": "NH1" <-> "NH2" Residue "A GLU 469": "OE1" <-> "OE2" Residue "A ARG 582": "NH1" <-> "NH2" Residue "A ARG 591": "NH1" <-> "NH2" Residue "A GLU 609": "OE1" <-> "OE2" Residue "A ARG 618": "NH1" <-> "NH2" Residue "A ARG 636": "NH1" <-> "NH2" Residue "A GLU 641": "OE1" <-> "OE2" Residue "A GLU 642": "OE1" <-> "OE2" Residue "A ARG 665": "NH1" <-> "NH2" Residue "A ARG 709": "NH1" <-> "NH2" Residue "A ARG 717": "NH1" <-> "NH2" Residue "A ARG 762": "NH1" <-> "NH2" Residue "A ARG 840": "NH1" <-> "NH2" Residue "A GLU 864": "OE1" <-> "OE2" Residue "A GLU 931": "OE1" <-> "OE2" Residue "A ARG 1012": "NH1" <-> "NH2" Residue "A ARG 1014": "NH1" <-> "NH2" Residue "A ARG 1064": "NH1" <-> "NH2" Residue "A ARG 1098": "NH1" <-> "NH2" Residue "A GLU 1106": "OE1" <-> "OE2" Residue "A ARG 1160": "NH1" <-> "NH2" Residue "A ARG 1208": "NH1" <-> "NH2" Residue "A ARG 1238": "NH1" <-> "NH2" Residue "A GLU 1263": "OE1" <-> "OE2" Residue "B ARG 91": "NH1" <-> "NH2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "B ARG 227": "NH1" <-> "NH2" Residue "B ARG 251": "NH1" <-> "NH2" Residue "B GLU 254": "OE1" <-> "OE2" Residue "B GLU 256": "OE1" <-> "OE2" Residue "B ARG 370": "NH1" <-> "NH2" Residue "B ARG 396": "NH1" <-> "NH2" Residue "B ARG 409": "NH1" <-> "NH2" Residue "B ARG 419": "NH1" <-> "NH2" Residue "B ARG 491": "NH1" <-> "NH2" Residue "B ARG 507": "NH1" <-> "NH2" Residue "B ARG 516": "NH1" <-> "NH2" Residue "B PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 606": "OE1" <-> "OE2" Residue "B ARG 713": "NH1" <-> "NH2" Residue "B GLU 785": "OE1" <-> "OE2" Residue "B PHE 849": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 863": "NH1" <-> "NH2" Residue "B ARG 1016": "NH1" <-> "NH2" Residue "B ARG 1021": "NH1" <-> "NH2" Residue "B ARG 1109": "NH1" <-> "NH2" Residue "B ARG 1134": "NH1" <-> "NH2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C ARG 15": "NH1" <-> "NH2" Residue "C PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 27": "NH1" <-> "NH2" Residue "C ARG 38": "NH1" <-> "NH2" Residue "C ARG 85": "NH1" <-> "NH2" Residue "C ARG 107": "NH1" <-> "NH2" Residue "C GLU 207": "OE1" <-> "OE2" Residue "E ARG 22": "NH1" <-> "NH2" Residue "E ARG 24": "NH1" <-> "NH2" Residue "E ARG 60": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 157": "NH1" <-> "NH2" Residue "E ARG 167": "NH1" <-> "NH2" Residue "E ARG 182": "NH1" <-> "NH2" Residue "F ARG 108": "NH1" <-> "NH2" Residue "H GLU 48": "OE1" <-> "OE2" Residue "I GLU 9": "OE1" <-> "OE2" Residue "I GLU 54": "OE1" <-> "OE2" Residue "I ARG 75": "NH1" <-> "NH2" Residue "I ARG 113": "NH1" <-> "NH2" Residue "J GLU 31": "OE1" <-> "OE2" Residue "K ARG 47": "NH1" <-> "NH2" Residue "K ARG 74": "NH1" <-> "NH2" Residue "L TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 28": "NH1" <-> "NH2" Residue "M ARG 54": "NH1" <-> "NH2" Residue "M ARG 58": "NH1" <-> "NH2" Residue "M ARG 69": "NH1" <-> "NH2" Residue "M ARG 98": "NH1" <-> "NH2" Residue "M GLU 127": "OE1" <-> "OE2" Residue "M ARG 209": "NH1" <-> "NH2" Residue "M ARG 221": "NH1" <-> "NH2" Residue "M ARG 258": "NH1" <-> "NH2" Residue "M ARG 323": "NH1" <-> "NH2" Residue "M GLU 397": "OE1" <-> "OE2" Residue "M GLU 410": "OE1" <-> "OE2" Residue "M ARG 417": "NH1" <-> "NH2" Residue "M ARG 453": "NH1" <-> "NH2" Residue "M ARG 468": "NH1" <-> "NH2" Residue "M PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 499": "NH1" <-> "NH2" Residue "M GLU 500": "OE1" <-> "OE2" Residue "M ARG 509": "NH1" <-> "NH2" Residue "M ARG 526": "NH1" <-> "NH2" Residue "M ARG 532": "NH1" <-> "NH2" Residue "M ARG 596": "NH1" <-> "NH2" Residue "M ARG 600": "NH1" <-> "NH2" Residue "M ARG 633": "NH1" <-> "NH2" Residue "M GLU 699": "OE1" <-> "OE2" Residue "M ARG 707": "NH1" <-> "NH2" Residue "M GLU 711": "OE1" <-> "OE2" Residue "M ARG 720": "NH1" <-> "NH2" Residue "M ARG 722": "NH1" <-> "NH2" Residue "M GLU 842": "OE1" <-> "OE2" Residue "M ARG 861": "NH1" <-> "NH2" Residue "M GLU 929": "OE1" <-> "OE2" Residue "M ARG 937": "NH1" <-> "NH2" Residue "M GLU 954": "OE1" <-> "OE2" Residue "M ARG 962": "NH1" <-> "NH2" Residue "M GLU 1034": "OE1" <-> "OE2" Residue "M ARG 1039": "NH1" <-> "NH2" Residue "M GLU 1067": "OE1" <-> "OE2" Residue "M ARG 1093": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 32686 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 7722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 7722 Classifications: {'peptide': 1060} Incomplete info: {'truncation_to_alanine': 161} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 1012} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 567 Unresolved non-hydrogen angles: 694 Unresolved non-hydrogen dihedrals: 457 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 8, 'ASP:plan': 27, 'PHE:plan': 3, 'GLU:plan': 30, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 346 Chain: "B" Number of atoms: 7861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1054, 7861 Classifications: {'peptide': 1054} Incomplete info: {'truncation_to_alanine': 151} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 1013} Chain breaks: 10 Unresolved non-hydrogen bonds: 540 Unresolved non-hydrogen angles: 656 Unresolved non-hydrogen dihedrals: 434 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 26, 'GLU:plan': 42, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 364 Chain: "C" Number of atoms: 2148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2148 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 12, 'TRANS': 278} Chain breaks: 1 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 17, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 114 Chain: "E" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1458 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 6, 'TRANS': 191} Chain breaks: 1 Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 250 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 7, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 138 Chain: "F" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 554 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 71} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "H" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 923 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 3, 'ARG:plan': 2, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 58 Chain: "I" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 819 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 4, 'TRANS': 108} Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 5, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 67 Chain: "J" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 472 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 1, 'TRANS': 60} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'TYR:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 34 Chain: "K" Number of atoms: 711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 711 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 3, 'TRANS': 90} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 45 Chain: "L" Number of atoms: 293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 293 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 41} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "M" Number of atoms: 8055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1052, 8055 Classifications: {'peptide': 1052} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PTRANS': 40, 'TRANS': 1011} Chain breaks: 3 Unresolved non-hydrogen bonds: 411 Unresolved non-hydrogen angles: 512 Unresolved non-hydrogen dihedrals: 333 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 5, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 19, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 262 Chain: "N" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 353 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "O" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 664 Classifications: {'RNA': 32} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 6, 'rna3p_pur': 8, 'rna3p_pyr': 17} Link IDs: {'rna2p': 6, 'rna3p': 25} Chain: "Q" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 561 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "R" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 82 Classifications: {'RNA': 4} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna3p': 3} Chain: "A" 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: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 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: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 329 SG CYS A 56 40.465 71.937 132.111 1.00 44.12 S ATOM 394 SG CYS A 67 41.325 74.870 129.408 1.00 36.96 S ATOM 6117 SG CYS A1031 130.908 59.988 87.955 1.00 43.17 S ATOM 6186 SG CYS A1044 129.169 61.814 90.521 1.00 21.45 S ATOM 15211 SG CYS B1108 51.869 86.840 141.400 1.00 42.54 S ATOM 15233 SG CYS B1111 55.162 83.832 141.966 1.00 49.31 S ATOM 15303 SG CYS B1133 51.477 83.351 142.231 1.00 51.21 S ATOM 15327 SG CYS B1136 51.962 85.702 144.216 1.00 50.56 S ATOM 16250 SG CYS C 90 10.597 88.609 73.299 1.00 33.61 S ATOM 16266 SG CYS C 93 7.780 85.951 73.146 1.00 48.83 S ATOM 16321 SG CYS C 102 12.517 85.276 72.448 1.00 30.81 S ATOM 21196 SG CYS I 76 106.607 96.137 69.380 1.00 21.63 S ATOM 21217 SG CYS I 79 102.526 96.334 68.713 1.00 24.95 S ATOM 21395 SG CYS I 103 103.676 93.926 71.177 1.00 11.99 S ATOM 21430 SG CYS I 108 104.608 94.243 67.606 1.00 13.46 S ATOM 20713 SG CYS I 7 120.977 30.961 93.195 1.00 36.75 S ATOM 20739 SG CYS I 10 117.375 29.064 95.516 1.00 46.88 S ATOM 20866 SG CYS I 29 119.609 32.031 96.440 1.00 42.76 S ATOM 20891 SG CYS I 32 120.947 29.279 95.969 1.00 48.26 S ATOM 21537 SG CYS J 7 40.262 78.526 59.346 1.00 12.08 S ATOM 21561 SG CYS J 10 39.038 81.661 56.305 1.00 8.91 S ATOM 21814 SG CYS J 44 42.457 80.900 56.825 1.00 10.37 S ATOM 21820 SG CYS J 45 39.715 78.793 55.634 1.00 7.44 S ATOM 22700 SG CYS L 12 28.818 43.442 85.970 1.00 25.02 S ATOM 22718 SG CYS L 15 27.839 40.756 82.462 1.00 32.97 S ATOM 22801 SG CYS L 29 27.772 40.860 87.122 1.00 32.08 S ATOM 22817 SG CYS L 32 29.316 39.178 85.014 1.00 35.00 S Time building chain proxies: 17.36, per 1000 atoms: 0.53 Number of scatterers: 32686 At special positions: 0 Unit cell: (178.08, 155.82, 162.18, 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 8 29.99 S 195 16.00 P 80 15.00 Mg 2 11.99 O 6136 8.00 N 5716 7.00 C 20549 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: 12.23 Conformation dependent library (CDL) restraints added in 5.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1601 " pdb="ZN ZN A1601 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1601 " - pdb=" NE2 HIS A 70 " pdb="ZN ZN A1601 " - pdb=" SG CYS A 56 " pdb=" ZN A1603 " pdb="ZN ZN A1603 " - pdb=" NE2 HIS A 985 " pdb="ZN ZN A1603 " - pdb=" ND1 HIS A 983 " pdb="ZN ZN A1603 " - pdb=" SG CYS A1044 " pdb="ZN ZN A1603 " - pdb=" SG CYS A1031 " pdb=" ZN B2001 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1133 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1136 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1108 " pdb="ZN ZN B2001 " - pdb=" SG CYS B1111 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 102 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 93 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 90 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 79 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 76 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 108 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 10 " pdb=" ZN J 200 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 200 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 32 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 15 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 29 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 12 " Number of angles added : 31 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7874 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 49 sheets defined 32.9% alpha, 17.7% beta 24 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 8.77 Creating SS restraints... Processing helix chain 'A' and resid 24 through 31 removed outlier: 3.556A pdb=" N ARG A 28 " --> pdb=" O ASN A 24 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASP A 29 " --> pdb=" O ASN A 25 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS A 30 " --> pdb=" O ASN A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.919A pdb=" N LYS A 210 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 274 removed outlier: 4.333A pdb=" N SER A 267 " --> pdb=" O THR A 263 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N SER A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 305 through 313 removed outlier: 3.700A pdb=" N MET A 309 " --> pdb=" O GLY A 305 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP A 311 " --> pdb=" O ARG A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 345 removed outlier: 3.542A pdb=" N LYS A 345 " --> pdb=" O GLU A 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 341 through 345' Processing helix chain 'A' and resid 416 through 418 No H-bonds generated for 'chain 'A' and resid 416 through 418' Processing helix chain 'A' and resid 437 through 439 No H-bonds generated for 'chain 'A' and resid 437 through 439' Processing helix chain 'A' and resid 440 through 445 removed outlier: 3.713A pdb=" N PHE A 444 " --> pdb=" O CYS A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 466 removed outlier: 3.804A pdb=" N GLU A 466 " --> pdb=" O GLN A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 471 removed outlier: 3.716A pdb=" N LEU A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 503 removed outlier: 3.688A pdb=" N ASN A 501 " --> pdb=" O ALA A 497 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU A 503 " --> pdb=" O LEU A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 517 Processing helix chain 'A' and resid 543 through 548 removed outlier: 3.528A pdb=" N PHE A 547 " --> pdb=" O GLY A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 596 Processing helix chain 'A' and resid 600 through 619 removed outlier: 3.621A pdb=" N TYR A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 629 removed outlier: 3.720A pdb=" N LEU A 627 " --> pdb=" O SER A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 658 removed outlier: 3.512A pdb=" N ARG A 636 " --> pdb=" O ASP A 632 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 669 Processing helix chain 'A' and resid 682 through 693 removed outlier: 3.746A pdb=" N PHE A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N CYS A 687 " --> pdb=" O LEU A 683 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER A 693 " --> pdb=" O GLU A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 706 removed outlier: 3.834A pdb=" N SER A 702 " --> pdb=" O GLU A 698 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A 703 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP A 706 " --> pdb=" O SER A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 713 No H-bonds generated for 'chain 'A' and resid 711 through 713' Processing helix chain 'A' and resid 714 through 719 Processing helix chain 'A' and resid 723 through 731 Processing helix chain 'A' and resid 736 through 745 removed outlier: 3.568A pdb=" N LEU A 740 " --> pdb=" O ASN A 736 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN A 742 " --> pdb=" O GLY A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 770 removed outlier: 3.520A pdb=" N TRP A 769 " --> pdb=" O THR A 765 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN A 770 " --> pdb=" O CYS A 766 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 765 through 770' Processing helix chain 'A' and resid 805 through 818 removed outlier: 4.439A pdb=" N ASP A 818 " --> pdb=" O VAL A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 840 removed outlier: 3.646A pdb=" N SER A 832 " --> pdb=" O PRO A 828 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE A 838 " --> pdb=" O ARG A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 891 removed outlier: 3.628A pdb=" N LEU A 885 " --> pdb=" O SER A 881 