Starting phenix.real_space_refine on Mon Dec 30 18:28:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ml2_23906/12_2024/7ml2_23906.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ml2_23906/12_2024/7ml2_23906.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ml2_23906/12_2024/7ml2_23906.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ml2_23906/12_2024/7ml2_23906.map" model { file = "/net/cci-nas-00/data/ceres_data/7ml2_23906/12_2024/7ml2_23906.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ml2_23906/12_2024/7ml2_23906.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.003 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: 8 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 17 6.06 5 P 112 5.49 5 Mg 1 5.21 5 S 359 5.16 5 C 40344 2.51 5 N 11343 2.21 5 O 12370 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 127 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 64550 Number of models: 1 Model: "" Number of chains: 55 Chain: "A" Number of atoms: 10997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1398, 10997 Classifications: {'peptide': 1398} Link IDs: {'PCIS': 2, 'PTRANS': 62, 'TRANS': 1333} Chain breaks: 5 Chain: "B" Number of atoms: 9178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1152, 9178 Classifications: {'peptide': 1152} Link IDs: {'PTRANS': 51, 'TRANS': 1100} Chain breaks: 7 Chain: "C" Number of atoms: 2061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2061 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 11, 'TRANS': 250} Chain: "D" Number of atoms: 1253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1253 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain breaks: 1 Chain: "E" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1744 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "F" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 670 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1340 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1089 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain breaks: 1 Chain: "I" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 944 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "J" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 904 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "L" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 358 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 2175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2175 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 10, 'TRANS': 268} Chain breaks: 2 Chain: "Q" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1144 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 141} Chain breaks: 3 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 9, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 77 Chain: "R" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1303 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 7, 'TRANS': 182} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 293 Unresolved non-hydrogen angles: 371 Unresolved non-hydrogen dihedrals: 253 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 6, 'TYR:plan': 6, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 158 Chain: "U" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 383 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "V" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 381 Classifications: {'peptide': 49} Link IDs: {'TRANS': 48} Chain breaks: 1 Chain: "W" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1469 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 8, 'TRANS': 182} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 58 Chain: "X" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 984 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 7, 'TRANS': 148} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 321 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 277 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 6, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 148 Chain: "T" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1140 Classifications: {'DNA': 56} Link IDs: {'rna3p': 55} Chain: "N" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1156 Classifications: {'DNA': 56} Link IDs: {'rna3p': 55} Chain: "O" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1416 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 171} Chain: "1" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 380 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 47} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "1" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Classifications: {'peptide': 4} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UNK:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "1" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 34 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'UNK:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "1" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Classifications: {'peptide': 3} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UNK:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "1" Number of atoms: 489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 489 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 61} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'PHE:plan': 1, 'UNK:plan-1': 17, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "1" Number of atoms: 247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 247 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 1, 'TRANS': 39} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'UNK:plan-1': 29} Unresolved non-hydrogen planarities: 29 Chain: "1" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 41 Classifications: {'peptide': 6} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UNK:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "1" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 57 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UNK:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "1" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 167 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 23} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 8 Chain: "1" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Classifications: {'peptide': 3} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'UNK:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "1" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 299 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'TRANS': 52} Chain breaks: 1 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'UNK:plan-1': 41} Unresolved non-hydrogen planarities: 41 Chain: "1" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 630 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 209 Unresolved non-hydrogen angles: 268 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 7, 'TYR:plan': 3, 'UNK:plan-1': 4, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 6, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 118 Chain: "4" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 506 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 3, 'TRANS': 69} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "4" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1535 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 8, 'TRANS': 202} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1, 'UNK:plan-1': 2, 'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 48 Chain: "0" Number of atoms: 6108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 754, 6108 Classifications: {'peptide': 754} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 721} Chain: "6" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2264 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 19, 'TRANS': 285} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 180 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'PHE:plan': 5, 'GLU:plan': 4, 'ARG:plan': 3, 'TYR:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 77 Chain: "6" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 263 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 1, 'TRANS': 44} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'TYR:plan': 1, 'UNK:plan-1': 13, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "2" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3011 Classifications: {'peptide': 460} Incomplete info: {'backbone_only': 154, 'truncation_to_alanine': 14} Link IDs: {'CIS': 2, 'PTRANS': 17, 'TRANS': 440} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 727 Unresolved non-hydrogen angles: 1042 Unresolved non-hydrogen dihedrals: 468 Unresolved non-hydrogen chiralities: 210 Planarities with less than four sites: {'GLN:plan1': 11, 'ARG:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 12, 'PHE:plan': 8, 'GLU:plan': 16, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 352 Chain: "5" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 498 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 62} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "7" Number of atoms: 4447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 4447 Classifications: {'peptide': 634} Incomplete info: {'backbone_only': 162} Link IDs: {'CIS': 3, 'PTRANS': 26, 'TRANS': 604} Chain breaks: 1 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 688 Unresolved non-hydrogen angles: 1003 Unresolved non-hydrogen dihedrals: 436 Unresolved non-hydrogen chiralities: 214 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 14, 'TYR:plan': 6, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 7, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 312 Chain: "3" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 860 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 5, 'TRANS': 132} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 298 Unresolved non-hydrogen angles: 379 Unresolved non-hydrogen dihedrals: 241 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 6, 'ASP:plan': 10, 'PHE:plan': 3, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 178 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: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "3" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 813 SG CYS A 107 122.059 124.501 105.380 1.00 0.00 S ATOM 837 SG CYS A 110 121.289 123.939 108.874 1.00 0.00 S ATOM 1142 SG CYS A 148 124.431 126.095 107.706 1.00 0.00 S ATOM 1211 SG CYS A 167 124.302 122.277 107.247 1.00 0.00 S ATOM 508 SG CYS A 67 75.978 115.902 117.892 1.00 0.00 S ATOM 530 SG CYS A 70 77.231 117.154 120.968 1.00 0.00 S ATOM 583 SG CYS A 77 76.123 119.327 118.298 1.00 0.00 S ATOM 19693 SG CYS B1163 90.890 119.885 128.378 1.00 0.00 S ATOM 19711 SG CYS B1166 91.714 120.783 124.826 1.00 0.00 S ATOM 19836 SG CYS B1182 89.687 117.752 125.757 1.00 0.00 S ATOM 19855 SG CYS B1185 93.692 118.144 126.316 1.00 0.00 S ATOM 20822 SG CYS C 86 18.150 152.828 118.268 1.00 0.00 S ATOM 20839 SG CYS C 88 18.654 149.388 117.129 1.00 0.00 S ATOM 20872 SG CYS C 92 15.538 150.822 115.979 1.00 0.00 S ATOM 20895 SG CYS C 95 18.637 152.335 114.584 1.00 0.00 S ATOM 28385 SG CYS I 7 123.466 165.267 52.323 1.00 0.00 S ATOM 28410 SG CYS I 10 123.232 161.242 51.918 1.00 0.00 S ATOM 28576 SG CYS I 29 123.730 163.268 55.403 1.00 0.00 S ATOM 28600 SG CYS I 32 126.120 162.788 52.749 1.00 0.00 S ATOM 28927 SG CYS I 75 97.367 200.660 61.064 1.00 0.00 S ATOM 28949 SG CYS I 78 96.268 200.993 57.524 1.00 0.00 S ATOM 29165 SG CYS I 103 93.949 198.720 60.513 1.00 0.00 S ATOM 29185 SG CYS I 106 96.776 198.175 58.277 1.00 0.00 S ATOM 29330 SG CYS J 7 36.792 173.563 99.743 1.00 0.00 S ATOM 29353 SG CYS J 10 34.115 175.323 100.761 1.00 0.00 S ATOM 29633 SG CYS J 45 36.772 177.259 101.193 1.00 0.00 S ATOM 29639 SG CYS J 46 33.952 176.214 98.606 1.00 0.00 S ATOM 30762 SG CYS L 31 35.704 135.431 78.824 1.00 30.00 S ATOM 30886 SG CYS L 48 37.819 133.570 76.699 1.00 0.00 S ATOM 30909 SG CYS L 51 36.766 135.872 74.386 1.00 0.00 S ATOM 31137 SG CYS M 24 52.433 118.673 127.968 1.00 0.00 S ATOM 31159 SG CYS M 27 48.686 118.747 128.239 1.00 0.00 S ATOM 31303 SG CYS M 45 50.592 120.959 125.807 1.00 0.00 S ATOM 31322 SG CYS M 48 50.660 122.306 128.546 1.00 0.00 S ATOM 37357 SG CYS W 124 74.395 97.478 121.256 1.00 0.00 S ATOM 37378 SG CYS W 127 75.138 100.841 119.576 1.00 0.00 S ATOM 37563 SG CYS W 149 75.179 100.680 123.477 1.00 0.00 S ATOM 37583 SG CYS W 152 72.048 99.976 121.742 1.00 0.00 S ATOM 46868 SG CYS 4 289 190.753 18.603 55.216 1.00 0.00 S ATOM 46887 SG CYS 4 292 193.909 18.618 57.249 1.00 0.00 S ATOM 46972 SG CYS 4 305 192.390 15.613 55.246 1.00 0.00 S ATOM 46988 SG CYS 4 308 191.662 16.602 58.915 1.00 0.00 S ATOM 48011 SG CYS 0 115 134.292 25.463 94.916 1.00117.61 S ATOM 48011 SG CYS 0 115 134.292 25.463 94.916 1.00117.61 S ATOM 48338 SG CYS 0 156 131.006 21.972 96.575 1.00 90.79 S ATOM 48153 SG CYS 0 133 131.777 23.222 99.607 1.00 46.59 S ATOM 55394 SG CYS 6 403 212.756 38.460 73.366 1.00 0.00 S ATOM 55416 SG CYS 6 406 213.662 41.837 71.720 1.00 0.00 S ATOM 55584 SG CYS 6 437 210.835 41.671 74.087 1.00 0.00 S ATOM 55600 SG CYS 6 440 210.622 40.149 70.598 1.00 0.00 S ATOM 55542 SG CYS 6 429 205.361 29.008 73.374 1.00 0.00 S ATOM 55558 SG CYS 6 432 209.142 29.059 73.047 1.00 0.00 S ATOM 55678 SG CYS 6 451 206.915 30.536 70.480 1.00 0.00 S ATOM 55693 SG CYS 6 454 206.890 26.777 70.639 1.00 0.00 S ATOM 55039 SG CYS 6 349 186.649 30.670 38.115 1.00 0.00 S ATOM 55060 SG CYS 6 352 185.847 32.236 34.464 1.00 0.00 S ATOM 55129 SG CYS 6 363 184.438 32.779 36.887 1.00 0.00 S ATOM 55147 SG CYS 6 366 183.827 29.064 36.605 1.00 0.00 S ATOM 54956 SG CYS 6 336 186.173 42.867 34.447 1.00 30.00 S ATOM 54967 SG CYS 6 338 185.515 41.644 37.609 1.00 30.00 S ATOM 55094 SG CYS 6 357 188.568 44.052 36.919 1.00 30.00 S ATOM 63695 SG CYS 3 13 103.586 65.744 116.387 1.00 0.00 S ATOM 63889 SG CYS 3 39 105.093 67.890 116.656 1.00 0.00 S ATOM 63842 SG CYS 3 34 103.134 57.944 123.080 1.00 0.00 S Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" P DT T 109 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT T 109 " occ=0.00 residue: pdb=" P DT T 111 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT T 111 " occ=0.00 residue: pdb=" P DT T 113 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT T 113 " occ=0.00 residue: pdb=" P DT T 115 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT T 115 " occ=0.00 residue: pdb=" P DA N 51 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA N 51 " occ=0.00 residue: pdb=" P DA N 53 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA N 53 " occ=0.00 residue: pdb=" P DA N 55 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA N 55 " occ=0.00 residue: pdb=" P DA N 57 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA N 57 " occ=0.00 Time building chain proxies: 26.06, per 1000 atoms: 0.40 Number of scatterers: 64550 At special positions: 0 Unit cell: (254.4, 230.02, 184.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 17 29.99 Fe 4 26.01 S 359 16.00 P 112 15.00 Mg 1 11.99 O 12370 8.00 N 11343 7.00 C 40344 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " UNK 1 219 " - " ARG 1 218 " " UNK 1 223 " - " LEU 1 222 " " UNK 1 228 " - " LYS 1 227 " " UNK 1 231 " - " PRO 1 230 " " UNK 1 297 " - " LEU 1 296 " " UNK 1 338 " - " ILE 1 337 " " UNK 1 344 " - " ILE 1 343 " " UNK 1 352 " - " GLY 1 351 " " UNK 1 388 " - " MET 1 387 " " UNK 1 391 " - " LYS 1 390 " " UNK 1 515 " - " ALA 1 514 " " UNK 6 412 " - " PRO 6 411 " Time building additional restraints: 13.46 Conformation dependent library (CDL) restraints added in 6.