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA A 888 " --> pdb=" O ALA A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 913 Processing helix chain 'A' and resid 930 through 936 removed outlier: 3.817A pdb=" N LEU A 933 " --> pdb=" O SER A 930 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER A 934 " --> pdb=" O GLU A 931 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS A 935 " --> pdb=" O TYR A 932 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS A 936 " --> pdb=" O LEU A 933 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 930 through 936' Processing helix chain 'A' and resid 938 through 951 Processing helix chain 'A' and resid 988 through 994 removed outlier: 3.861A pdb=" N LYS A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1010 removed outlier: 3.945A pdb=" N VAL A1002 " --> pdb=" O ALA A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1059 through 1066 removed outlier: 3.897A pdb=" N ILE A1063 " --> pdb=" O GLU A1059 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1073 removed outlier: 3.646A pdb=" N LEU A1071 " --> pdb=" O LEU A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1121 through 1127 Processing helix chain 'A' and resid 1146 through 1151 Processing helix chain 'A' and resid 1155 through 1172 removed outlier: 3.862A pdb=" N SER A1161 " --> pdb=" O ASP A1157 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE A1162 " --> pdb=" O ALA A1158 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A1172 " --> pdb=" O GLU A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1173 through 1175 No H-bonds generated for 'chain 'A' and resid 1173 through 1175' Processing helix chain 'A' and resid 1179 through 1190 removed outlier: 3.901A pdb=" N LEU A1183 " --> pdb=" O LEU A1179 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A1185 " --> pdb=" O GLU A1181 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A1186 " --> pdb=" O HIS A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1212 removed outlier: 3.651A pdb=" N GLN A1207 " --> pdb=" O GLY A1203 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG A1208 " --> pdb=" O TRP A1204 " (cutoff:3.500A) Processing helix chain 'A' and resid 1215 through 1223 removed outlier: 3.585A pdb=" N GLN A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A1223 " --> pdb=" O GLN A1219 " (cutoff:3.500A) Processing helix chain 'A' and resid 1224 through 1236 removed outlier: 3.662A pdb=" N CYS A1228 " --> pdb=" O SER A1224 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS A1231 " --> pdb=" O GLN A1227 " (cutoff:3.500A) Processing helix chain 'A' and resid 1244 through 1249 Processing helix chain 'B' and resid 29 through 46 removed outlier: 3.899A pdb=" N LYS B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 62 removed outlier: 3.886A pdb=" N SER B 55 " --> pdb=" O HIS B 51 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR B 56 " --> pdb=" O GLN B 52 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE B 59 " --> pdb=" O SER B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 70 removed outlier: 4.104A pdb=" N ASN B 66 " --> pdb=" O HIS B 62 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER B 70 " --> pdb=" O ASN B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 124 Processing helix chain 'B' and resid 278 through 285 removed outlier: 3.523A pdb=" N LEU B 282 " --> pdb=" O PRO B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 298 removed outlier: 3.776A pdb=" N ILE B 298 " --> pdb=" O ALA B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 322 removed outlier: 4.149A pdb=" N THR B 308 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN B 309 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER B 310 " --> pdb=" O SER B 306 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS B 322 " --> pdb=" O ALA B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 341 removed outlier: 3.957A pdb=" N THR B 333 " --> pdb=" O ASN B 329 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR B 334 " --> pdb=" O ASN B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 357 removed outlier: 3.739A pdb=" N LEU B 354 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N HIS B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 384 Processing helix chain 'B' and resid 407 through 419 removed outlier: 3.880A pdb=" N VAL B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS B 414 " --> pdb=" O GLU B 410 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N HIS B 417 " --> pdb=" O VAL B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 427 removed outlier: 3.925A pdb=" N THR B 423 " --> pdb=" O ARG B 419 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG B 424 " --> pdb=" O ARG B 420 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA B 425 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 430 No H-bonds generated for 'chain 'B' and resid 428 through 430' Processing helix chain 'B' and resid 445 through 459 removed outlier: 4.207A pdb=" N THR B 449 " --> pdb=" O ALA B 445 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY B 451 " --> pdb=" O VAL B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 490 removed outlier: 3.823A pdb=" N THR B 486 " --> pdb=" O ASN B 482 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 490 " --> pdb=" O THR B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 514 removed outlier: 3.764A pdb=" N TRP B 514 " --> pdb=" O PRO B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 553 Processing helix chain 'B' and resid 587 through 599 removed outlier: 3.867A pdb=" N ALA B 592 " --> pdb=" O GLU B 588 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU B 593 " --> pdb=" O SER B 589 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER B 596 " --> pdb=" O ALA B 592 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG B 597 " --> pdb=" O GLU B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 656 Processing helix chain 'B' and resid 692 through 697 removed outlier: 3.647A pdb=" N PHE B 695 " --> pdb=" O ASP B 692 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU B 696 " --> pdb=" O LEU B 693 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU B 697 " --> pdb=" O SER B 694 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 692 through 697' Processing helix chain 'B' and resid 711 through 721 removed outlier: 3.703A pdb=" N LEU B 716 " --> pdb=" O GLY B 712 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR B 717 " --> pdb=" O ARG B 713 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN B 718 " --> pdb=" O ARG B 714 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN B 720 " --> pdb=" O LEU B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 726 Processing helix chain 'B' and resid 755 through 761 Processing helix chain 'B' and resid 763 through 767 removed outlier: 3.875A pdb=" N LEU B 766 " --> pdb=" O LYS B 763 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE B 767 " --> pdb=" O GLU B 764 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 763 through 767' Processing helix chain 'B' and resid 792 through 796 removed outlier: 3.696A pdb=" N GLU B 796 " --> pdb=" O LYS B 792 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 792 through 796' Processing helix chain 'B' and resid 929 through 933 removed outlier: 3.724A pdb=" N PHE B 933 " --> pdb=" O GLN B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 955 removed outlier: 4.139A pdb=" N SER B 953 " --> pdb=" O HIS B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 971 Processing helix chain 'B' and resid 990 through 994 removed outlier: 3.769A pdb=" N THR B 994 " --> pdb=" O PRO B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 996 through 1007 removed outlier: 3.524A pdb=" N ILE B1000 " --> pdb=" O GLY B 996 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN B1003 " --> pdb=" O GLU B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1043 through 1047 removed outlier: 3.647A pdb=" N ASP B1046 " --> pdb=" O MET B1043 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1085 removed outlier: 3.625A pdb=" N ALA B1085 " --> pdb=" O ASP B1081 " (cutoff:3.500A) Processing helix chain 'B' and resid 1089 through 1095 Processing helix chain 'B' and resid 1148 through 1159 removed outlier: 3.687A pdb=" N LYS B1152 " --> pdb=" O PRO B1148 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 44 removed outlier: 3.809A pdb=" N ALA C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG C 38 " --> pdb=" O ALA C 34 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER C 43 " --> pdb=" O ARG C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 73 removed outlier: 3.829A pdb=" N ILE C 67 " --> pdb=" O ASN C 63 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA C 68 " --> pdb=" O ASP C 64 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY C 72 " --> pdb=" O ALA C 68 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU C 73 " --> pdb=" O HIS C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 215 Processing helix chain 'C' and resid 243 through 251 Processing helix chain 'C' and resid 277 through 303 removed outlier: 4.025A pdb=" N VAL C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 25 removed outlier: 3.628A pdb=" N ARG E 12 " --> pdb=" O LYS E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 42 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 111 through 116 Processing helix chain 'E' and resid 147 through 159 removed outlier: 3.634A pdb=" N THR E 153 " --> pdb=" O GLU E 149 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR E 158 " --> pdb=" O LEU E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 178 removed outlier: 3.704A pdb=" N PHE E 178 " --> pdb=" O ILE E 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 83 removed outlier: 3.555A pdb=" N ARG F 72 " --> pdb=" O TYR F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 108 removed outlier: 3.534A pdb=" N LYS F 103 " --> pdb=" O GLU F 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 removed outlier: 3.782A pdb=" N LEU J 27 " --> pdb=" O ASP J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 52 removed outlier: 4.118A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET J 50 " --> pdb=" O ARG J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 39 through 51 removed outlier: 3.538A pdb=" N GLY K 43 " --> pdb=" O ASP K 39 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 110 removed outlier: 3.535A pdb=" N LEU K 94 " --> pdb=" O ALA K 90 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS K 96 " --> pdb=" O ASN K 92 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU K 97 " --> pdb=" O ASP K 93 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA K 110 " --> pdb=" O GLU K 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 34 removed outlier: 3.515A pdb=" N LEU M 26 " --> pdb=" O VAL M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 76 removed outlier: 3.627A pdb=" N LYS M 67 " --> pdb=" O THR M 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 230 through 234 Processing helix chain 'M' and resid 247 through 252 Processing helix chain 'M' and resid 283 through 288 removed outlier: 3.589A pdb=" N LEU M 287 " --> pdb=" O ASN M 283 " (cutoff:3.500A) Processing helix chain 'M' and resid 292 through 305 removed outlier: 3.818A pdb=" N GLN M 298 " --> pdb=" O GLU M 294 " (cutoff:3.500A) Processing helix chain 'M' and resid 309 through 314 removed outlier: 3.691A pdb=" N ALA M 313 " --> pdb=" O SER M 309 " (cutoff:3.500A) Processing helix chain 'M' and resid 315 through 320 removed outlier: 3.650A pdb=" N ILE M 319 " --> pdb=" O ASP M 315 " (cutoff:3.500A) Processing helix chain 'M' and resid 328 through 340 removed outlier: 3.727A pdb=" N LEU M 334 " --> pdb=" O ALA M 330 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS M 336 " --> pdb=" O VAL M 332 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU M 337 " --> pdb=" O ILE M 333 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS M 338 " --> pdb=" O LEU M 334 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN M 340 " --> pdb=" O LYS M 336 " (cutoff:3.500A) Processing helix chain 'M' and resid 346 through 355 removed outlier: 3.741A pdb=" N PHE M 350 " --> pdb=" O ASP M 346 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL M 351 " --> pdb=" O PRO M 347 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS M 352 " --> pdb=" O VAL M 348 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET M 355 " --> pdb=" O VAL M 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 368 through 372 Processing helix chain 'M' and resid 372 through 377 removed outlier: 4.148A pdb=" N GLN M 376 " --> pdb=" O ARG M 372 " (cutoff:3.500A) Processing helix chain 'M' and resid 402 through 408 Processing helix chain 'M' and resid 411 through 413 No H-bonds generated for 'chain 'M' and resid 411 through 413' Processing helix chain 'M' and resid 448 through 460 removed outlier: 3.585A pdb=" N ASN M 452 " --> pdb=" O THR M 448 " (cutoff:3.500A) Processing helix chain 'M' and resid 475 through 481 removed outlier: 4.039A pdb=" N ARG M 480 " --> pdb=" O ALA M 476 " (cutoff:3.500A) Processing helix chain 'M' and resid 494 through 503 removed outlier: 3.687A pdb=" N ARG M 499 " --> pdb=" O ALA M 495 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N MET M 502 " --> pdb=" O ILE M 498 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY M 503 " --> pdb=" O ARG M 499 " (cutoff:3.500A) Processing helix chain 'M' and resid 512 through 517 Processing helix chain 'M' and resid 519 through 523 removed outlier: 3.742A pdb=" N PHE M 522 " --> pdb=" O GLY M 519 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER M 523 " --> pdb=" O GLN M 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 519 through 523' Processing helix chain 'M' and resid 561 through 570 removed outlier: 3.726A pdb=" N ALA M 565 " --> pdb=" O SER M 561 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS M 566 " --> pdb=" O LEU M 562 " (cutoff:3.500A) Processing helix chain 'M' and resid 632 through 640 Processing helix chain 'M' and resid 647 through 661 removed outlier: 3.917A pdb=" N ALA M 651 " --> pdb=" O ALA M 647 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN M 653 " --> pdb=" O PHE M 649 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N HIS M 656 " --> pdb=" O MET M 652 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N MET M 659 " --> pdb=" O VAL M 655 " (cutoff:3.500A) Processing helix chain 'M' and resid 662 through 664 No H-bonds generated for 'chain 'M' and resid 662 through 664' Processing helix chain 'M' and resid 668 through 673 removed outlier: 3.774A pdb=" N ASN M 672 " --> pdb=" O ASP M 668 " (cutoff:3.500A) Processing helix chain 'M' and resid 684 through 692 removed outlier: 3.907A pdb=" N MET M 689 " --> pdb=" O LEU M 685 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU M 690 " --> pdb=" O LEU M 686 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU M 691 " --> pdb=" O VAL M 687 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN M 692 " --> pdb=" O LYS M 688 " (cutoff:3.500A) Processing helix chain 'M' and resid 699 through 719 removed outlier: 4.075A pdb=" N MET M 705 " --> pdb=" O TYR M 701 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU M 717 " --> pdb=" O GLN M 713 " (cutoff:3.500A) Processing helix chain 'M' and resid 788 through 792 removed outlier: 3.604A pdb=" N ILE M 792 " --> pdb=" O PRO M 789 " (cutoff:3.500A) Processing helix chain 'M' and resid 800 through 805 Processing helix chain 'M' and resid 870 through 878 Processing helix chain 'M' and resid 884 through 899 removed outlier: 3.676A pdb=" N ILE M 888 " --> pdb=" O THR M 884 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N SER M 889 " --> pdb=" O LEU M 885 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N THR M 890 " --> pdb=" O GLY M 886 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP M 897 " --> pdb=" O LEU M 893 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP M 899 " --> pdb=" O HIS M 895 " (cutoff:3.500A) Processing helix chain 'M' and resid 905 through 919 removed outlier: 3.715A pdb=" N LEU M 911 " --> pdb=" O LYS M 907 " (cutoff:3.500A) Processing helix chain 'M' and resid 955 through 966 removed outlier: 3.547A pdb=" N LYS M 959 " --> pdb=" O SER M 955 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL M 964 " --> pdb=" O LEU M 960 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS M 965 " --> pdb=" O TYR M 961 " (cutoff:3.500A) Processing helix chain 'M' and resid 999 through 1011 Processing helix chain 'M' and resid 1011 through 1018 removed outlier: 4.104A pdb=" N ILE M1015 " --> pdb=" O THR M1011 " (cutoff:3.500A) Processing helix chain 'M' and resid 1021 through 1028 removed outlier: 3.827A pdb=" N ILE M1025 " --> pdb=" O ASN M1021 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR M1027 " --> pdb=" O GLU M1023 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY M1028 " --> pdb=" O GLU M1024 " (cutoff:3.500A) Processing helix chain 'M' and resid 1040 through 1070 removed outlier: 3.647A pdb=" N MET M1047 " --> pdb=" O ARG M1043 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR M1052 " --> pdb=" O LYS M1048 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP M1057 " --> pdb=" O LEU M1053 " (cutoff:3.500A) Processing helix chain 'M' and resid 1075 through 1089 removed outlier: 3.759A pdb=" N LEU M1079 " --> pdb=" O GLN M1075 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER M1081 " --> pdb=" O LYS M1077 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ALA M1082 " --> pdb=" O LYS M1078 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP M1083 " --> pdb=" O LEU M1079 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR M1087 " --> pdb=" O TRP M1083 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1238 through 1239 Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 81 removed outlier: 10.430A pdb=" N PHE A 76 " --> pdb=" O PRO A 224 " (cutoff:3.500A) removed outlier: 10.076A pdb=" N TYR A 78 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N SER A 222 " --> pdb=" O TYR A 78 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 316 through 318 removed outlier: 3.601A pdb=" N SER A 318 " --> pdb=" O ILE B1073 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ILE B1073 " --> pdb=" O SER A 318 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 321 through 328 removed outlier: 3.520A pdb=" N ILE A 421 " --> pdb=" O MET A 409 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR A 324 " --> pdb=" O LEU A 453 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 350 Processing sheet with id=AA6, first strand: chain 'A' and resid 528 through 529 removed outlier: 3.802A pdb=" N ILE A 529 " --> pdb=" O GLN A 540 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 557 through 559 removed outlier: 6.623A pdb=" N VAL A 565 " --> pdb=" O LEU A 572 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 748 through 751 removed outlier: 3.587A pdb=" N GLY A 748 " --> pdb=" O ILE A 796 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 843 through 844 Processing sheet with id=AB1, first strand: chain 'A' and resid 925 through 926 removed outlier: 3.569A pdb=" N HIS A1143 " --> pdb=" O SER A 926 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 954 through 955 removed outlier: 6.787A pdb=" N LEU A 954 " --> pdb=" O VAL A1076 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1022 through 1028 removed outlier: 4.410A pdb=" N ASP A1022 " --> pdb=" O VAL A1050 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N VAL A1049 " --> pdb=" O TRP A 980 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N TRP A 980 " --> pdb=" O VAL A1049 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR A 962 " --> pdb=" O HIS A 985 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR I 44 " --> pdb=" O ILE A 965 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N PHE A 967 " --> pdb=" O CYS I 42 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N CYS I 42 " --> pdb=" O PHE A 967 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1082 through 1090 removed outlier: 3.549A pdb=" N ASN A1086 " --> pdb=" O LYS A1110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 95 through 102 removed outlier: 5.586A pdb=" N PHE B 97 " --> pdb=" O GLN B 137 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLN B 137 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N GLU B 99 " --> pdb=" O ASN B 135 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY B 174 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL B 134 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N LEU B 172 " --> pdb=" O VAL B 134 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 106 through 108 Processing sheet with id=AB7, first strand: chain 'B' and resid 208 through 209 Processing sheet with id=AB8, first strand: chain 'B' and resid 398 through 401 removed outlier: 5.964A pdb=" N ALA B 219 " --> pdb=" O ARG B 494 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 229 through 231 removed outlier: 3.922A pdb=" N TRP B 235 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 579 through 584 removed outlier: 5.374A pdb=" N TRP B 580 " --> pdb=" O LEU B 576 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU B 576 " --> pdb=" O TRP B 580 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY B 582 " --> pdb=" O VAL B 574 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LYS B 573 " --> pdb=" O VAL B 618 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ILE B 620 " --> pdb=" O LYS B 573 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU B 575 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU B 617 " --> pdb=" O ASP B 612 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP B 612 " --> pdb=" O GLU B 617 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 628 through 632 Processing sheet with id=AC3, first strand: chain 'B' and resid 741 through 745 removed outlier: 3.605A pdb=" N SER B 802 " --> pdb=" O ARG B 906 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA B 898 " --> pdb=" O ALA B 810 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N PHE B 897 " --> pdb=" O LEU B 888 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LEU B 888 " --> pdb=" O PHE B 897 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ALA B 899 " --> pdb=" O VAL B 886 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL B 886 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N SER B 901 " --> pdb=" O GLN B 884 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 741 through 745 removed outlier: 3.605A pdb=" N SER B 802 " --> pdb=" O ARG B 906 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA B 898 " --> pdb=" O ALA B 810 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N PHE B 897 " --> pdb=" O LEU B 888 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LEU B 888 " --> pdb=" O PHE B 897 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ALA B 899 " --> pdb=" O VAL B 886 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL B 886 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N SER B 901 " --> pdb=" O GLN B 884 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N VAL B 886 " --> pdb=" O LYS L 39 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 914 through 916 removed outlier: 8.649A pdb=" N ILE B 944 " --> pdb=" O ASN B 771 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE B 773 " --> pdb=" O ILE B 944 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ILE B 946 " --> pdb=" O ILE B 773 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA B 775 " --> pdb=" O ILE B 946 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE B 788 " --> pdb=" O GLY B 925 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU B 927 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N MET B 790 " --> pdb=" O LEU B 927 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 859 through 861 Processing sheet with id=AC7, first strand: chain 'B' and resid 935 through 936 Processing sheet with id=AC8, first strand: chain 'B' and resid 1014 through 1015 Processing sheet with id=AC9, first strand: chain 'B' and resid 1105 through 1108 Processing sheet with id=AD1, first strand: chain 