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 0 801 " pdb="FE3 SF4 0 801 " - pdb=" SG CYS 0 133 " pdb="FE2 SF4 0 801 " - pdb=" SG CYS 0 156 " pdb="FE1 SF4 0 801 " - pdb=" SG CYS 0 115 " Number of angles added : 9 Zn2+ tetrahedral coordination pdb=" ZN 3 401 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 39 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 13 " pdb=" ZN 3 402 " pdb="ZN ZN 3 402 " - pdb=" ND1 HIS 3 36 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 34 " pdb=" ZN 4 401 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 292 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 305 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 289 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 308 " pdb=" ZN 6 501 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 406 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 437 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 440 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 403 " pdb=" ZN 6 502 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 451 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 429 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 432 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 454 " pdb=" ZN 6 503 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 349 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 363 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 352 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 366 " pdb=" ZN 6 504 " pdb="ZN ZN 6 504 " - pdb=" ND1 HIS 6 339 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 336 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 357 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 338 " pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 148 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 45 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 24 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 27 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 48 " pdb=" ZN W 501 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 152 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 124 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 149 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 127 " Number of angles added : 78 15864 Ramachandran restraints generated. 7932 Oldfield, 0 Emsley, 7932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14958 Finding SS restraints... Secondary structure from input PDB file: 314 helices and 76 sheets defined 44.9% alpha, 13.1% beta 46 base pairs and 84 stacking pairs defined. Time for finding SS restraints: 18.86 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 95 through 104 removed outlier: 4.143A pdb=" N GLU A 104 " --> pdb=" O LYS A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 removed outlier: 3.793A pdb=" N ARG A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 144 removed outlier: 4.071A pdb=" N ARG A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 135 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N THR A 144 " --> pdb=" O THR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 213 removed outlier: 3.563A pdb=" N ILE A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N HIS A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 224 Processing helix chain 'A' and resid 230 through 233 Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 260 through 282 removed outlier: 3.654A pdb=" N PHE A 264 " --> pdb=" O ASP A 260 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 305 removed outlier: 3.951A pdb=" N GLU A 293 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 removed outlier: 3.560A pdb=" N LEU A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 384 through 394 removed outlier: 3.584A pdb=" N ARG A 393 " --> pdb=" O THR A 389 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN A 394 " --> pdb=" O GLN A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 471 through 475 removed outlier: 3.622A pdb=" N VAL A 474 " --> pdb=" O ASN A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 507 through 510 Processing helix chain 'A' and resid 525 through 535 removed outlier: 3.734A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.584A pdb=" N ASN A 548 " --> pdb=" O ASP A 544 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.691A pdb=" N ILE A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 661 removed outlier: 3.581A pdb=" N VAL A 632 " --> pdb=" O GLY A 628 " (cutoff:3.500A) Proline residue: A 639 - end of helix removed outlier: 3.840A pdb=" N CYS A 642 " --> pdb=" O GLY A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 672 through 699 removed outlier: 3.753A pdb=" N VAL A 693 " --> pdb=" O LYS A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 737 removed outlier: 3.640A pdb=" N PHE A 721 " --> pdb=" O ASN A 717 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU A 732 " --> pdb=" O LYS A 728 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 737 " --> pdb=" O ALA A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 749 Processing helix chain 'A' and resid 754 through 762 removed outlier: 3.700A pdb=" N ILE A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 807 removed outlier: 3.669A pdb=" N GLY A 807 " --> pdb=" O TYR A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 845 removed outlier: 3.505A pdb=" N GLY A 819 " --> pdb=" O PHE A 815 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 824 " --> pdb=" O GLY A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 909 through 914 removed outlier: 3.531A pdb=" N LEU A 912 " --> pdb=" O ASP A 909 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N GLU A 914 " --> pdb=" O SER A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 920 Processing helix chain 'A' and resid 923 through 947 removed outlier: 3.533A pdb=" N VAL A 927 " --> pdb=" O LEU A 923 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU A 928 " --> pdb=" O LYS A 924 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A 942 " --> pdb=" O LYS A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 972 removed outlier: 3.764A pdb=" N ILE A 963 " --> pdb=" O ASN A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 995 removed outlier: 3.594A pdb=" N LEU A 988 " --> pdb=" O LYS A 984 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY A 989 " --> pdb=" O ASP A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1015 Processing helix chain 'A' and resid 1015 through 1026 Processing helix chain 'A' and resid 1027 through 1034 Processing helix chain 'A' and resid 1038 through 1057 Processing helix chain 'A' and resid 1063 through 1074 removed outlier: 3.777A pdb=" N ILE A1072 " --> pdb=" O ALA A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1106 Processing helix chain 'A' and resid 1127 through 1139 removed outlier: 3.756A pdb=" N ALA A1137 " --> pdb=" O LEU A1133 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU A1139 " --> pdb=" O ARG A1135 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1175 Processing helix chain 'A' and resid 1198 through 1205 Processing helix chain 'A' and resid 1208 through 1220 removed outlier: 3.622A pdb=" N VAL A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1256 through 1271 removed outlier: 3.795A pdb=" N ILE A1271 " --> pdb=" O MET A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1318 removed outlier: 3.678A pdb=" N THR A1318 " --> pdb=" O SER A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1360 removed outlier: 4.465A pdb=" N ILE A1335 " --> pdb=" O SER A1331 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ILE A1341 " --> pdb=" O GLU A1337 " (cutoff:3.500A) removed outlier: 9.425A pdb=" N GLU A1342 " --> pdb=" O VAL A1338 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA A1343 " --> pdb=" O LEU A1339 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL A1355 " --> pdb=" O GLU A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1376 removed outlier: 4.010A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR A1376 " --> pdb=" O VAL A1372 " (cutoff:3.500A) Processing helix chain 'A' and resid 1385 through 1390 removed outlier: 3.534A pdb=" N PHE A1389 " --> pdb=" O THR A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1403 removed outlier: 3.555A pdb=" N PHE A1402 " --> pdb=" O MET A1398 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLU A1403 " --> pdb=" O ARG A1399 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1415 removed outlier: 3.514A pdb=" N ILE A1408 " --> pdb=" O GLU A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1423 through 1431 Processing helix chain 'A' and resid 1436 through 1440 Processing helix chain 'A' and resid 1447 through 1452 removed outlier: 3.654A pdb=" N VAL A1451 " --> pdb=" O GLU A1448 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 41 removed outlier: 4.079A pdb=" N SER B 30 " --> pdb=" O THR B 26 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TRP B 31 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 57 removed outlier: 3.686A pdb=" N PHE B 54 " --> pdb=" O SER B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 66 removed outlier: 4.362A pdb=" N ASP B 66 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 179 through 183 removed outlier: 3.926A pdb=" N GLU B 183 " --> pdb=" O TYR B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 289 Processing helix chain 'B' and resid 293 through 302 removed outlier: 3.515A pdb=" N HIS B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE B 301 " --> pdb=" O ILE B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 323 Proline residue: B 316 - end of helix removed outlier: 3.562A pdb=" N GLU B 319 " --> pdb=" O LYS B 315 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY B 321 " --> pdb=" O CYS B 317 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL B 323 " --> pdb=" O GLU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 336 Processing helix chain 'B' and resid 344 through 359 removed outlier: 4.418A pdb=" N GLN B 350 " --> pdb=" O GLU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 390 removed outlier: 3.743A pdb=" N ASN B 383 " --> pdb=" O GLY B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 438 removed outlier: 3.565A pdb=" N ASP B 427 " --> pdb=" O LYS B 423 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B 429 " --> pdb=" O THR B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 450 through 463 removed outlier: 3.586A pdb=" N THR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY B 456 " --> pdb=" O THR B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.542A pdb=" N LEU B 495 " --> pdb=" O THR B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 560 Processing helix chain 'B' and resid 570 through 574 Processing helix chain 'B' and resid 592 through 606 removed outlier: 3.918A pdb=" N LEU B 596 " --> pdb=" O ASN B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 666 Processing helix chain 'B' and resid 680 through 687 removed outlier: 3.529A pdb=" N LEU B 684 " --> pdb=" O THR B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 695 through 699 removed outlier: 3.583A pdb=" N GLU B 699 " --> pdb=" O ALA B 695 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 695 through 699' Processing helix chain 'B' and resid 706 through 711 Processing helix chain 'B' and resid 744 through 748 Processing helix chain 'B' and resid 752 through 756 Processing helix chain 'B' and resid 763 through 775 removed outlier: 3.832A pdb=" N ASN B 767 " --> pdb=" O GLN B 763 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 788 removed outlier: 4.504A pdb=" N ASN B 786 " --> pdb=" O THR B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 817 Processing helix chain 'B' and resid 843 through 848 removed outlier: 3.643A pdb=" N ASP B 847 " --> pdb=" O GLN B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 924 removed outlier: 3.895A pdb=" N GLU B 923 " --> pdb=" O SER B 919 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU B 924 " --> pdb=" O PRO B 920 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 919 through 924' Processing helix chain 'B' and resid 927 through 932 removed outlier: 4.446A pdb=" N TYR B 931 " --> pdb=" O GLN B 927 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS B 932 " --> pdb=" O ARG B 928 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 927 through 932' Processing helix chain 'B' and resid 995 through 999 Processing helix chain 'B' and resid 1013 through 1021 Proline residue: B1018 - end of helix Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.529A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1062 removed outlier: 3.765A pdb=" N ILE B1055 " --> pdb=" O THR B1051 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B1058 " --> pdb=" O GLY B1054 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS B1062 " --> pdb=" O LEU B1058 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1131 through 1141 removed outlier: 3.762A pdb=" N ARG B1135 " --> pdb=" O GLY B1131 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP B1136 " --> pdb=" O GLU B1132 " (cutoff:3.500A) Processing helix chain 'B' and resid 1143 through 1153 removed outlier: 3.512A pdb=" N GLU B1149 " --> pdb=" O SER B1145 " (cutoff:3.500A) Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 through 69 removed outlier: 3.741A pdb=" N LEU C 69 " --> pdb=" O HIS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 204 through 209 removed outlier: 3.733A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 263 removed outlier: 3.864A pdb=" N SER C 257 " --> pdb=" O LYS C 253 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE C 258 " --> pdb=" O LYS C 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 34 Processing helix chain 'D' and resid 53 through 74 removed outlier: 3.898A pdb=" N ILE D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS D 60 " --> pdb=" O ARG D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 134 removed outlier: 3.893A pdb=" N GLU D 131 " --> pdb=" O ASP D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 152 removed outlier: 3.562A pdb=" N LYS D 142 " --> pdb=" O ASN D 138 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN D 150 " --> pdb=" O GLN D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 169 removed outlier: 3.811A pdb=" N VAL D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 182 Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 196 through 199 Processing helix chain 'D' and resid 203 through 218 removed outlier: 3.530A pdb=" N LEU D 207 " --> pdb=" O SER D 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 27 removed outlier: 3.517A pdb=" N SER E 10 " --> pdb=" O GLU E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 47 removed outlier: 3.512A pdb=" N PHE E 42 " --> pdb=" O PRO E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 104 removed outlier: 3.503A pdb=" N PHE E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 124 removed outlier: 3.830A pdb=" N MET E 121 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS E 122 " --> pdb=" O PRO E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 142 removed outlier: 3.666A pdb=" N VAL E 142 " --> pdb=" O ALA E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 169 removed outlier: 3.589A pdb=" N LEU E 165 " --> pdb=" O LYS E 161 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS E 166 " --> pdb=" O ARG E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.532A pdb=" N GLN E 174 " --> pdb=" O LYS E 171 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 171 through 175' Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 86 through 102 removed outlier: 4.107A pdb=" N ALA F 98 " --> pdb=" O LEU F 94 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU F 99 " --> pdb=" O GLY F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'F' and resid 149 through 151 No H-bonds generated for 'chain 'F' and resid 149 through 151' Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 19 through 20 No H-bonds generated for 'chain 'G' and resid 19 through 20' Processing helix chain 'G' and resid 21 through 32 Processing helix chain 'H' and resid 129 through 133 Processing helix chain 'J' and resid 16 through 29 removed outlier: 4.056A pdb=" N SER J 20 " --> pdb=" O ASP J 16 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU J 25 " --> pdb=" O TYR J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 45 through 50 removed outlier: 3.530A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 51 through 53 No H-bonds generated for 'chain 'J' and resid 51 through 53' Processing helix chain 'J' and resid 59 through 63 Processing helix chain 'K' and resid 6 through 10 Processing helix chain 'K' and resid 39 through 51 removed outlier: 3.669A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 