'C' and resid 11 through 17 removed outlier: 3.646A pdb=" N LYS C 13 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LYS C 23 " --> pdb=" O ARG C 15 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU C 17 " --> pdb=" O TYR C 21 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N TYR C 21 " --> pdb=" O LEU C 17 " (cutoff:3.500A) removed outlier: 11.345A pdb=" N ILE C 195 " --> pdb=" O PRO C 261 " (cutoff:3.500A) removed outlier: 10.608A pdb=" N ASP C 263 " --> pdb=" O ASP C 193 " (cutoff:3.500A) removed outlier: 12.081A pdb=" N ASP C 193 " --> pdb=" O ASP C 263 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N SER C 265 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 126 through 127 removed outlier: 4.841A pdb=" N CYS C 112 " --> pdb=" O GLN C 161 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N GLN C 161 " --> pdb=" O CYS C 112 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU C 52 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ARG C 170 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ILE C 50 " --> pdb=" O ARG C 170 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLY C 172 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N VAL C 48 " --> pdb=" O GLY C 172 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL C 53 " --> pdb=" O TYR L 48 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR L 48 " --> pdb=" O VAL C 53 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 118 through 120 Processing sheet with id=AD4, first strand: chain 'C' and resid 221 through 223 Processing sheet with id=AD5, first strand: chain 'E' and resid 55 through 58 removed outlier: 3.711A pdb=" N THR E 55 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARG E 96 " --> pdb=" O GLN E 66 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR E 68 " --> pdb=" O ARG E 96 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA E 97 " --> pdb=" O GLU E 123 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N PHE E 125 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU E 99 " --> pdb=" O PHE E 125 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 142 through 145 removed outlier: 3.777A pdb=" N GLU E 142 " --> pdb=" O ILE E 189 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TYR E 198 " --> pdb=" O ARG E 190 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE E 168 " --> pdb=" O VAL E 205 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 113 through 117 Processing sheet with id=AD8, first strand: chain 'H' and resid 9 through 17 removed outlier: 3.578A pdb=" N VAL H 13 " --> pdb=" O ARG H 33 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLU H 31 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LEU H 17 " --> pdb=" O ARG H 29 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ARG H 29 " --> pdb=" O LEU H 17 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU H 43 " --> pdb=" O VAL H 30 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP H 44 " --> pdb=" O LEU H 120 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU H 120 " --> pdb=" O ASP H 44 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N TYR H 113 " --> pdb=" O TYR H 98 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN H 137 " --> pdb=" O LEU H 97 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 14 through 19 removed outlier: 3.677A pdb=" N ILE I 24 " --> pdb=" O ASP I 19 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 70 through 71 Processing sheet with id=AE2, first strand: chain 'K' and resid 19 through 20 removed outlier: 3.568A pdb=" N ILE K 75 " --> pdb=" O ALA K 31 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY K 60 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE K 58 " --> pdb=" O HIS K 76 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 39 through 43 removed outlier: 3.786A pdb=" N LYS M 13 " --> pdb=" O SER M 89 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 218 through 221 removed outlier: 3.999A pdb=" N MET M 218 " --> pdb=" O VAL M 195 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS M 155 " --> pdb=" O PHE M 192 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N CYS M 153 " --> pdb=" O ARG M 194 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TRP M 146 " --> pdb=" O ARG M 133 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N TRP M 148 " --> pdb=" O GLY M 131 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N GLY M 131 " --> pdb=" O TRP M 148 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ALA M 125 " --> pdb=" O PHE M 115 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N PHE M 115 " --> pdb=" O ALA M 125 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N GLU M 127 " --> pdb=" O VAL M 113 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL M 113 " --> pdb=" O GLU M 127 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ILE M 109 " --> pdb=" O GLY M 131 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ARG M 133 " --> pdb=" O ASP M 107 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASP M 107 " --> pdb=" O ARG M 133 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N TRP M 135 " --> pdb=" O ARG M 105 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ARG M 105 " --> pdb=" O TRP M 135 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA M 180 " --> pdb=" O SER M 168 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N SER M 168 " --> pdb=" O ALA M 180 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU M 182 " --> pdb=" O THR M 166 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR M 166 " --> pdb=" O LEU M 182 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYS M 184 " --> pdb=" O ILE M 164 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ARG M 258 " --> pdb=" O ILE M 164 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N THR M 166 " --> pdb=" O ARG M 258 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASP M 260 " --> pdb=" O THR M 166 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER M 168 " --> pdb=" O ASP M 260 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 218 through 221 removed outlier: 3.999A pdb=" N MET M 218 " --> pdb=" O VAL M 195 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS M 155 " --> pdb=" O PHE M 192 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N CYS M 153 " --> pdb=" O ARG M 194 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TRP M 146 " --> pdb=" O ARG M 133 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N TRP M 148 " --> pdb=" O GLY M 131 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N GLY M 131 " --> pdb=" O TRP M 148 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N PHE M 123 " --> pdb=" O VAL M 267 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 391 through 400 removed outlier: 5.321A pdb=" N LEU M 393 " --> pdb=" O TYR M 385 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N TYR M 385 " --> pdb=" O LEU M 393 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLY M 395 " --> pdb=" O ARG M 383 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG M 383 " --> pdb=" O GLY M 395 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N PHE M 415 " --> pdb=" O SER M 380 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLN M 382 " --> pdb=" O PHE M 415 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR M 419 " --> pdb=" O ALA M 384 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 435 through 438 Processing sheet with id=AE8, first strand: chain 'M' and resid 526 through 530 removed outlier: 4.298A pdb=" N LEU M 618 " --> pdb=" O THR M 528 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE M 581 " --> pdb=" O ILE M 592 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR M 585 " --> pdb=" O TYR M 588 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS M 559 " --> pdb=" O SER M 603 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER M 603 " --> pdb=" O LYS M 559 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 543 through 546 Processing sheet with id=AF1, first strand: chain 'M' and resid 627 through 628 Processing sheet with id=AF2, first strand: chain 'M' and resid 734 through 735 removed outlier: 7.460A pdb=" N CYS M 734 " --> pdb=" O PHE M 814 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'M' and resid 745 through 746 Processing sheet with id=AF4, first strand: chain 'M' and resid 749 through 751 1049 hydrogen bonds defined for protein. 