85 No H-bonds generated for 'chain 'K' and resid 83 through 85' Processing helix chain 'K' and resid 86 through 102 removed outlier: 4.005A pdb=" N SER K 93 " --> pdb=" O ASN K 89 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE K 95 " --> pdb=" O CYS K 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 110 removed outlier: 4.527A pdb=" N GLU K 108 " --> pdb=" O ASN K 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 66 removed outlier: 4.378A pdb=" N THR M 65 " --> pdb=" O GLU M 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 113 Processing helix chain 'M' and resid 114 through 116 No H-bonds generated for 'chain 'M' and resid 114 through 116' Processing helix chain 'M' and resid 122 through 140 removed outlier: 4.005A pdb=" N ALA M 129 " --> pdb=" O GLU M 125 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE M 130 " --> pdb=" O VAL M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 143 through 157 removed outlier: 3.776A pdb=" N LYS M 147 " --> pdb=" O PRO M 143 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TYR M 154 " --> pdb=" O ALA M 150 " (cutoff:3.500A) Processing helix chain 'M' and resid 169 through 183 removed outlier: 4.010A pdb=" N GLY M 179 " --> pdb=" O SER M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 188 through 194 removed outlier: 3.658A pdb=" N ILE M 192 " --> pdb=" O THR M 188 " (cutoff:3.500A) Processing helix chain 'M' and resid 200 through 218 Processing helix chain 'M' and resid 237 through 246 removed outlier: 4.456A pdb=" N ARG M 241 " --> pdb=" O THR M 237 " (cutoff:3.500A) Processing helix chain 'M' and resid 249 through 267 removed outlier: 4.023A pdb=" N THR M 253 " --> pdb=" O PRO M 249 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS M 264 " --> pdb=" O ALA M 260 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU M 265 " --> pdb=" O LYS M 261 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE M 266 " --> pdb=" O LYS M 262 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS M 267 " --> pdb=" O CYS M 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 274 through 288 Processing helix chain 'M' and resid 294 through 303 Processing helix chain 'M' and resid 305 through 320 removed outlier: 4.222A pdb=" N ILE M 309 " --> pdb=" O THR M 305 " (cutoff:3.500A) Processing helix chain 'Q' and resid 27 through 35 Processing helix chain 'Q' and resid 107 through 114 removed outlier: 4.350A pdb=" N LEU Q 111 " --> pdb=" O PRO Q 107 " (cutoff:3.500A) Processing helix chain 'Q' and resid 129 through 134 removed outlier: 3.942A pdb=" N HIS Q 134 " --> pdb=" O VAL Q 130 " (cutoff:3.500A) Processing helix chain 'Q' and resid 337 through 346 Processing helix chain 'Q' and resid 409 through 414 removed outlier: 3.626A pdb=" N ASP Q 414 " --> pdb=" O GLU Q 410 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 80 Processing helix chain 'R' and resid 234 through 245 Processing helix chain 'R' and resid 258 through 266 removed outlier: 3.543A pdb=" N THR R 262 " --> pdb=" O THR R 258 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N HIS R 265 " --> pdb=" O VAL R 261 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N THR R 266 " --> pdb=" O THR R 262 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 310 Processing helix chain 'R' and resid 314 through 323 Processing helix chain 'R' and resid 325 through 337 removed outlier: 3.683A pdb=" N LYS R 335 " --> pdb=" O GLU R 331 " (cutoff:3.500A) Processing helix chain 'W' and resid 5 through 20 Processing helix chain 'W' and resid 22 through 35 removed outlier: 3.553A pdb=" N VAL W 26 " --> pdb=" O GLY W 22 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N HIS W 35 " --> pdb=" O ALA W 31 " (cutoff:3.500A) Processing helix chain 'W' and resid 39 through 48 Processing helix chain 'W' and resid 50 through 53 Processing helix chain 'W' and resid 54 through 64 Processing helix chain 'W' and resid 90 through 114 removed outlier: 3.528A pdb=" N ASP W 114 " --> pdb=" O LYS W 110 " (cutoff:3.500A) Processing helix chain 'W' and resid 133 through 138 Processing helix chain 'W' and resid 162 through 190 Proline residue: W 181 - end of helix Processing helix chain 'X' and resid 124 through 139 removed outlier: 3.851A pdb=" N LEU X 128 " --> pdb=" O ASP X 124 " (cutoff:3.500A) Processing helix chain 'X' and resid 143 through 152 removed outlier: 3.799A pdb=" N LEU X 151 " --> pdb=" O LEU X 147 " (cutoff:3.500A) Processing helix chain 'X' and resid 156 through 166 removed outlier: 3.833A pdb=" N ILE X 160 " --> pdb=" O ASP X 156 " (cutoff:3.500A) Processing helix chain 'X' and resid 188 through 199 Processing helix chain 'X' and resid 207 through 212 Processing helix chain 'X' and resid 216 through 224 Processing helix chain 'X' and resid 256 through 265 Processing helix chain 'X' and resid 272 through 282 Processing helix chain 'O' and resid 81 through 89 Processing helix chain 'O' and resid 128 through 147 removed outlier: 3.522A pdb=" N ILE O 146 " --> pdb=" O ILE O 142 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY O 147 " --> pdb=" O ILE O 143 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 179 Processing helix chain 'O' and resid 219 through 238 Proline residue: O 232 - end of helix Processing helix chain '1' and resid 170 through 176 Processing helix chain '1' and resid 177 through 188 removed outlier: 3.698A pdb=" N LEU 1 184 " --> pdb=" O LEU 1 180 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN 1 188 " --> pdb=" O LEU 1 184 " (cutoff:3.500A) Processing helix chain '1' and resid 188 through 197 Processing helix chain '1' and resid 205 through 213 Processing helix chain '1' and resid 213 through 225 Processing helix chain '1' and resid 230 through 237 No H-bonds generated for 'chain '1' and resid 230 through 237' Processing helix chain '1' and resid 251 through 263 removed outlier: 3.605A pdb=" N GLU 1 261 " --> pdb=" O LEU 1 257 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN 1 262 " --> pdb=" O ASN 1 258 " (cutoff:3.500A) Processing helix chain '1' and resid 263 through 273 removed outlier: 4.073A pdb=" N LYS 1 267 " --> pdb=" O TYR 1 263 " (cutoff:3.500A) Processing helix chain '1' and resid 279 through 292 removed outlier: 3.790A pdb=" N SER 1 289 " --> pdb=" O ALA 1 285 " (cutoff:3.500A) Processing helix chain '1' and resid 308 through 328 removed outlier: 4.028A pdb=" N UNK 1 320 " --> pdb=" O UNK 1 316 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N UNK 1 328 " --> pdb=" O LYS 1 324 " (cutoff:3.500A) Processing helix chain '1' and resid 371 through 388 Processing helix chain '1' and resid 467 through 483 removed outlier: 3.517A pdb=" N UNK 1 477 " --> pdb=" O UNK 1 473 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N UNK 1 478 " --> pdb=" O UNK 1 474 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N UNK 1 480 " --> pdb=" O UNK 1 476 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N UNK 1 481 " --> pdb=" O UNK 1 477 " (cutoff:3.500A) Processing helix chain '1' and resid 496 through 516 Processing helix chain '1' and resid 540 through 565 removed outlier: 3.639A pdb=" N LEU 1 561 " --> pdb=" O CYS 1 557 " (cutoff:3.500A) Processing helix chain '1' and resid 575 through 604 Processing helix chain '1' and resid 606 through 616 Processing helix chain '1' and resid 616 through 639 Processing helix chain '4' and resid 35 through 43 Processing helix chain '4' and resid 49 through 68 removed outlier: 4.250A pdb=" N VAL 4 53 " --> pdb=" O SER 4 49 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN 4 68 " --> pdb=" O HIS 4 64 " (cutoff:3.500A) Processing helix chain '4' and resid 116 through 135 Processing helix chain '4' and resid 137 through 143 removed outlier: 3.556A pdb=" N ASN 4 143 " --> pdb=" O GLN 4 139 " (cutoff:3.500A) Processing helix chain '4' and resid 148 through 167 Processing helix chain '4' and resid 192 through 206 removed outlier: 3.827A pdb=" N ILE 4 196 " --> pdb=" O GLN 4 192 " (cutoff:3.500A) Processing helix chain '4' and resid 221 through 231 Processing helix chain '4' and resid 244 through 252 Processing helix chain '4' and resid 313 through 321 Processing helix chain '0' and resid 18 through 34 removed outlier: 3.954A pdb=" N VAL 0 34 " --> pdb=" O LYS 0 30 " (cutoff:3.500A) Processing helix chain '0' and resid 47 through 63 removed outlier: 3.773A pdb=" N LEU 0 55 " --> pdb=" O SER 0 51 " (cutoff:3.500A) Processing helix chain '0' and resid 75 through 98 Processing helix chain '0' and resid 117 through 123 removed outlier: 3.773A pdb=" N GLU 0 123 " --> pdb=" O GLU 0 119 " (cutoff:3.500A) Processing helix chain '0' and resid 125 through 137 removed outlier: 3.834A pdb=" N VAL 0 129 " --> pdb=" O LYS 0 125 " (cutoff:3.500A) Processing helix chain '0' and resid 140 through 147 Processing helix chain '0' and resid 157 through 166 Processing helix chain '0' and resid 177 through 188 removed outlier: 3.706A pdb=" N LYS 0 183 " --> pdb=" O GLU 0 179 " (cutoff:3.500A) Processing helix chain '0' and resid 191 through 199 removed outlier: 3.687A pdb=" N ARG 0 198 " --> pdb=" O PHE 0 194 " (cutoff:3.500A) Processing helix chain '0' and resid 209 through 215 removed outlier: 3.728A pdb=" N LEU 0 213 " --> pdb=" O SER 0 209 " (cutoff:3.500A) Processing helix chain '0' and resid 223 through 228 Processing helix chain '0' and resid 239 through 249 removed outlier: 3.759A pdb=" N VAL 0 243 " --> pdb=" O ASN 0 239 " (cutoff:3.500A) Processing helix chain '0' and resid 253 through 279 removed outlier: 3.699A pdb=" N SER 0 272 " --> pdb=" O ASP 0 268 " (cutoff:3.500A) Processing helix chain '0' and resid 279 through 291 Processing helix chain '0' and resid 322 through 326 removed outlier: 3.853A pdb=" N ARG 0 326 " --> pdb=" O GLY 0 323 " (cutoff:3.500A) Processing helix chain '0' and resid 327 through 347 removed outlier: 4.502A pdb=" N GLU 0 340 " --> pdb=" O LYS 0 336 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR 0 341 " --> pdb=" O ARG 0 337 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU 0 342 " --> pdb=" O LEU 0 338 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS 0 343 " --> pdb=" O ILE 0 339 " (cutoff:3.500A) Processing helix chain '0' and resid 355 through 367 Processing helix chain '0' and resid 370 through 376 removed outlier: 3.697A pdb=" N PHE 0 376 " --> pdb=" O LYS 0 372 " (cutoff:3.500A) Processing helix chain '0' and resid 376 through 389 Processing helix chain '0' and resid 393 through 395 No H-bonds generated for 'chain '0' and resid 393 through 395' Processing helix chain '0' and resid 396 through 412 removed outlier: 3.633A pdb=" N ILE 0 402 " --> pdb=" O ALA 0 398 " (cutoff:3.500A) Processing helix chain '0' and resid 424 through 428 removed outlier: 3.663A pdb=" N ALA 0 428 " --> pdb=" O ILE 0 425 " (cutoff:3.500A) Processing helix chain '0' and resid 442 through 453 removed outlier: 3.632A pdb=" N ILE 0 446 " --> pdb=" O ALA 0 442 " (cutoff:3.500A) Proline residue: 0 448 - end of helix Processing helix chain '0' and resid 467 through 474 Processing helix chain '0' and resid 515 through 533 Processing helix chain '0' and resid 543 through 557 Processing helix chain '0' and resid 558 through 567 removed outlier: 3.679A pdb=" N GLU 0 562 " --> pdb=" O GLY 0 558 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL 0 563 " --> pdb=" O ILE 0 559 " (cutoff:3.500A) Processing helix chain '0' and resid 575 through 592 removed outlier: 3.680A pdb=" N THR 0 585 " --> pdb=" O LEU 0 581 " (cutoff:3.500A) Processing helix chain '0' and resid 605 through 610 removed outlier: 4.115A pdb=" N GLY 0 609 " --> pdb=" O LYS 0 605 " (cutoff:3.500A) Processing helix chain '0' and resid 633 through 645 Processing helix chain '0' and resid 649 through 667 removed outlier: 3.717A pdb=" N GLY 0 667 " --> pdb=" O ALA 0 663 " (cutoff:3.500A) Processing helix chain '0' and resid 668 through 670 No H-bonds generated for 'chain '0' and resid 668 through 670' Processing helix chain '0' and resid 683 through 688 Processing helix chain '0' and resid 694 through 701 removed outlier: 3.733A pdb=" N GLY 0 700 " --> pdb=" O TRP 0 696 " (cutoff:3.500A) Processing helix chain '0' and resid 702 through 706 Processing helix chain '0' and resid 709 through 726 removed outlier: 3.585A pdb=" N ALA 0 713 " --> pdb=" O SER 0 709 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER 0 715 " --> pdb=" O ASP 0 711 " (cutoff:3.500A) Processing helix chain '0' and resid 733 through 738 Processing helix chain '0' and resid 747 through 752 Processing helix chain '6' and resid 133 through 138 Processing helix chain '6' and resid 144 through 164 removed outlier: 3.542A pdb=" N MET 6 148 " --> pdb=" O ASN 6 144 " (cutoff:3.500A) Processing helix chain '6' and resid 188 through 202 removed outlier: 3.862A pdb=" N HIS 6 192 " --> pdb=" O ASN 6 188 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE 6 199 " --> pdb=" O ALA 6 195 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG 6 200 " --> pdb=" O LEU 6 196 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS 6 201 " --> pdb=" O LYS 6 197 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN 6 202 " --> pdb=" O SER 6 198 " (cutoff:3.500A) Processing helix chain '6' and resid 209 through 221 removed outlier: 3.613A pdb=" N GLY 6 219 " --> pdb=" O GLU 6 215 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU 6 221 " --> pdb=" O ALA 6 217 " (cutoff:3.500A) Processing helix chain '6' and resid 247 through 257 Processing helix chain '6' and resid 270 through 281 Processing helix chain '6' and resid 293 through 303 Processing helix chain '6' and resid 373 through 384 removed outlier: 4.189A pdb=" N ALA 6 377 " --> pdb=" O SER 6 373 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG 6 378 " --> pdb=" O THR 6 374 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER 6 379 " --> pdb=" O HIS 6 375 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS 6 381 " --> pdb=" O ALA 6 377 " (cutoff:3.500A) Processing helix chain '6' and resid 418 through 423 removed outlier: 4.585A pdb=" N UNK 6 423 " --> pdb=" O UNK 6 419 " (cutoff:3.500A) Processing helix chain '6' and resid 437 through 445 Processing helix chain '6' and resid 451 through 456 Processing helix chain '2' and resid 10 through 17 Processing helix chain '2' and resid 18 through 26 Processing helix chain '2' and resid 28 through 36 removed outlier: 3.635A pdb=" N TYR 2 36 " --> pdb=" O CYS 2 32 " (cutoff:3.500A) Processing helix chain '2' and resid 40 through 53 removed outlier: 3.740A pdb=" N ALA 2 49 " --> pdb=" O PHE 2 45 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N MET 2 50 " --> pdb=" O PHE 2 46 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE 2 52 " --> pdb=" O MET 2 48 " (cutoff:3.500A) Processing helix chain '2' and resid 59 through 66 removed outlier: 3.562A pdb=" N VAL 2 66 " --> pdb=" O LEU 2 62 " (cutoff:3.500A) Processing helix chain '2' and resid 70 through 84 removed outlier: 3.606A pdb=" N LEU 2 84 " --> pdb=" O SER 2 80 " (cutoff:3.500A) Processing helix chain '2' and resid 101 through 113 removed outlier: 3.589A pdb=" N LYS 2 105 " --> pdb=" O ASN 2 101 " (cutoff:3.500A) Processing helix chain '2' and resid 119 through 123 removed outlier: 4.428A pdb=" N VAL 2 123 " --> pdb=" O SER 2 120 " (cutoff:3.500A) Processing helix chain '2' and resid 135 through 152 removed outlier: 3.800A pdb=" N SER 2 139 " --> pdb=" O LEU 2 135 " (cutoff:3.500A) Processing helix chain '2' and resid 160 through 170 Processing helix chain '2' and resid 185 through 192 Processing helix chain '2' and resid 196 through 211 removed outlier: 3.582A pdb=" N LEU 2 204 " --> pdb=" O LEU 2 200 " (cutoff:3.500A) Processing helix chain '2' and resid 217 through 231 removed outlier: 3.785A pdb=" N LEU 2 231 " --> pdb=" O MET 2 227 " (cutoff:3.500A) Processing helix chain '2' and resid 243 through 256 Processing helix chain '2' and resid 272 through 281 removed outlier: 4.105A pdb=" N LEU 2 276 " --> pdb=" O THR 2 272 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N THR 2 279 " --> pdb=" O ALA 2 275 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP 2 281 " --> pdb=" O MET 2 277 " (cutoff:3.500A) Processing helix chain '2' and resid 353 through 362 Processing helix chain '2' and resid 379 through 388 removed outlier: 4.207A pdb=" N ALA 2 386 " --> pdb=" O SER 2 382 " (cutoff:3.500A) Processing helix chain '2' and resid 394 through 403 removed outlier: 3.821A pdb=" N ALA 2 398 " --> pdb=" O ASP 2 394 " (cutoff:3.500A) Processing helix chain '2' and resid 404 through 417 removed outlier: 6.678A pdb=" N ARG 2 410 " --> pdb=" O PRO 2 406 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N LEU 2 411 " --> pdb=" O GLN 2 407 " (cutoff:3.500A) Processing helix chain '2' and resid 421 through 426 removed outlier: 3.841A pdb=" N ASN 2 425 " --> pdb=" O GLU 2 421 " (cutoff:3.500A) Processing helix chain '2' and resid 434 through 448 removed outlier: 4.451A pdb=" N VAL 2 438 " --> pdb=" O PRO 2 434 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN 2 440 " --> pdb=" O THR 2 436 " (cutoff:3.500A) Processing helix chain '2' and resid 464 through 479 Processing helix chain '2' and resid 495 through 507 removed outlier: 3.541A pdb=" N GLN 2 500 " --> pdb=" O GLU 2 496 " (cutoff:3.500A) Processing helix chain '5' and resid 13 through 27 Processing helix chain '5' and resid 43 through 62 removed outlier: 3.702A pdb=" N VAL 5 47 " --> pdb=" O ASN 5 43 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLU 5 48 " --> pdb=" O PRO 5 44 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N PHE 5 49 " --> pdb=" O SER 5 45 " (cutoff:3.500A) Processing helix chain '7' and resid 104 through 109 removed outlier: 4.100A pdb=" N SER 7 108 " --> pdb=" O PHE 7 104 " (cutoff:3.500A) Processing helix chain '7' and resid 124 through 128 removed outlier: 3.594A pdb=" N ALA 7 128 " --> pdb=" O PRO 7 125 " (cutoff:3.500A) Processing helix chain '7' and resid 149 through 161 Processing helix chain '7' and resid 176 through 185 Processing helix chain '7' and resid 189 through 201 Processing helix chain '7' and resid 206 through 219 Processing helix chain '7' and resid 238 through 247 Processing helix chain '7' and resid 262 through 268 Processing helix chain '7' and resid 322 through 333 removed outlier: 3.688A pdb=" N VAL 7 326 " --> pdb=" O SER 7 322 " (cutoff:3.500A) Processing helix chain '7' and resid 363 through 375 removed outlier: 3.783A pdb=" N GLU 7 367 " --> pdb=" O ARG 7 363 " (cutoff:3.500A) Processing helix chain '7' and resid 391 through 404 removed outlier: 4.337A pdb=" N VAL 7 395 " --> pdb=" O GLY 7 391 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY 7 396 " --> pdb=" O LYS 7 392 " (cutoff:3.500A) Processing helix chain '7' and resid 413 through 424 Processing helix chain '7' and resid 457 through 461 Processing helix chain '7' and resid 467 through 480 removed outlier: 3.605A pdb=" N GLN 7 471 " --> pdb=" O SER 7 467 " (cutoff:3.500A) Processing helix chain '7' and resid 494 through 499 Processing helix chain '7' and resid 527 through 532 removed outlier: 3.584A pdb=" N ILE 7 531 " --> pdb=" O LEU 7 527 " (cutoff:3.500A) Processing helix chain '7' and resid 543 through 547 Processing helix chain '7' and resid 562 through 572 removed outlier: 3.821A pdb=" N TYR 7 566 " --> pdb=" O THR 7 562 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU 7 572 " --> pdb=" O GLU 7 568 " (cutoff:3.500A) Processing helix chain '7' and resid 574 through 576 No H-bonds generated for 'chain '7' and resid 574 through 576' Processing helix chain '7' and resid 577 through 583 Processing helix chain '7' and resid 584 through 601 Processing helix chain '7' and resid 612 through 623 Processing helix chain '7' and resid 632 through 645 removed outlier: 3.578A pdb=" N TYR 7 645 " --> pdb=" O GLN 7 641 " (cutoff:3.500A) Processing helix chain '7' and resid 679 through 691 removed outlier: 3.527A pdb=" N GLU 7 683 " --> pdb=" O SER 7 679 " (cutoff:3.500A) Processing helix chain '7' and resid 715 through 730 removed outlier: 3.556A pdb=" N ALA 7 724 " --> pdb=" O THR 7 720 " (cutoff:3.500A) Processing helix chain '7' and resid 752 through 765 removed outlier: 3.581A pdb=" N LEU 7 765 " --> pdb=" O GLN 7 761 " (cutoff:3.500A) Processing helix chain '3' and resid 39 through 50 Processing helix chain '3' and resid 76 through 92 removed outlier: 3.596A pdb=" N ARG 3 87 " --> pdb=" O ASP 3 83 " (cutoff:3.500A) Processing helix chain '3' and resid 103 through 123 removed outlier: 3.684A pdb=" N ASP 3 115 " --> pdb=" O GLU 3 111 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE 3 117 " --> pdb=" O VAL 3 113 " (cutoff:3.500A) Processing helix chain '3' and resid 127 through 145 Processing sheet with id=AA1, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 34 removed outlier: 5.933A pdb=" N ALA A 33 " --> pdb=" O HIS A 83 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ASP A 85 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR A 237 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 10.113A pdb=" N LYS A 88 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 9.979A pdb=" N ILE A 235 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 177 removed outlier: 3.684A pdb=" N VAL A 182 " --> pdb=" O ARG A 175 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 249 through 252 Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 345 Processing sheet with id=AA6, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.839A pdb=" N HIS B1104 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET A 456 " --> pdb=" O PHE A 444 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N VAL A 364 " --> pdb=" O LYS A 461 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE A 463 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N VAL A 366 " --> pdb=" O ILE A 463 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N PHE A 468 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL A 352 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N LEU A 470 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N SER A 354 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.647A pdb=" N ARG A 434 " --> pdb=" O TYR A 376 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 512 through 513 removed outlier: 3.652A pdb=" N LYS A 518 " --> pdb=" O SER A 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 541 through 542 Processing sheet with id=AB1, first strand: chain 'A' and resid 565 through 566 removed outlier: 3.845A pdb=" N ILE A 566 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL H 96 " --> pdb=" O ILE A 566 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 587 through 590 removed outlier: 6.981A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 849 through 850 removed outlier: 3.589A pdb=" N MET A 849 " --> pdb=" O ARG A 857 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N THR A 856 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 879 through 882 Processing sheet with id=AB5, first strand: chain 'A' and resid 1116 through 1120 removed outlier: 4.264A pdb=" N TYR A1119 " --> pdb=" O ARG A1326 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ARG A1326 " --> pdb=" O TYR A1119 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1141 through 1142 removed outlier: 6.606A pdb=" N THR A1141 " --> pdb=" O LEU A1273 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1147 through 1151 removed outlier: 6.227A pdb=" N GLU A1196 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N SER A1150 " --> pdb=" O ARG A1194 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG A1194 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A1195 " --> pdb=" O ILE A1238 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1284 through 1292 Processing sheet with id=AB9, first strand: chain 'A' and resid 1442 through 1444 Processing sheet with id=AC1, first strand: chain 'B' and resid 164 through 171 removed outlier: 6.147A pdb=" N LYS B 164 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP B 131 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ILE B 70 " --> pdb=" O LYS Q 333 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AC3, first strand: chain 'B' and resid 203 through 204 Processing sheet with id=AC4, first strand: chain 'B' and resid 217 through 218 Processing sheet with id=AC5, first strand: chain 'B' and resid 223 through 227 removed outlier: 4.110A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS B 270 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 544 through 547 removed outlier: 6.823A pdb=" N CYS B 544 " --> pdb=" O VAL B 633 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL B 633 " --> pdb=" O CYS B 544 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N SER B 546 " --> pdb=" O GLY B 631 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 650 through 651 Processing sheet with id=AC8, first strand: chain 'B' and resid 585 through 590 removed outlier: 4.998A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ARG B 579 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ILE B 626 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE B 581 " --> pdb=" O ILE B 626 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU B 623 " --> pdb=" O ASP B 618 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER B 614 " --> pdb=" O PHE B 627 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 793 through 796 removed outlier: 3.559A pdb=" N LYS B 965 " --> pdb=" O LEU B 953 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN B 951 " --> pdb=" O ARG B 967 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 793 through 796 removed outlier: 3.559A pdb=" N LYS B 965 " --> pdb=" O LEU B 953 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN B 951 " --> pdb=" O ARG B 967 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU L 56 " --> pdb=" O VAL B 954 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 821 through 827 removed outlier: 3.500A pdb=" N LEU B1010 " --> pdb=" O ILE B 824 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 873 through 874 Processing sheet with id=AD4, first strand: chain 'B' and resid 910 through 912 removed outlier: 3.705A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR B 939 " --> pdb=" O ILE B 912 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD6, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD7, first strand: chain 'C' and resid 7 through 13 removed outlier: 6.661A pdb=" N ASP C 19 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ALA C 13 " --> pdb=" O ASN C 17 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ASN C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN C 231 " --> pdb=" O GLU C 177 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 43 through 54 removed outlier: 5.975A pdb=" N VAL C 158 " --> pdb=" O ASP C 47 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N VAL C 49 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR C 156 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL C 51 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LYS C 154 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLU C 152 " --> pdb=" O THR C 53 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 72 through 74 removed outlier: 4.299A pdb=" N GLN C 73 " --> pdb=" O GLY C 130 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 111 through 114 removed outlier: 4.014A pdb=" N CYS C 145 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 37 through 38 Processing sheet with id=AE3, first strand: chain 'E' and resid 60 through 62 removed outlier: 3.649A pdb=" N PHE E 60 " --> pdb=" O VAL E 80 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TRP E 79 " --> pdb=" O THR E 107 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 177 through 178 Processing sheet with id=AE5, first strand: chain 'G' and resid 2 through 13 removed outlier: 7.929A pdb=" N ARG G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL G 48 " --> pdb=" O ARG G 75 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL G 77 " --> pdb=" O LEU G 46 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 2 through 13 Processing sheet with id=AE7, first strand: chain 'G' and resid 106 through 111 removed outlier: 3.727A pdb=" N GLY G 98 " --> pdb=" O SER G 95 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLN G 102 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N VAL G 91 " --> pdb=" O GLN G 102 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS G 146 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE G 160 " --> pdb=" O GLU G 148 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N CYS G 150 " --> pdb=" O HIS G 158 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N HIS G 158 " --> pdb=" O CYS G 150 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N SER G 152 " --> pdb=" O SER G 156 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N SER G 156 " --> pdb=" O SER G 152 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 106 through 111 removed outlier: 3.727A pdb=" N GLY G 98 " --> pdb=" O SER G 95 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLN G 102 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N VAL G 91 " --> pdb=" O GLN G 102 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY G 169 " --> pdb=" O ARG G 144 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.677A pdb=" N THR G 120 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN G 122 " --> pdb=" O SER G 129 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER G 129 " --> pdb=" O ASN G 122 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 11 through 16 removed outlier: 6.203A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE H 42 " --> pdb=" O CYS H 24 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU H 125 " --> pdb=" O VAL H 114 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL H 114 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 14 through 19 Processing sheet with id=AF3, first strand: chain 'I' and resid 70 through 71 removed outlier: 4.548A pdb=" N SER I 71 " --> pdb=" O ASN I 83 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ASN I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 21 through 22 removed outlier: 3.691A pdb=" N PHE K 71 " --> pdb=" O PHE K 35 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 35 through 37 removed outlier: 6.302A pdb=" N VAL M 43 " --> pdb=" O LEU M 52 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Q' and resid 98 through 99 Processing sheet with id=AF7, first strand: chain 'Q' and resid 391 through 392 removed outlier: 3.949A pdb=" N LYS Q 391 " --> pdb=" O THR Q 116 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR R 136 " --> pdb=" O ILE R 214 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILE R 214 " --> pdb=" O THR R 136 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Q' and resid 140 through 141 removed outlier: 4.623A pdb=" N THR Q 360 " --> pdb=" O ARG Q 398 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Q' and resid 384 through 388 removed outlier: 3.565A pdb=" N THR Q 385 " --> pdb=" O SER Q 377 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N CYS R 222 " --> pdb=" O VAL R 68 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N LEU R 70 " --> pdb=" O CYS R 222 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N VAL R 224 " --> pdb=" O LEU R 70 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ARG R 72 " --> pdb=" O VAL R 224 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLN R 223 " --> pdb=" O LEU R 124 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LEU R 124 " --> pdb=" O GLN R 223 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'U' and resid 243 through 252 removed outlier: 7.634A pdb=" N MET U 244 " --> pdb=" O VAL U 267 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N VAL U 267 " --> pdb=" O MET U 244 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N CYS U 246 " --> pdb=" O GLY U 265 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLY U 265 " --> pdb=" O CYS U 246 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N TYR U 248 " --> pdb=" O LYS U 263 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LYS U 263 " --> pdb=" O TYR U 248 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS U 250 " --> pdb=" O SER U 261 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N SER U 261 " --> pdb=" O GLN U 280 