2991 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 57 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 15.21 Time building geometry restraints manager: 13.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9888 1.34 - 1.46: 5634 1.46 - 1.57: 17483 1.57 - 1.69: 157 1.69 - 1.81: 296 Bond restraints: 33458 Sorted by residual: bond pdb=" O3' DA Q 15 " pdb=" P DC Q 16 " ideal model delta sigma weight residual 1.607 1.691 -0.084 1.50e-02 4.44e+03 3.14e+01 bond pdb=" O3' DC Q 7 " pdb=" P DG Q 8 " ideal model delta sigma weight residual 1.607 1.664 -0.057 1.50e-02 4.44e+03 1.46e+01 bond pdb=" C LEU A 442 " pdb=" N PRO A 443 " ideal model delta sigma weight residual 1.336 1.379 -0.043 1.20e-02 6.94e+03 1.27e+01 bond pdb=" N CYS A 59 " pdb=" CA CYS A 59 " ideal model delta sigma weight residual 1.453 1.489 -0.036 1.31e-02 5.83e+03 7.55e+00 bond pdb=" N CYS C 99 " pdb=" CA CYS C 99 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.29e-02 6.01e+03 7.08e+00 ... (remaining 33453 not shown) Histogram of bond angle deviations from ideal: 76.97 - 89.46: 1 89.46 - 101.94: 161 101.94 - 114.43: 20876 114.43 - 126.92: 24185 126.92 - 139.40: 519 Bond angle restraints: 45742 Sorted by residual: angle pdb=" O3' DA Q 15 " pdb=" P DC Q 16 " pdb=" O5' DC Q 16 " ideal model delta sigma weight residual 104.00 137.38 -33.38 1.50e+00 4.44e-01 4.95e+02 angle pdb=" C3' DA Q 15 " pdb=" O3' DA Q 15 " pdb=" P DC Q 16 " ideal model delta sigma weight residual 120.20 139.40 -19.20 1.50e+00 4.44e-01 1.64e+02 angle pdb=" O3' DA Q 15 " pdb=" P DC Q 16 " pdb=" OP2 DC Q 16 " ideal model delta sigma weight residual 108.00 76.97 31.03 3.00e+00 1.11e-01 1.07e+02 angle pdb=" C ASP C 176 " pdb=" N HIS C 177 " pdb=" CA HIS C 177 " ideal model delta sigma weight residual 121.54 131.06 -9.52 1.91e+00 2.74e-01 2.48e+01 angle pdb=" C SER A 916 " pdb=" N LYS A 917 " pdb=" CA LYS A 917 " ideal model delta sigma weight residual 122.61 129.49 -6.88 1.56e+00 4.11e-01 1.94e+01 ... (remaining 45737 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.31: 19369 35.31 - 70.62: 451 70.62 - 105.93: 29 105.93 - 141.23: 1 141.23 - 176.54: 2 Dihedral angle restraints: 19852 sinusoidal: 7723 harmonic: 12129 Sorted by residual: dihedral pdb=" O4' C O 11 " pdb=" C1' C O 11 " pdb=" N1 C O 11 " pdb=" C2 C O 11 " ideal model delta sinusoidal sigma weight residual 200.00 87.03 112.97 1 1.50e+01 4.44e-03 5.93e+01 dihedral pdb=" O4' U O 26 " pdb=" C1' U O 26 " pdb=" N1 U O 26 " pdb=" C2 U O 26 " ideal model delta sinusoidal sigma weight residual -160.00 -75.88 -84.12 1 1.50e+01 4.44e-03 3.83e+01 dihedral pdb=" O4' U O 13 " pdb=" C1' U O 13 " pdb=" N1 U O 13 " pdb=" C2 U O 13 " ideal model delta sinusoidal sigma weight residual -160.00 -79.02 -80.98 1 1.50e+01 4.44e-03 3.60e+01 ... (remaining 19849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 4402 0.055 - 0.110: 795 0.110 - 0.165: 149 0.165 - 0.220: 6 0.220 - 0.275: 4 Chirality restraints: 5356 Sorted by residual: chirality pdb=" CB ILE A 415 " pdb=" CA ILE A 415 " pdb=" CG1 ILE A 415 " pdb=" CG2 ILE A 415 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C3' U O 17 " pdb=" C4' U O 17 " pdb=" O3' U O 17 " pdb=" C2' U O 17 " both_signs ideal model delta sigma weight residual False -2.48 -2.20 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CB ILE M 812 " pdb=" CA ILE M 812 " pdb=" CG1 ILE M 812 " pdb=" CG2 ILE M 812 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 5353 not shown) Planarity restraints: 5571 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS M 822 " 0.046 5.00e-02 4.00e+02 6.92e-02 7.65e+00 pdb=" N PRO M 823 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO M 823 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO M 823 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR M 387 " 0.043 5.00e-02 4.00e+02 6.44e-02 6.63e+00 pdb=" N PRO M 388 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO M 388 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO M 388 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 525 " -0.035 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO A 526 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 526 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 526 " -0.029 5.00e-02 4.00e+02 ... (remaining 5568 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 51 2.42 - 3.04: 16194 3.04 - 3.66: 46902 3.66 - 4.28: 70087 4.28 - 4.90: 117925 Nonbonded interactions: 251159 Sorted by model distance: nonbonded pdb=" O4 DT N 31 " pdb=" N1 DA Q 17 " model vdw 1.797 2.496 nonbonded pdb=" N2 DG N 32 " pdb=" O2 DC Q 16 " model vdw 2.051 2.496 nonbonded pdb=" OD1 ASP M 830 " pdb="MG MG M2001 " model vdw 2.073 2.170 nonbonded pdb=" OD1 ASP M 832 " pdb="MG MG M2001 " model vdw 2.080 2.170 nonbonded pdb=" OD2 ASP M 834 " pdb="MG MG M2001 " model vdw 2.101 2.170 ... (remaining 251154 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: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 7.680 Check model and map are aligned: 0.480 Set scattering table: 0.260 Process input model: 94.590 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.130 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.084 33458 Z= 0.186 Angle : 0.735 33.383 45742 Z= 0.428 Chirality : 0.045 0.275 5356 Planarity : 0.005 0.069 5571 Dihedral : 14.667 176.543 11978 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: -4.58 (0.10), residues: 4096 helix: -3.71 (0.08), residues: 1291 sheet: -2.10 (0.18), residues: 670 loop : -2.93 (0.10), residues: 2135 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 3697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 633 time to evaluate : 3.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 638 average time/residue: 0.5142 time to fit residues: 499.2973 Evaluate side-chains 433 residues out of total 3697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 430 time to evaluate : 3.617 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.5487 time to fit residues: 7.4413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 353 optimal weight: 4.9990 chunk 317 optimal weight: 5.9990 chunk 176 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 214 optimal weight: 0.6980 chunk 169 optimal weight: 2.9990 chunk 328 optimal weight: 2.9990 chunk 127 optimal weight: 0.1980 chunk 199 optimal weight: 3.9990 chunk 244 optimal weight: 0.0050 chunk 380 optimal weight: 2.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 HIS A 462 GLN A 491 GLN A 634 GLN A 923 GLN A1149 GLN A1182 HIS B 220 GLN B 222 GLN B 417 HIS B 495 GLN B 577 ASN B 600 GLN B 688 HIS B 711 HIS B 718 GLN ** B 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 768 ASN B 877 HIS B 949 HIS ** B1052 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1091 ASN B1106 HIS C 284 ASN F 107 GLN H 124 GLN K 51 HIS L 17 GLN ** L 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 47 GLN ** M 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 304 HIS M 339 GLN M 407 ASN M 431 ASN M 788 HIS M 873 HIS M1092 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 33458 Z= 0.214 Angle : 0.523 9.065 45742 Z= 0.272 Chirality : 0.042 0.162 5356 Planarity : 0.004 0.063 5571 Dihedral : 11.896 177.567 5334 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer Outliers : 1.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.11), residues: 4096 helix: -2.00 (0.12), residues: 1306 sheet: -1.78 (0.18), residues: 705 loop : -2.50 (0.11), residues: 2085 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 434 time to evaluate : 3.