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLN U 280 " --> pdb=" O SER U 261 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS U 263 " --> pdb=" O LYS U 278 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LYS U 278 " --> pdb=" O LYS U 263 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY U 265 " --> pdb=" O PHE U 276 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE U 276 " --> pdb=" O GLY U 265 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER V 58 " --> pdb=" O THR U 275 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N LEU V 60 " --> pdb=" O GLN U 277 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ALA U 279 " --> pdb=" O LEU V 60 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N VAL V 62 " --> pdb=" O ALA U 279 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL U 281 " --> pdb=" O VAL V 62 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLY V 64 " --> pdb=" O VAL U 281 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LYS V 59 " --> pdb=" O VAL V 87 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL V 87 " --> pdb=" O LYS V 59 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N THR V 61 " --> pdb=" O VAL V 85 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL V 85 " --> pdb=" O THR V 61 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LYS V 63 " --> pdb=" O CYS V 83 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N CYS V 83 " --> pdb=" O LYS V 63 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN V 65 " --> pdb=" O LYS V 81 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE V 79 " --> pdb=" O ASP V 67 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR V 69 " --> pdb=" O THR V 77 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N THR V 77 " --> pdb=" O TYR V 69 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE V 71 " --> pdb=" O VAL V 75 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL V 75 " --> pdb=" O PHE V 71 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ASP V 109 " --> pdb=" O ASN V 82 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLN V 84 " --> pdb=" O SER V 107 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N SER V 107 " --> pdb=" O GLN V 84 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N THR V 86 " --> pdb=" O VAL V 105 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL V 105 " --> pdb=" O THR V 86 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET U 244 " --> pdb=" O ARG V 112 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL V 114 " --> pdb=" O MET U 244 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N CYS U 246 " --> pdb=" O VAL V 114 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N CYS V 116 " --> pdb=" O CYS U 246 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 68 through 72 removed outlier: 4.081A pdb=" N TYR W 86 " --> pdb=" O HIS W 70 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLN W 72 " --> pdb=" O ARG W 84 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG W 84 " --> pdb=" O GLN W 72 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'W' and resid 122 through 123 Processing sheet with id=AG4, first strand: chain 'O' and resid 92 through 93 removed outlier: 3.573A pdb=" N THR O 111 " --> pdb=" O ILE O 106 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS O 120 " --> pdb=" O PHE O 116 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY O 125 " --> pdb=" O ILE O 70 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ILE O 70 " --> pdb=" O GLY O 125 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL O 161 " --> pdb=" O GLN O 68 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE O 70 " --> pdb=" O ASN O 159 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ASN O 159 " --> pdb=" O ILE O 70 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ALA O 72 " --> pdb=" O ILE O 157 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE O 157 " --> pdb=" O ALA O 72 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL O 74 " --> pdb=" O PHE O 155 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N PHE O 155 " --> pdb=" O VAL O 74 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain '4' and resid 83 through 85 removed outlier: 3.541A pdb=" N ALA 4 78 " --> pdb=" O ILE 4 30 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU 4 177 " --> pdb=" O THR 4 27 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE 4 29 " --> pdb=" O LEU 4 177 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU 4 179 " --> pdb=" O ILE 4 29 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU 4 31 " --> pdb=" O LEU 4 179 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N CYS 4 181 " --> pdb=" O GLU 4 31 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASP 4 211 " --> pdb=" O LEU 4 176 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N LEU 4 236 " --> pdb=" O ILE 4 210 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL 4 212 " --> pdb=" O LEU 4 236 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain '4' and resid 287 through 288 Processing sheet with id=AG7, first strand: chain '0' and resid 2 through 4 removed outlier: 3.743A pdb=" N PHE 0 3 " --> pdb=" O VAL 0 10 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain '0' and resid 39 through 41 removed outlier: 3.736A pdb=" N SER 0 460 " --> pdb=" O LEU 0 40 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL 0 232 " --> pdb=" O ILE 0 457 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N THR 0 459 " --> pdb=" O VAL 0 232 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N PHE 0 234 " --> pdb=" O THR 0 459 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE 0 69 " --> pdb=" O ILE 0 206 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N TYR 0 208 " --> pdb=" O ILE 0 69 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N TYR 0 71 " --> pdb=" O TYR 0 208 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU 0 106 " --> pdb=" O ILE 0 205 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE 0 207 " --> pdb=" O LEU 0 106 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain '0' and resid 416 through 421 Processing sheet with id=AH1, first strand: chain '0' and resid 493 through 496 removed outlier: 6.089A pdb=" N LEU 0 493 " --> pdb=" O MET 0 679 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU 0 681 " --> pdb=" O LEU 0 493 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N MET 0 495 " --> pdb=" O LEU 0 681 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL 0 538 " --> pdb=" O THR 0 619 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU 0 599 " --> pdb=" O LEU 0 570 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain '6' and resid 178 through 186 removed outlier: 6.224A pdb=" N ILE 6 171 " --> pdb=" O VAL 6 182 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLN 6 184 " --> pdb=" O MET 6 169 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N MET 6 169 " --> pdb=" O GLN 6 184 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N LEU 6 126 " --> pdb=" O GLY 6 170 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N ILE 6 172 " --> pdb=" O LEU 6 126 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LEU 6 128 " --> pdb=" O ILE 6 172 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N MET 6 174 " --> pdb=" O LEU 6 128 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU 6 233 " --> pdb=" O ILE 6 127 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ARG 6 230 " --> pdb=" O ARG 6 260 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N LYS 6 262 " --> pdb=" O ARG 6 230 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL 6 232 " --> pdb=" O LYS 6 262 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain '6' and resid 326 through 327 Processing sheet with id=AH4, first strand: chain '6' and resid 390 through 391 Processing sheet with id=AH5, first strand: chain '2' and resid 57 through 58 Processing sheet with id=AH6, first strand: chain '2' and resid 492 through 493 Processing sheet with id=AH7, first strand: chain '5' and resid 8 through 11 removed outlier: 6.079A pdb=" N HIS 5 39 " --> pdb=" O LEU 5 35 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain '7' and resid 133 through 134 removed outlier: 3.629A pdb=" N TRP 7 133 " --> pdb=" O ILE 7 142 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE 7 142 " --> pdb=" O TRP 7 133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain '7' and resid 383 through 384 removed outlier: 7.613A pdb=" N ILE 7 383 " --> pdb=" O LEU 7 535 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH9 Processing sheet with id=AI1, first strand: chain '7' and resid 453 through 456 removed outlier: 7.034A pdb=" N VAL 7 407 " --> pdb=" O VAL 7 453 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N SER 7 455 " --> pdb=" O VAL 7 407 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N VAL 7 409 " --> pdb=" O SER 7 455 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain '7' and resid 557 through 559 removed outlier: 5.885A pdb=" N VAL 7 607 " --> pdb=" O LEU 7 654 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain '7' and resid 557 through 559 removed outlier: 6.117A pdb=" N CYS 7 554 " --> pdb=" O LYS 7 734 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain '3' and resid 52 through 53 2693 hydrogen bonds defined for protein. 7611 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 102 hydrogen bonds 192 hydrogen bond angles 0 basepair planarities 46 basepair parallelities 84 stacking parallelities Total time for adding SS restraints: 34.38 Time building geometry restraints manager: 15.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.37: 22328 1.37 - 1.60: 42813 1.60 - 1.83: 691 1.83 - 2.06: 6 2.06 - 2.29: 12 Bond restraints: 65850 Sorted by residual: bond pdb=" CE LYS 3 61 " pdb=" NZ LYS 3 61 " ideal model delta sigma weight residual 1.489 1.286 0.203 3.00e-02 1.11e+03 4.56e+01 bond pdb=" CD GLU A1074 " pdb=" OE2 GLU A1074 " ideal model delta sigma weight residual 1.249 1.138 0.111 1.90e-02 2.77e+03 3.43e+01 bond pdb=" CA ARG F 135 " pdb=" CB ARG F 135 " ideal model delta sigma weight residual 1.527 1.390 0.137 2.48e-02 1.63e+03 3.07e+01 bond pdb=" CA GLU C 166 " pdb=" CB GLU C 166 " ideal model delta sigma weight residual 1.528 1.440 0.088 1.66e-02 3.63e+03 2.82e+01 bond pdb=" C LEU B 112 " pdb=" N TYR B 113 " ideal model delta sigma weight residual 1.331 1.225 0.106 2.07e-02 2.33e+03 2.65e+01 ... (remaining 65845 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 87779 3.54 - 7.08: 1389 7.08 - 10.61: 158 10.61 - 14.15: 25 14.15 - 17.69: 5 Bond angle restraints: 89356 Sorted by residual: angle pdb=" N VAL 7 501 " pdb=" CA VAL 7 501 " pdb=" C VAL 7 501 " ideal model delta sigma weight residual 112.83 101.38 11.45 9.90e-01 1.02e+00 1.34e+02 angle pdb=" N GLY 2 70 " pdb=" CA GLY 2 70 " pdb=" C GLY 2 70 " ideal model delta sigma weight residual 114.48 103.97 10.51 1.19e+00 7.06e-01 7.80e+01 angle pdb=" C TYR J 63 " pdb=" N ASN J 64 " pdb=" CA ASN J 64 " ideal model delta sigma weight residual 120.49 108.93 11.56 1.42e+00 4.96e-01 6.63e+01 angle pdb=" N ARG J 6 " pdb=" CA ARG J 6 " pdb=" C ARG J 6 " ideal model delta sigma weight residual 110.35 121.11 -10.76 1.40e+00 5.10e-01 5.91e+01 angle pdb=" NE ARG K 6 " pdb=" CZ ARG K 6 " pdb=" NH1 ARG K 6 " ideal model delta sigma weight residual 121.50 114.12 7.38 1.00e+00 1.00e+00 5.45e+01 ... (remaining 89351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.35: 38641 35.35 - 70.70: 913 70.70 - 106.04: 47 106.04 - 141.39: 0 141.39 - 176.74: 2 Dihedral angle restraints: 39603 sinusoidal: 16277 harmonic: 23326 Sorted by residual: dihedral pdb=" CA HIS B 363 " pdb=" C HIS B 363 " pdb=" N ILE B 364 " pdb=" CA ILE B 364 " ideal model delta harmonic sigma weight residual -180.00 -130.01 -49.99 0 5.00e+00 4.00e-02 1.00e+02 dihedral pdb=" CA LYS M 272 " pdb=" C LYS M 272 " pdb=" N SER M 273 " pdb=" CA SER M 273 " ideal model delta harmonic sigma weight residual -180.00 -131.03 -48.97 0 5.00e+00 4.00e-02 9.59e+01 dihedral pdb=" CA ASP 3 125 " pdb=" C ASP 3 125 " pdb=" N VAL 3 126 " pdb=" CA VAL 3 126 " ideal model delta harmonic sigma weight residual -180.00 -131.66 -48.34 0 5.00e+00 4.00e-02 9.35e+01 ... (remaining 39600 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 9958 0.160 - 0.319: 105 0.319 - 0.479: 5 0.479 - 0.639: 0 0.639 - 0.798: 1 Chirality restraints: 10069 Sorted by residual: chirality pdb=" CG LEU 0 162 " pdb=" CB LEU 0 162 " pdb=" CD1 LEU 0 162 " pdb=" CD2 LEU 0 162 " both_signs ideal model delta sigma weight residual False -2.59 -1.79 -0.80 2.00e-01 2.50e+01 1.59e+01 chirality pdb=" CA ARG J 6 " pdb=" N ARG J 6 " pdb=" C ARG J 6 " pdb=" CB ARG J 6 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CG LEU A 450 " pdb=" CB LEU A 450 " pdb=" CD1 LEU A 450 " pdb=" CD2 LEU A 450 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.35 2.00e-01 2.50e+01 3.15e+00 ... (remaining 10066 not shown) Planarity restraints: 11234 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 451 " 0.049 2.00e-02 2.50e+03 4.49e-02 3.03e+01 pdb=" CG HIS A 451 " -0.090 2.00e-02 2.50e+03 pdb=" ND1 HIS A 451 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 HIS A 451 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS A 451 " -0.007 2.00e-02 2.50e+03 pdb=" NE2 HIS A 451 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 797 " -0.045 2.00e-02 2.50e+03 3.19e-02 2.04e+01 pdb=" CG TYR B 797 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR B 797 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR B 797 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR B 797 " 0.031 2.00e-02 2.50e+03 pdb=" CE2 TYR B 797 " 0.021 2.00e-02 2.50e+03 pdb=" CZ TYR B 797 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR B 797 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS 3 61 " 0.019 2.00e-02 2.50e+03 3.84e-02 1.48e+01 pdb=" C LYS 3 61 " -0.067 2.00e-02 2.50e+03 pdb=" O LYS 3 61 " 0.025 2.00e-02 2.50e+03 pdb=" N ILE 3 62 " 0.022 2.00e-02 2.50e+03 ... (remaining 11231 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 685 2.44 - 3.06: 50232 3.06 - 3.67: 105147 3.67 - 4.29: 156265 4.29 - 4.90: 238155 Nonbonded interactions: 550484 Sorted by model distance: nonbonded pdb=" NZ LYS B 649 " pdb=" O THR B 736 " model vdw 1.825 3.120 nonbonded pdb=" O GLY L 52 " pdb=" NH1 ARG L 54 " model vdw 1.897 3.120 nonbonded pdb=" N CYS 3 16 " pdb="ZN ZN 3 401 " model vdw 1.899 2.310 nonbonded pdb=" OE1 GLU A 870 " pdb=" OG SER E 202 " model vdw 1.944 3.040 nonbonded pdb=" OG SER A1189 " pdb=" OE1 GLU A1256 " model vdw 1.977 3.040 ... (remaining 550479 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.00 max=1.00 mean=0.99 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: 7.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 2.090 Check model and map are aligned: 0.380 Set scattering table: 0.460 Process input model: 157.370 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.230 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:2.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 170.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4591 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 : 0.008 0.203 65850 Z= 0.539 Angle : 1.137 17.690 89356 Z= 0.617 Chirality : 0.057 0.798 10069 Planarity : 0.007 0.080 11222 Dihedral : 15.234 176.741 24609 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 40.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 13.10 % Favored : 86.72 % Rotamer: Outliers : 0.09 % Allowed : 0.72 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 1.77 % Twisted General : 0.39 % 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: -4.05 (0.08), residues: 7932 helix: -2.19 (0.08), residues: 2897 sheet: -2.61 (0.16), residues: 884 loop : -3.13 (0.09), residues: 4151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.004 TRP C 192 HIS 0.041 0.003 HIS A 451 PHE 0.054 0.004 PHE A 252 TYR 0.051 0.004 TYR B 797 ARG 0.050 0.002 ARG K 6 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15864 Ramachandran restraints generated. 7932 Oldfield, 0 Emsley, 7932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15864 Ramachandran restraints generated. 