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 25 residues processed: 459 average time/residue: 0.4691 time to fit residues: 343.2823 Evaluate side-chains 415 residues out of total 3697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 390 time to evaluate : 3.651 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.3119 time to fit residues: 19.2247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 211 optimal weight: 7.9990 chunk 118 optimal weight: 0.0070 chunk 316 optimal weight: 5.9990 chunk 259 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 381 optimal weight: 40.0000 chunk 411 optimal weight: 9.9990 chunk 339 optimal weight: 10.0000 chunk 378 optimal weight: 30.0000 chunk 129 optimal weight: 0.9990 chunk 305 optimal weight: 9.9990 overall best weight: 2.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 ASN B 600 GLN ** B 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 GLN F 107 GLN ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 84 HIS ** M 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 340 GLN M 411 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 33458 Z= 0.317 Angle : 0.580 9.945 45742 Z= 0.299 Chirality : 0.044 0.191 5356 Planarity : 0.004 0.056 5571 Dihedral : 11.962 178.109 5334 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer Outliers : 1.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.12), residues: 4096 helix: -1.13 (0.14), residues: 1310 sheet: -1.58 (0.18), residues: 694 loop : -2.26 (0.12), residues: 2092 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 392 time to evaluate : 3.827 Fit side-chains revert: symmetry clash outliers start: 54 outliers final: 31 residues processed: 430 average time/residue: 0.4595 time to fit residues: 319.1507 Evaluate side-chains 398 residues out of total 3697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 367 time to evaluate : 3.644 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.2914 time to fit residues: 22.4526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 376 optimal weight: 7.9990 chunk 286 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 181 optimal weight: 2.9990 chunk 255 optimal weight: 0.8980 chunk 382 optimal weight: 50.0000 chunk 405 optimal weight: 7.9990 chunk 199 optimal weight: 0.4980 chunk 362 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 GLN A 658 GLN ** A1219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1242 GLN B 600 GLN B 733 ASN ** B 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1042 HIS H 42 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 33458 Z= 0.233 Angle : 0.520 12.930 45742 Z= 0.267 Chirality : 0.042 0.166 5356 Planarity : 0.004 0.051 5571 Dihedral : 11.851 178.754 5334 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer Outliers : 1.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.12), residues: 4096 helix: -0.64 (0.15), residues: 1304 sheet: -1.45 (0.18), residues: 700 loop : -2.06 (0.12), residues: 2092 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 375 time to evaluate : 3.929 Fit side-chains revert: symmetry clash outliers start: 41 outliers final: 29 residues processed: 403 average time/residue: 0.4550 time to fit residues: 298.3180 Evaluate side-chains 383 residues out of total 3697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 354 time to evaluate : 3.910 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.3077 time to fit residues: 22.2018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 337 optimal weight: 9.9990 chunk 229 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 301 optimal weight: 0.0770 chunk 167 optimal weight: 0.7980 chunk 345 optimal weight: 7.9990 chunk 279 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 206 optimal weight: 0.1980 chunk 363 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 overall best weight: 0.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 GLN A 462 GLN B 600 GLN ** B 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 GLN B1003 GLN M 16 ASN ** M 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 33458 Z= 0.133 Angle : 0.465 11.974 45742 Z= 0.239 Chirality : 0.040 0.158 5356 Planarity : 0.003 0.045 5571 Dihedral : 11.659 178.237 5334 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: -1.78 (0.13), residues: 4096 helix: -0.18 (0.15), residues: 1305 sheet: -1.13 (0.19), residues: 698 loop : -1.86 (0.12), residues: 2093 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 394 time to evaluate : 3.717 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 11 residues processed: 409 average time/residue: 0.4703 time to fit residues: 311.2619 Evaluate side-chains 371 residues out of total 3697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 360 time to evaluate : 3.731 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2993 time to fit residues: 11.3428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 136 optimal weight: 6.9990 chunk 364 optimal weight: 8.9990 chunk 80 optimal weight: 0.9980 chunk 237 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 405 optimal weight: 1.9990 chunk 336 optimal weight: 9.9990 chunk 187 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 134 optimal weight: 10.0000 chunk 212 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 GLN A 587 ASN A 923 GLN ** B 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 33458 Z= 0.331 Angle : 0.582 11.072 45742 Z= 0.298 Chirality : 0.045 0.237 5356 Planarity : 0.004 0.084 5571 Dihedral : 11.879 179.573 5334 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: -1.88 (0.13), residues: 4096 helix: -0.34 (0.15), residues: 1328 sheet: -1.23 (0.19), residues: 709 loop : -1.86 (0.13), residues: 2059 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8192 Ramachandran restraints generated. 4096 Oldfield, 0 Emsley, 4096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 362 time to evaluate : 3.696 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 22 residues processed: 386 average time/residue: 0.4491 time to fit residues: 282.1044 Evaluate side-chains 368 residues out of total 3697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 346 time to evaluate : 3.662 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2928 time to fit residues: 17.2193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.8257 > 50: distance: 59 - 62: 13.066 distance: 62 - 63: 16.948 distance: 62 - 68: 22.157 distance: 63 - 64: 19.001 distance: 63 - 66: 14.668 distance: 64 - 65: 27.969 distance: 64 - 69: 32.162 distance: 66 - 67: 18.145 distance: 67 - 68: 7.663 distance: 69 - 70: 7.987 distance: 70 - 71: 16.574 distance: 70 - 73: 21.438 distance: 71 - 72: 7.649 distance: 71 - 75: 6.628 distance: 73 - 74: 8.031 distance: 75 - 76: 6.568 distance: 76 - 77: 5.453 distance: 76 - 79: 3.471 distance: 77 - 78: 8.220 distance: 77 - 84: 5.409 distance: 79 - 80: 5.371 distance: 80 - 81: 3.038 distance: 81 - 82: 3.606 distance: 84 - 85: 9.005 distance: 85 - 86: 5.248 distance: 85 - 88: 5.780 distance: 86 - 87: 3.691 distance: 88 - 89: 3.418 distance: 92 - 93: 8.865 distance: 93 - 94: 18.979 distance: 93 - 96: 25.669 distance: 94 - 95: 18.183 distance: 94 - 100: 16.658 distance: 96 - 97: 19.750 distance: 97 - 98: 19.628 distance: 97 - 99: 12.689 distance: 100 - 101: 19.982 distance: 100 - 106: 17.995 distance: 101 - 102: 44.460 distance: 101 - 104: 25.230 distance: 102 - 103: 30.546 distance: 102 - 107: 45.689 distance: 104 - 105: 29.556 distance: 105 - 106: 19.545 distance: 107 - 108: 37.108 distance: 107 - 113: 19.856 distance: 108 - 109: 3.586 distance: 108 - 111: 25.299 distance: 109 - 110: 41.809 distance: 109 - 114: 27.958 distance: 111 - 112: 45.114 distance: 112 - 113: 29.441 distance: 114 - 115: 8.120 distance: 115 - 116: 13.262 distance: 115 - 118: 23.301 distance: 116 - 117: 19.335 distance: 116 - 122: 17.127 distance: 118 - 119: 19.301 distance: 119 - 120: 23.726 distance: 120 - 121: 8.351 distance: 122 - 123: 29.712 distance: 123 - 124: 7.756 distance: 123 - 126: 23.849 distance: 124 - 125: 32.381 distance: 124 - 130: 33.453 distance: 126 - 127: 9.617 distance: 127 - 128: 14.484 distance: 127 - 129: 11.997 distance: 130 - 131: 11.980 distance: 131 - 132: 14.486 distance: 131 - 134: 21.996 distance: 132 - 133: 13.323 distance: 132 - 135: 17.904