7932 Oldfield, 0 Emsley, 7932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 7227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 282 time to evaluate : 5.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 244 MET cc_start: -0.0985 (ptt) cc_final: -0.1629 (ptp) REVERT: 1 385 MET cc_start: -0.0901 (ttm) cc_final: -0.1216 (ttp) REVERT: 0 61 MET cc_start: 0.2715 (mtm) cc_final: 0.1842 (ptp) REVERT: 0 485 MET cc_start: 0.0028 (mmm) cc_final: -0.0254 (mmm) REVERT: 6 322 MET cc_start: 0.1656 (pmm) cc_final: 0.1431 (pmm) REVERT: 3 61 LYS cc_start: 0.0291 (tmtt) cc_final: -0.0183 (tmtt) outliers start: 6 outliers final: 4 residues processed: 288 average time/residue: 0.5920 time to fit residues: 297.9791 Evaluate side-chains 239 residues out of total 7227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 235 time to evaluate : 5.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 40 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 668 optimal weight: 4.9990 chunk 600 optimal weight: 50.0000 chunk 333 optimal weight: 10.0000 chunk 205 optimal weight: 6.9990 chunk 404 optimal weight: 20.0000 chunk 320 optimal weight: 2.9990 chunk 620 optimal weight: 8.9990 chunk 240 optimal weight: 1.9990 chunk 377 optimal weight: 4.9990 chunk 462 optimal weight: 20.0000 chunk 719 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 ASN ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 ASN A 548 ASN A 626 ASN A 650 GLN A 659 HIS A 717 ASN A1059 HIS ** A1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1354 ASN B 887 HIS B 932 HIS B1025 HIS C 167 HIS E 143 ASN H 21 ASN ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN I 79 HIS ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 ASN ** M 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 300 GLN W 141 ASN ** 1 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 159 HIS 0 480 GLN ** 0 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 163 GLN 6 164 ASN ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 469 ASN 7 345 ASN ** 7 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 761 GLN 3 36 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4426 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 65850 Z= 0.290 Angle : 0.807 12.478 89356 Z= 0.424 Chirality : 0.049 0.375 10069 Planarity : 0.006 0.080 11222 Dihedral : 13.498 173.876 10051 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.06 % Favored : 90.83 % Rotamer: Outliers : 0.73 % Allowed : 7.00 % Favored : 92.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 0.88 % Twisted General : 0.23 % 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: -2.78 (0.09), residues: 7932 helix: -0.88 (0.09), residues: 3176 sheet: -2.15 (0.15), residues: 965 loop : -2.63 (0.09), residues: 3791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 192 HIS 0.026 0.002 HIS A 451 PHE 0.033 0.002 PHE A 252 TYR 0.038 0.002 TYR 7 365 ARG 0.008 0.001 ARG A1012 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15864 Ramachandran restraints generated. 7932 Oldfield, 0 Emsley, 7932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15864 Ramachandran restraints generated. 7932 Oldfield, 0 Emsley, 7932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 7227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 252 time to evaluate : 5.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 HIS cc_start: 0.5914 (OUTLIER) cc_final: 0.5198 (m170) REVERT: M 105 ARG cc_start: 0.5308 (tmm-80) cc_final: 0.3781 (mpt-90) REVERT: U 244 MET cc_start: -0.0764 (ptt) cc_final: -0.1230 (ptt) REVERT: 4 153 MET cc_start: 0.2866 (ppp) cc_final: 0.2581 (ppp) REVERT: 4 206 MET cc_start: 0.2547 (mpp) cc_final: 0.2041 (mpp) REVERT: 0 61 MET cc_start: 0.3106 (mtm) cc_final: 0.1852 (ptp) REVERT: 0 435 MET cc_start: 0.1669 (mmp) cc_final: 0.1318 (mmp) outliers start: 47 outliers final: 13 residues processed: 280 average time/residue: 0.5951 time to fit residues: 294.9566 Evaluate side-chains 249 residues out of total 7227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 235 time to evaluate : 5.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain G residue 44 TYR Chi-restraints excluded: chain I residue 79 HIS Chi-restraints excluded: chain Q residue 380 ASP Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain 0 residue 148 ASP Chi-restraints excluded: chain 0 residue 284 ASP Chi-restraints excluded: chain 0 residue 468 MET Chi-restraints excluded: chain 2 residue 373 MET Chi-restraints excluded: chain 7 residue 501 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 399 optimal weight: 9.9990 chunk 223 optimal weight: 6.9990 chunk 598 optimal weight: 30.0000 chunk 489 optimal weight: 20.0000 chunk 198 optimal weight: 10.0000 chunk 720 optimal weight: 50.0000 chunk 778 optimal weight: 5.9990 chunk 641 optimal weight: 50.0000 chunk 714 optimal weight: 30.0000 chunk 245 optimal weight: 1.9990 chunk 578 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 HIS A 760 GLN ** A1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1354 ASN ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 GLN ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 212 ASN ** 6 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4485 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 65850 Z= 0.326 Angle : 0.741 13.527 89356 Z= 0.388 Chirality : 0.046 0.450 10069 Planarity : 0.005 0.073 11222 Dihedral : 13.269 172.799 10044 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.32 % Favored : 90.61 % Rotamer: Outliers : 1.26 % Allowed : 9.90 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 0.59 % Twisted General : 0.17 % 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: -2.29 (0.09), residues: 7932 helix: -0.40 (0.09), residues: 3181 sheet: -2.09 (0.16), residues: 922 loop : -2.36 (0.10), residues: 3829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 170 HIS 0.017 0.002 HIS A 451 PHE 0.030 0.002 PHE 3 47 TYR 0.031 0.002 TYR 7 365 ARG 0.010 0.001 ARG J 6 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15864 Ramachandran restraints generated. 7932 Oldfield, 0 Emsley, 7932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15864 Ramachandran restraints generated. 7932 Oldfield, 0 Emsley, 7932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 7227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 243 time to evaluate : 6.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 85 MET cc_start: 0.6439 (ttp) cc_final: 0.6008 (ptm) REVERT: J 49 MET cc_start: 0.5658 (mtp) cc_final: 0.5406 (mtp) REVERT: M 105 ARG cc_start: 0.5256 (tmm-80) cc_final: 0.3818 (mpt-90) REVERT: U 244 MET cc_start: -0.0588 (ptt) cc_final: -0.1203 (ptt) REVERT: 0 61 MET cc_start: 0.2736 (mtm) cc_final: 0.1376 (ptm) REVERT: 0 199 MET cc_start: -0.4005 (OUTLIER) cc_final: -0.4494 (mtp) REVERT: 0 485 MET cc_start: -0.0296 (mmt) cc_final: -0.1276 (mmt) REVERT: 7 622 MET cc_start: -0.0950 (OUTLIER) cc_final: -0.1616 (mmm) REVERT: 3 61 LYS cc_start: -0.0661 (tmtt) cc_final: -0.1120 (tmtt) outliers start: 81 outliers final: 31 residues processed: 308 average time/residue: 0.5754 time to fit residues: 316.2903 Evaluate side-chains 267 residues out of total 7227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 234 time to evaluate : 5.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 797 TYR Chi-restraints excluded: chain B residue 1113 VAL Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain G residue 44 TYR Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain M residue 308 THR Chi-restraints excluded: chain Q residue 380 ASP Chi-restraints excluded: chain O residue 111 THR Chi-restraints excluded: chain 4 residue 197 MET Chi-restraints excluded: chain 0 residue 148 ASP Chi-restraints excluded: chain 0 residue 167 VAL Chi-restraints excluded: chain 0 residue 199 MET Chi-restraints excluded: chain 0 residue 290 VAL Chi-restraints excluded: chain 2 residue 373 MET Chi-restraints excluded: chain 7 residue 348 ARG Chi-restraints excluded: chain 7 residue 349 ASN Chi-restraints excluded: chain 7 residue 501 VAL Chi-restraints excluded: chain 7 residue 622 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 711 optimal weight: 8.9990 chunk 541 optimal weight: 7.9990 chunk 373 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 343 optimal weight: 8.9990 chunk 483 optimal weight: 20.0000 chunk 723 optimal weight: 10.0000 chunk 765 optimal weight: 9.9990 chunk 377 optimal weight: 4.9990 chunk 685 optimal weight: 20.0000 chunk 206 optimal weight: 1.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 ASN A1059 HIS A1171 GLN ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 ASN H 11 GLN ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN ** I 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 84 ASN M 90 ASN ** M 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 188 ASN ** 4 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 349 ASN ** 7 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4498 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 65850 Z= 0.303 Angle : 0.700 9.983 89356 Z= 0.366 Chirality : 0.045 0.317 10069 Planarity : 0.005 0.073 11222 Dihedral : 13.126 171.289 10044 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.05 % Favored : 90.87 % Rotamer: Outliers : 1.74 % Allowed : 11.99 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 0.59 % Twisted General : 0.16 % 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: -1.98 (0.09), residues: 7932 helix: -0.09 (0.09), residues: 3201 sheet: -2.07 (0.16), residues: 956 loop : -2.21 (0.10), residues: 3775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 170 HIS 0.011 0.001 HIS L 53 PHE 0.027 0.002 PHE 3 47 TYR 0.030 0.002 TYR 7 365 ARG 0.011 0.001 ARG Q 138 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15864 Ramachandran restraints generated. 7932 Oldfield, 0 Emsley, 7932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15864 Ramachandran restraints generated. 7932 Oldfield, 0 Emsley, 7932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 7227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 234 time to evaluate : 5.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 57 MET cc_start: 0.6120 (ppp) cc_final: 0.5759 (ppp) REVERT: F 85 MET cc_start: 0.6378 (ttp) cc_final: 0.6153 (ttp) REVERT: M 105 ARG cc_start: 0.5227 (tmm-80) cc_final: 0.3887 (mpt-90) REVERT: U 244 MET cc_start: -0.0502 (ptt) cc_final: -0.1286 (ptt) REVERT: 4 153 MET cc_start: 0.3063 (ppp) cc_final: 0.2511 (ppp) REVERT: 0 61 MET cc_start: 0.2674 (mtm) cc_final: 0.1430 (ptm) REVERT: 0 199 MET cc_start: -0.4078 (OUTLIER) cc_final: -0.4516 (mtp) REVERT: 0 435 MET cc_start: 0.1951 (mmp) cc_final: 0.1272 (mmp) REVERT: 0 485 MET cc_start: -0.0533 (mmt) cc_final: -0.1094 (mmt) REVERT: 0 495 MET cc_start: 0.3484 (pmm) cc_final: 0.2182 (pmm) REVERT: 0 539 VAL cc_start: 0.5232 (OUTLIER) cc_final: 0.5015 (m) REVERT: 7 622 MET cc_start: -0.1082 (OUTLIER) cc_final: -0.1516 (mmm) REVERT: 3 61 LYS cc_start: -0.0256 (tmtt) cc_final: -0.0828 (tmtt) outliers start: 112 outliers final: 58 residues processed: 326 average time/residue: 0.5658 time to fit residues: 329.7076 Evaluate side-chains 291 residues out of total 7227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 230 time to evaluate : 6.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 1004 ASN Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 797 TYR Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 921 ASP Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 1113 VAL Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain G residue 44 TYR Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 78 CYS Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 38 GLU Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 287 LEU Chi-restraints excluded: chain M residue 308 THR Chi-restraints excluded: chain Q residue 380 ASP Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain O residue 111 THR Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain 4 residue 197 MET Chi-restraints excluded: chain 4 residue 244 LEU Chi-restraints excluded: chain 0 residue 1 MET Chi-restraints excluded: chain 0 residue 148 ASP Chi-restraints excluded: chain 0 residue 167 VAL Chi-restraints excluded: chain 0 residue 199 MET Chi-restraints excluded: chain 0 residue 290 VAL Chi-restraints excluded: chain 0 residue 349 LEU Chi-restraints excluded: chain 0 residue 539 VAL Chi-restraints excluded: chain 6 residue 126 LEU Chi-restraints excluded: chain 2 residue 52 PHE Chi-restraints excluded: chain 2 residue 371 VAL Chi-restraints excluded: chain 2 residue 373 MET Chi-restraints excluded: chain 7 residue 337 VAL Chi-restraints excluded: chain 7 residue 348 ARG Chi-restraints excluded: chain 7 residue 365 TYR Chi-restraints excluded: chain 7 residue 622 MET Chi-restraints excluded: chain 7 residue 742 MET Chi-restraints excluded: chain 3 residue 30 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 637 optimal weight: 20.0000 chunk 434 optimal weight: 50.0000 chunk 11 optimal weight: 9.9990 chunk 570 optimal weight: 30.0000 chunk 315 optimal weight: 10.0000 chunk 653 optimal weight: 9.9990 chunk 529 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 390 optimal weight: 7.9990 chunk 687 optimal weight: 30.0000 chunk 193 optimal weight: 9.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1171 GLN ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 ASN ** B 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 986 GLN ** B1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN E 101 GLN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 79 HIS ** I 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 104 ASN ** M 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 138 GLN X 251 ASN ** O 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 633 GLN ** 7 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 702 ASN ** 7 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4647 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.105 65850 Z= 0.442 Angle : 0.830 12.180 89356 Z= 0.428 Chirality : 0.048 0.294 10069 Planarity : 0.006 0.073 11222 Dihedral : 13.298 172.747 10044 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 22.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.64 % Favored : 89.27 % Rotamer: Outliers : 2.63 % Allowed : 13.82 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 0.29 % Twisted General : 0.14 % 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: -2.20 (0.09), residues: 7932 helix: -0.25 (0.09), residues: 3193 sheet: -2.08 (0.16), residues: 926 loop : -2.39 (0.10), residues: 3813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 170 HIS 0.019 0.002 HIS A 399 PHE 0.037 0.002 PHE O 116 TYR 0.030 0.002 TYR 7 365 ARG 0.011 0.001 ARG B 261 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15864 Ramachandran restraints generated. 7932 Oldfield, 0 Emsley, 7932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15864 Ramachandran restraints generated. 7932 Oldfield, 0 Emsley, 7932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 7227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 228 time to evaluate : 6.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 923 LEU cc_start: 0.6638 (OUTLIER) cc_final: 0.6305 (mm) REVERT: B 809 MET cc_start: 0.5057 (ptm) cc_final: 0.4800 (ptm) REVERT: E 57 MET cc_start: 0.6213 (ppp) cc_final: 0.5956 (ppp) REVERT: L 50 ASP cc_start: 0.2747 (OUTLIER) cc_final: 0.1920 (t70) REVERT: U 244 MET cc_start: -0.0547 (ptt) cc_final: -0.1399 (ptt) REVERT: 4 153 MET cc_start: 0.2377 (ppp) cc_final: 0.2052 (ppp) REVERT: 0 61 MET cc_start: 0.2777 (mtm) cc_final: 0.1372 (ptm) REVERT: 0 199 MET cc_start: -0.3996 (OUTLIER) cc_final: -0.4475 (mtp) REVERT: 0 485 MET cc_start: -0.0624 (OUTLIER) cc_final: -0.1346 (mmt) REVERT: 0 659 MET cc_start: -0.0018 (mmt) cc_final: -0.0559 (mmt) REVERT: 6 192 HIS cc_start: 0.0672 (OUTLIER) cc_final: 0.0349 (m170) REVERT: 7 622 MET cc_start: -0.0977 (OUTLIER) cc_final: -0.1635 (mmm) outliers start: 169 outliers final: 86 residues processed: 372 average time/residue: 0.5744 time to fit residues: 380.7131 Evaluate side-chains 316 residues out of total 7227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 224 time to evaluate : 5.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 1004 ASN Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1287 TYR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 797 TYR Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 921 ASP Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 1113 VAL Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain G residue 44 TYR Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 78 CYS Chi-restraints excluded: chain I residue 79 HIS Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 38 GLU Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain L residue 47 ARG Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 287 LEU Chi-restraints excluded: chain M residue 308 THR Chi-restraints excluded: chain Q residue 380 ASP Chi-restraints excluded: chain O residue 104 MET Chi-restraints excluded: chain O residue 111 THR Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain 4 residue 197 MET Chi-restraints excluded: chain 4 residue 215 ILE Chi-restraints excluded: chain 0 residue 1 MET Chi-restraints excluded: chain 0 residue 148 ASP Chi-restraints excluded: chain 0 residue 167 VAL Chi-restraints excluded: chain 0 residue 199 MET Chi-restraints excluded: chain 0 residue 290 VAL Chi-restraints excluded: chain 0 residue 349 LEU Chi-restraints excluded: chain 0 residue 485 MET Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 6 residue 126 LEU Chi-restraints excluded: chain 6 residue 192 HIS Chi-restraints excluded: chain 6 residue 290 ILE Chi-restraints excluded: chain 6 residue 448 LEU Chi-restraints excluded: chain 2 residue 48 MET Chi-restraints excluded: chain 2 residue 371 VAL Chi-restraints excluded: chain 2 residue 373 MET Chi-restraints excluded: chain 7 residue 337 VAL Chi-restraints excluded: chain 7 residue 348 ARG Chi-restraints excluded: chain 7 residue 365 TYR Chi-restraints excluded: chain 7 residue 501 VAL Chi-restraints excluded: chain 7 residue 622 MET Chi-restraints excluded: chain 7 residue 742 MET Chi-restraints excluded: chain 7 residue 745 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 257 optimal weight: 1.9990 chunk 689 optimal weight: 50.0000 chunk 151 optimal weight: 6.9990 chunk 449 optimal weight: 50.0000 chunk 188 optimal weight: 3.9990 chunk 766 optimal weight: 30.0000 chunk 636 optimal weight: 40.0000 chunk 354 optimal weight: 9.9990 chunk 63 optimal weight: 0.9980 chunk 253 optimal weight: 1.9990 chunk 402 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 HIS ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 GLN ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 ASN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN I 79 HIS I 83 ASN ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 212 ASN ** Q 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 138 GLN ** O 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 566 HIS ** 0 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 699 GLN 0 707 ASN 6 163 GLN ** 2 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4511 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 65850 Z= 0.217 Angle : 0.673 11.832 89356 Z= 0.349 Chirality : 0.044 0.306 10069 Planarity : 0.005 0.073 11222 Dihedral : 13.051 171.517 10044 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.97 % Favored : 91.96 % Rotamer: Outliers : 1.83 % Allowed : 15.17 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 0.59 % Twisted General : 0.14 % 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: -1.75 (0.09), residues: 7932 helix: 0.15 (0.09), residues: 3201 sheet: -1.90 (0.16), residues: 968 loop : -2.15 (0.10), residues: 3763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 192 HIS 0.034 0.001 HIS I 79 PHE 0.030 0.002 PHE 3 47 TYR 0.033 0.001 TYR 7 365 ARG 0.006 0.000 ARG B 261 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15864 Ramachandran restraints generated. 7932 Oldfield, 0 Emsley, 7932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15864 Ramachandran restraints generated. 7932 Oldfield, 0 Emsley, 7932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 7227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 233 time to evaluate : 6.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 75 MET cc_start: 0.5347 (mmp) cc_final: 0.5116 (mmp) REVERT: M 105 ARG cc_start: 0.5248 (tmm-80) cc_final: 0.4027 (mpt-90) REVERT: U 244 MET cc_start: -0.0432 (ptt) cc_final: -0.1309 (ptt) REVERT: 4 153 MET cc_start: 0.2350 (ppp) cc_final: 0.2044 (ppp) REVERT: 4 305 CYS cc_start: 0.0209 (OUTLIER) cc_final: -0.1701 (t) REVERT: 0 61 MET cc_start: 0.2615 (mtm) cc_final: 0.1227 (ptm) REVERT: 0 199 MET cc_start: -0.4236 (OUTLIER) cc_final: -0.4652 (mtp) REVERT: 0 346 MET cc_start: -0.1561 (tpp) cc_final: -0.2637 (tmm) REVERT: 0 485 MET cc_start: -0.0410 (OUTLIER) cc_final: -0.0664 (mmt) REVERT: 0 659 MET cc_start: -0.0030 (mmt) cc_final: -0.0479 (mmt) REVERT: 6 322 MET cc_start: 0.0810 (pmm) cc_final: 0.0450 (pmm) REVERT: 7 304 GLU cc_start: -0.1991 (OUTLIER) cc_final: -0.2609 (pt0) REVERT: 7 622 MET cc_start: -0.1000 (OUTLIER) cc_final: -0.1254 (mmm) outliers start: 118 outliers final: 73 residues processed: 326 average time/residue: 0.5583 time to fit residues: 327.6893 Evaluate side-chains 304 residues out of total 7227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 226 time to evaluate : 5.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 529 CYS Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 873 MET Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1287 TYR Chi-restraints excluded: chain A residue 1387 HIS Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 376 PHE Chi-restraints excluded: chain B residue 797 TYR Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 1113 VAL Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 44 TYR Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain I residue 10 CYS Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 79 HIS Chi-restraints excluded: chain I residue 101 PHE Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 119 MET Chi-restraints excluded: chain M residue 308 THR Chi-restraints excluded: chain Q residue 380 ASP Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain O residue 104 MET Chi-restraints excluded: chain O residue 197 MET Chi-restraints excluded: chain O residue 203 VAL Chi-restraints excluded: chain 4 residue 197 MET Chi-restraints excluded: chain 4 residue 305 CYS Chi-restraints excluded: chain 0 residue 1 MET Chi-restraints excluded: chain 0 residue 148 ASP Chi-restraints excluded: chain 0 residue 167 VAL Chi-restraints excluded: chain 0 residue 199 MET Chi-restraints excluded: chain 0 residue 231 ILE Chi-restraints excluded: chain 0 residue 290 VAL Chi-restraints excluded: chain 0 residue 485 MET Chi-restraints excluded: chain 0 residue 622 MET Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 6 residue 126 LEU Chi-restraints excluded: chain 6 residue 263 VAL Chi-restraints excluded: chain 6 residue 290 ILE Chi-restraints excluded: chain 6 residue 310 VAL Chi-restraints excluded: chain 6 residue 440 CYS Chi-restraints excluded: chain 2 residue 371 VAL Chi-restraints excluded: chain 2 residue 373 MET Chi-restraints excluded: chain 7 residue 304 GLU Chi-restraints excluded: chain 7 residue 337 VAL Chi-restraints excluded: chain 7 residue 343 PHE Chi-restraints excluded: chain 7 residue 348 ARG Chi-restraints excluded: chain 7 residue 365 TYR Chi-restraints excluded: chain 7 residue 501 VAL Chi-restraints excluded: chain 7 residue 514 THR Chi-restraints excluded: chain 7 residue 561 MET Chi-restraints excluded: chain 7 residue 622 MET Chi-restraints excluded: chain 7 residue 742 MET Chi-restraints excluded: chain 3 residue 30 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 738 optimal weight: 6.9990 chunk 86 optimal weight: 0.5980 chunk 436 optimal weight: 5.9990 chunk 559 optimal weight: 40.0000 chunk 433 optimal weight: 7.9990 chunk 645 optimal weight: 2.9990 chunk 427 optimal weight: 0.5980 chunk 763 optimal weight: 20.0000 chunk 477 optimal weight: 40.0000 chunk 465 optimal weight: 30.0000 chunk 352 optimal weight: 0.0970 overall best weight: 2.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 HIS ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 79 HIS ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 251 ASN X 265 ASN ** O 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 76 ASN ** 2 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4470 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 65850 Z= 0.187 Angle : 0.650 16.995 89356 Z= 0.334 Chirality : 0.043 0.307 10069 Planarity : 0.004 0.072 11222 Dihedral : 12.859 173.464 10044 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.02 % Favored : 91.92 % Rotamer: Outliers : 1.80 % Allowed : 15.58 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 0.29 % Twisted General : 0.09 % 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: -1.49 (0.09), residues: 7932 helix: 0.38 (0.09), residues: 3214 sheet: -1.71 (0.16), residues: 978 loop : -2.03 (0.10), residues: 3740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 192 HIS 0.040 0.001 HIS I 79 PHE 0.024 0.001 PHE 3 47 TYR 0.032 0.001 TYR 7 365 ARG 0.005 0.000 ARG 0 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15864 Ramachandran restraints generated. 7932 Oldfield, 0 Emsley, 7932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15864 Ramachandran restraints generated. 7932 Oldfield, 0 Emsley, 7932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 7227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 230 time to evaluate : 5.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 147 TYR cc_start: 0.3208 (OUTLIER) cc_final: 0.2972 (t80) REVERT: D 189 ASP cc_start: 0.1552 (OUTLIER) cc_final: 0.1344 (t0) REVERT: M 105 ARG cc_start: 0.4961 (tmm-80) cc_final: 0.3773 (mpt-90) REVERT: U 244 MET cc_start: -0.0440 (ptt) cc_final: -0.1403 (ptt) REVERT: 4 153 MET cc_start: 0.2283 (ppp) cc_final: 0.2052 (ppp) REVERT: 4 305 CYS cc_start: -0.0043 (OUTLIER) cc_final: -0.1971 (t) REVERT: 0 61 MET cc_start: 0.2426 (mtm) cc_final: 0.1003 (ptm) REVERT: 0 199 MET cc_start: -0.4218 (OUTLIER) cc_final: -0.4638 (mtp) REVERT: 0 485 MET cc_start: -0.0360 (OUTLIER) cc_final: -0.0648 (mmt) REVERT: 0 659 MET cc_start: -0.0207 (mmt) cc_final: -0.0618 (mmt) REVERT: 6 192 HIS cc_start: 0.0594 (OUTLIER) cc_final: 0.0349 (m170) REVERT: 7 304 GLU cc_start: -0.1979 (OUTLIER) cc_final: -0.2601 (pt0) REVERT: 7 622 MET cc_start: -0.0634 (OUTLIER) cc_final: -0.1212 (mmm) outliers start: 116 outliers final: 73 residues processed: 322 average time/residue: 0.5697 time to fit residues: 326.8605 Evaluate side-chains 306 residues out of total 7227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 225 time to evaluate : 5.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 529 CYS Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1287 TYR Chi-restraints excluded: chain B residue 376 PHE Chi-restraints excluded: chain B residue 797 TYR Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 1006 ILE Chi-restraints excluded: chain B residue 1113 VAL Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 44 TYR Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain I residue 10 CYS Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 78 CYS Chi-restraints excluded: chain I residue 79 HIS Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 119 MET Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 188 THR Chi-restraints excluded: chain M residue 301 THR Chi-restraints excluded: chain M residue 308 THR Chi-restraints excluded: chain Q residue 380 ASP Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain O residue 104 MET Chi-restraints excluded: chain O residue 203 VAL Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain 4 residue 197 MET Chi-restraints excluded: chain 4 residue 305 CYS Chi-restraints excluded: chain 0 residue 1 MET Chi-restraints excluded: chain 0 residue 34 VAL Chi-restraints excluded: chain 0 residue 148 ASP Chi-restraints excluded: chain 0 residue 167 VAL Chi-restraints excluded: chain 0 residue 199 MET Chi-restraints excluded: chain 0 residue 231 ILE Chi-restraints excluded: chain 0 residue 290 VAL Chi-restraints excluded: chain 0 residue 485 MET Chi-restraints excluded: chain 0 residue 538 VAL Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 6 residue 126 LEU Chi-restraints excluded: chain 6 residue 192 HIS Chi-restraints excluded: chain 6 residue 263 VAL Chi-restraints excluded: chain 6 residue 290 ILE Chi-restraints excluded: chain 6 residue 310 VAL Chi-restraints excluded: chain 2 residue 52 PHE Chi-restraints excluded: chain 2 residue 371 VAL Chi-restraints excluded: chain 2 residue 373 MET Chi-restraints excluded: chain 7 residue 304 GLU Chi-restraints excluded: chain 7 residue 337 VAL Chi-restraints excluded: chain 7 residue 343 PHE Chi-restraints excluded: chain 7 residue 348 ARG Chi-restraints excluded: chain 7 residue 514 THR Chi-restraints excluded: chain 7 residue 561 MET Chi-restraints excluded: chain 7 residue 622 MET Chi-restraints excluded: chain 7 residue 742 MET Chi-restraints excluded: chain 3 residue 30 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 472 optimal weight: 50.0000 chunk 304 optimal weight: 7.9990 chunk 455 optimal weight: 30.0000 chunk 229 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 chunk 147 optimal weight: 3.9990 chunk 485 optimal weight: 50.0000 chunk 520 optimal weight: 10.0000 chunk 377 optimal weight: 3.9990 chunk 71 optimal weight: 20.0000 chunk 600 optimal weight: 20.0000 overall best weight: 7.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 ASN A 650 GLN ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1093 GLN ** B1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 ASN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 79 HIS ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 251 ASN ** O 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 188 ASN ** 4 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4614 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 65850 Z= 0.369 Angle : 0.749 15.313 89356 Z= 0.383 Chirality : 0.046 0.301 10069 Planarity : 0.005 0.073 11222 Dihedral : 13.020 174.832 10044 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 19.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.61 % Favored : 90.32 % Rotamer: Outliers : 2.16 % Allowed : 15.75 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 0.59 % Twisted General : 0.09 % 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: -1.70 (0.09), residues: 7932 helix: 0.21 (0.09), residues: 3209 sheet: -1.80 (0.16), residues: 926 loop : -2.17 (0.10), residues: 3797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 170 HIS 0.042 0.002 HIS I 79 PHE 0.024 0.002 PHE 3 47 TYR 0.032 0.002 TYR 7 365 ARG 0.007 0.001 ARG H 146 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15864 Ramachandran restraints generated. 7932 Oldfield, 0 Emsley, 7932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15864 Ramachandran restraints generated. 7932 Oldfield, 0 Emsley, 7932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 7227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 222 time to evaluate : 5.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 PHE cc_start: 0.6229 (OUTLIER) cc_final: 0.5568 (m-80) REVERT: D 189 ASP cc_start: 0.2004 (OUTLIER) cc_final: 0.1738 (t0) REVERT: E 57 MET cc_start: 0.6048 (ppp) cc_final: 0.5842 (ppp) REVERT: G 119 LEU cc_start: -0.1074 (OUTLIER) cc_final: -0.1418 (mt) REVERT: U 244 MET cc_start: -0.0431 (ptt) cc_final: -0.1365 (ptt) REVERT: 1 350 ARG cc_start: -0.1393 (OUTLIER) cc_final: -0.2371 (pmt-80) REVERT: 4 305 CYS cc_start: -0.0287 (OUTLIER) cc_final: -0.2191 (t) REVERT: 0 61 MET cc_start: 0.2718 (mtm) cc_final: 0.1256 (ptm) REVERT: 0 199 MET cc_start: -0.4039 (OUTLIER) cc_final: -0.4474 (mpp) REVERT: 0 346 MET cc_start: -0.1328 (tpp) cc_final: -0.2572 (tmm) REVERT: 0 485 MET cc_start: -0.0597 (OUTLIER) cc_final: -0.0931 (mmt) REVERT: 0 659 MET cc_start: 0.0094 (mmt) cc_final: -0.0293 (mmt) REVERT: 6 192 HIS cc_start: 0.0495 (OUTLIER) cc_final: 0.0283 (m170) REVERT: 7 304 GLU cc_start: -0.1807 (OUTLIER) cc_final: -0.2399 (pt0) outliers start: 139 outliers final: 98 residues processed: 338 average time/residue: 0.6015 time to fit residues: 363.8130 Evaluate side-chains 328 residues out of total 7227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 221 time to evaluate : 5.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 PHE Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 529 CYS Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1240 CYS Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1287 TYR Chi-restraints excluded: chain A residue 1387 HIS Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 797 TYR Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 1006 ILE Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1113 VAL Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 44 TYR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 10 CYS Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 79 HIS Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 58 ASP Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 119 MET Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 188 THR Chi-restraints excluded: chain M residue 301 THR Chi-restraints excluded: chain M residue 308 THR Chi-restraints excluded: chain Q residue 380 ASP Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain W residue 142 PHE Chi-restraints excluded: chain O residue 104 MET Chi-restraints excluded: chain O residue 203 VAL Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain 1 residue 350 ARG Chi-restraints excluded: chain 4 residue 32 ILE Chi-restraints excluded: chain 4 residue 197 MET Chi-restraints excluded: chain 4 residue 305 CYS Chi-restraints excluded: chain 0 residue 1 MET Chi-restraints excluded: chain 0 residue 34 VAL Chi-restraints excluded: chain 0 residue 65 GLU Chi-restraints excluded: chain 0 residue 148 ASP Chi-restraints excluded: chain 0 residue 167 VAL Chi-restraints excluded: chain 0 residue 199 MET Chi-restraints excluded: chain 0 residue 231 ILE Chi-restraints excluded: chain 0 residue 290 VAL Chi-restraints excluded: chain 0 residue 349 LEU Chi-restraints excluded: chain 0 residue 485 MET Chi-restraints excluded: chain 0 residue 538 VAL Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 6 residue 192 HIS Chi-restraints excluded: chain 6 residue 290 ILE Chi-restraints excluded: chain 6 residue 310 VAL Chi-restraints excluded: chain 2 residue 48 MET Chi-restraints excluded: chain 2 residue 52 PHE Chi-restraints excluded: chain 2 residue 371 VAL Chi-restraints excluded: chain 2 residue 373 MET Chi-restraints excluded: chain 7 residue 304 GLU Chi-restraints excluded: chain 7 residue 337 VAL Chi-restraints excluded: chain 7 residue 343 PHE Chi-restraints excluded: chain 7 residue 348 ARG Chi-restraints excluded: chain 7 residue 365 TYR Chi-restraints excluded: chain 7 residue 449 GLU Chi-restraints excluded: chain 7 residue 501 VAL Chi-restraints excluded: chain 7 residue 514 THR Chi-restraints excluded: chain 7 residue 561 MET Chi-restraints excluded: chain 7 residue 745 ILE Chi-restraints excluded: chain 3 residue 30 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 694 optimal weight: 20.0000 chunk 731 optimal weight: 9.9990 chunk 667 optimal weight: 9.9990 chunk 711 optimal weight: 40.0000 chunk 428 optimal weight: 6.9990 chunk 309 optimal weight: 0.8980 chunk 558 optimal weight: 9.9990 chunk 218 optimal weight: 6.9990 chunk 642 optimal weight: 50.0000 chunk 672 optimal weight: 3.9990 chunk 708 optimal weight: 8.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 ASN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 79 HIS ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 188 ASN ** 4 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 577 GLN ** 0 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4580 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 65850 Z= 0.290 Angle : 0.701 16.378 89356 Z= 0.359 Chirality : 0.044 0.305 10069 Planarity : 0.005 0.071 11222 Dihedral : 13.012 173.799 10044 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.71 % Favored : 91.21 % Rotamer: Outliers : 1.80 % Allowed : 16.39 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 0.29 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.09), residues: 7932 helix: 0.29 (0.09), residues: 3218 sheet: -1.75 (0.16), residues: 962 loop : -2.11 (0.10), residues: 3752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 170 HIS 0.023 0.001 HIS I 79 PHE 0.025 0.002 PHE 3 47 TYR 0.033 0.002 TYR 7 365 ARG 0.006 0.000 ARG 7 466 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15864 Ramachandran restraints generated. 7932 Oldfield, 0 Emsley, 7932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15864 Ramachandran restraints generated. 7932 Oldfield, 0 Emsley, 7932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 7227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 223 time to evaluate : 6.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 189 ASP cc_start: 0.1906 (OUTLIER) cc_final: 0.1555 (t0) REVERT: M 105 ARG cc_start: 0.5340 (tmm-80) cc_final: 0.3933 (mpt-90) REVERT: U 244 MET cc_start: -0.0591 (ptt) cc_final: -0.1493 (ptt) REVERT: 0 61 MET cc_start: 0.2712 (mtm) cc_final: 0.1265 (ptm) REVERT: 0 199 MET cc_start: -0.4040 (mpp) cc_final: -0.4289 (mpp) REVERT: 0 346 MET cc_start: -0.1427 (tpp) cc_final: -0.3061 (tmm) REVERT: 0 485 MET cc_start: -0.0560 (OUTLIER) cc_final: -0.0906 (mmt) REVERT: 0 659 MET cc_start: 0.0493 (mmt) cc_final: 0.0144 (mmt) REVERT: 6 192 HIS cc_start: 0.0437 (OUTLIER) cc_final: 0.0195 (m170) REVERT: 7 304 GLU cc_start: -0.1595 (OUTLIER) cc_final: -0.2304 (pt0) REVERT: 7 561 MET cc_start: -0.2867 (OUTLIER) cc_final: -0.3461 (tmm) outliers start: 116 outliers final: 92 residues processed: 324 average time/residue: 0.5701 time to fit residues: 333.4665 Evaluate side-chains 320 residues out of total 7227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 223 time to evaluate : 5.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 529 CYS Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1278 ASN Chi-restraints excluded: chain A residue 1287 TYR Chi-restraints excluded: chain A residue 1387 HIS Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 797 TYR Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 1006 ILE Chi-restraints excluded: chain B residue 1113 VAL Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 44 TYR Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain I residue 10 CYS Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 78 CYS Chi-restraints excluded: chain I residue 79 HIS Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 119 MET Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 188 THR Chi-restraints excluded: chain M residue 301 THR Chi-restraints excluded: chain M residue 308 THR Chi-restraints excluded: chain Q residue 380 ASP Chi-restraints excluded: chain Q residue 386 MET Chi-restraints excluded: chain R residue 121 ASP Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain O residue 104 MET Chi-restraints excluded: chain O residue 203 VAL Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain 4 residue 32 ILE Chi-restraints excluded: chain 4 residue 197 MET Chi-restraints excluded: chain 4 residue 238 VAL Chi-restraints excluded: chain 0 residue 1 MET Chi-restraints excluded: chain 0 residue 34 VAL Chi-restraints excluded: chain 0 residue 65 GLU Chi-restraints excluded: chain 0 residue 148 ASP Chi-restraints excluded: chain 0 residue 231 ILE Chi-restraints excluded: chain 0 residue 485 MET Chi-restraints excluded: chain 0 residue 538 VAL Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 6 residue 126 LEU Chi-restraints excluded: chain 6 residue 192 HIS Chi-restraints excluded: chain 6 residue 263 VAL Chi-restraints excluded: chain 6 residue 290 ILE Chi-restraints excluded: chain 6 residue 310 VAL Chi-restraints excluded: chain 2 residue 48 MET Chi-restraints excluded: chain 2 residue 371 VAL Chi-restraints excluded: chain 7 residue 304 GLU Chi-restraints excluded: chain 7 residue 337 VAL Chi-restraints excluded: chain 7 residue 343 PHE Chi-restraints excluded: chain 7 residue 365 TYR Chi-restraints excluded: chain 7 residue 449 GLU Chi-restraints excluded: chain 7 residue 501 VAL Chi-restraints excluded: chain 7 residue 514 THR Chi-restraints excluded: chain 7 residue 561 MET Chi-restraints excluded: chain 7 residue 745 ILE Chi-restraints excluded: chain 3 residue 30 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 467 optimal weight: 2.9990 chunk 752 optimal weight: 8.9990 chunk 459 optimal weight: 50.0000 chunk 356 optimal weight: 10.0000 chunk 522 optimal weight: 50.0000 chunk 789 optimal weight: 30.0000 chunk 726 optimal weight: 50.0000 chunk 628 optimal weight: 20.0000 chunk 65 optimal weight: 6.9990 chunk 485 optimal weight: 40.0000 chunk 385 optimal weight: 9.9990 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 ASN ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1093 GLN ** B1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 12 ASN ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 269 GLN ** 6 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 405 HIS ** 7 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4669 moved from start: 0.5201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.118 65850 Z= 0.389 Angle : 0.788 19.021 89356 Z= 0.401 Chirality : 0.046 0.378 10069 Planarity : 0.005 0.075 11222 Dihedral : 13.244 174.649 10044 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 21.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.53 % Favored : 89.38 % Rotamer: Outliers : 1.85 % Allowed : 16.48 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 0.59 % Twisted General : 0.14 % 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: -1.86 (0.09), residues: 7932 helix: 0.06 (0.09), residues: 3214 sheet: -1.83 (0.16), residues: 916 loop : -2.26 (0.10), residues: 3802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 170 HIS 0.073 0.002 HIS I 79 PHE 0.026 0.002 PHE 0 612 TYR 0.033 0.002 TYR 7 365 ARG 0.015 0.001 ARG A1194 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15864 Ramachandran restraints generated. 7932 Oldfield, 0 Emsley, 7932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15864 Ramachandran restraints generated. 7932 Oldfield, 0 Emsley, 7932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 7227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 222 time to evaluate : 5.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 923 LEU cc_start: 0.6579 (OUTLIER) cc_final: 0.6239 (mm) REVERT: B 1098 MET cc_start: 0.5852 (mpp) cc_final: 0.5473 (mpp) REVERT: U 244 MET cc_start: -0.0685 (ptt) cc_final: -0.2041 (ptt) REVERT: O 240 MET cc_start: 0.4256 (mmm) cc_final: 0.4046 (mmm) REVERT: 0 61 MET cc_start: 0.2445 (mtm) cc_final: 0.1208 (ptm) REVERT: 0 199 MET cc_start: -0.3818 (mpp) cc_final: -0.4078 (mpp) REVERT: 0 346 MET cc_start: -0.1556 (tpp) cc_final: -0.3146 (tmm) REVERT: 0 485 MET cc_start: -0.0656 (OUTLIER) cc_final: -0.1016 (mmt) REVERT: 0 547 MET cc_start: 0.1722 (ptp) cc_final: 0.1495 (ptp) REVERT: 0 659 MET cc_start: 0.0534 (mmt) cc_final: 0.0158 (mmt) REVERT: 7 304 GLU cc_start: -0.1511 (OUTLIER) cc_final: -0.2145 (pt0) REVERT: 7 561 MET cc_start: -0.3035 (OUTLIER) cc_final: -0.3382 (tmm) outliers start: 119 outliers final: 95 residues processed: 323 average time/residue: 0.5618 time to fit residues: 328.0782 Evaluate side-chains 320 residues out of total 7227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 221 time to evaluate : 5.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 529 CYS Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1278 ASN Chi-restraints excluded: chain A residue 1287 TYR Chi-restraints excluded: chain A residue 1387 HIS Chi-restraints excluded: chain A residue 1433 MET Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 797 TYR Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 1006 ILE Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1113 VAL Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 44 TYR Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain I residue 10 CYS Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 78 CYS Chi-restraints excluded: chain I residue 79 HIS Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 23 THR Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 58 ASP Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 119 MET Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 188 THR Chi-restraints excluded: chain M residue 301 THR Chi-restraints excluded: chain M residue 308 THR Chi-restraints excluded: chain Q residue 386 MET Chi-restraints excluded: chain R residue 121 ASP Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain O residue 104 MET Chi-restraints excluded: chain O residue 203 VAL Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain 4 residue 32 ILE Chi-restraints excluded: chain 4 residue 197 MET Chi-restraints excluded: chain 4 residue 238 VAL Chi-restraints excluded: chain 0 residue 1 MET Chi-restraints excluded: chain 0 residue 34 VAL Chi-restraints excluded: chain 0 residue 148 ASP Chi-restraints excluded: chain 0 residue 156 CYS Chi-restraints excluded: chain 0 residue 167 VAL Chi-restraints excluded: chain 0 residue 290 VAL Chi-restraints excluded: chain 0 residue 485 MET Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 6 residue 126 LEU Chi-restraints excluded: chain 6 residue 263 VAL Chi-restraints excluded: chain 6 residue 290 ILE Chi-restraints excluded: chain 6 residue 310 VAL Chi-restraints excluded: chain 2 residue 371 VAL Chi-restraints excluded: chain 7 residue 304 GLU Chi-restraints excluded: chain 7 residue 337 VAL Chi-restraints excluded: chain 7 residue 343 PHE Chi-restraints excluded: chain 7 residue 365 TYR Chi-restraints excluded: chain 7 residue 449 GLU Chi-restraints excluded: chain 7 residue 501 VAL Chi-restraints excluded: chain 7 residue 514 THR Chi-restraints excluded: chain 7 residue 561 MET Chi-restraints excluded: chain 7 residue 745 ILE Chi-restraints excluded: chain 3 residue 30 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 499 optimal weight: 50.0000 chunk 669 optimal weight: 0.9990 chunk 192 optimal weight: 9.9990 chunk 579 optimal weight: 50.0000 chunk 92 optimal weight: 5.9990 chunk 174 optimal weight: 8.9990 chunk 629 optimal weight: 5.9990 chunk 263 optimal weight: 6.9990 chunk 646 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 115 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.056106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.047250 restraints weight = 819607.427| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 5.53 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3795 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3795 r_free = 0.3795 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 363 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3794 r_free = 0.3794 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 363 | |-----------------------------------------------------------------------------| r_final: 0.3794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.370 65850 Z= 0.396 Angle : 0.825 65.899 89356 Z= 0.433 Chirality : 0.046 0.547 10069 Planarity : 0.006 0.281 11222 Dihedral : 13.242 174.634 10044 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 22.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.45 % Favored : 89.46 % Rotamer: Outliers : 1.74 % Allowed : 16.76 % Favored : 81.50 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.07 % Twisted Proline : 0.59 % Twisted General : 0.14 % 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: -1.86 (0.09), residues: 7932 helix: 0.06 (0.09), residues: 3210 sheet: -1.84 (0.16), residues: 916 loop : -2.26 (0.10), residues: 3806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 170 HIS 0.068 0.002 HIS I 79 PHE 0.024 0.002 PHE 0 612 TYR 0.033 0.002 TYR 7 365 ARG 0.009 0.000 ARG A1194 =============================================================================== Job complete usr+sys time: 9273.58 seconds wall clock time: 167 minutes 38.84 seconds (10058.84 seconds total)