Starting phenix.real_space_refine on Mon Dec 30 08:16:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ml4_23908/12_2024/7ml4_23908.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ml4_23908/12_2024/7ml4_23908.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ml4_23908/12_2024/7ml4_23908.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ml4_23908/12_2024/7ml4_23908.map" model { file = "/net/cci-nas-00/data/ceres_data/7ml4_23908/12_2024/7ml4_23908.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ml4_23908/12_2024/7ml4_23908.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.002 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 15 6.06 5 P 90 5.49 5 Mg 1 5.21 5 S 347 5.16 5 C 39269 2.51 5 N 11015 2.21 5 O 11992 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 185 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 62733 Number of models: 1 Model: "" Number of chains: 55 Chain: "Q" Number of atoms: 1141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1141 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 141} Chain breaks: 3 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 108 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: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1039 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 7, 'TRANS': 146} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 352 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 6, 'TYR:plan': 6, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 152 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: "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: "M" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1805 Classifications: {'peptide': 234} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 224} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 11039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1405, 11039 Classifications: {'peptide': 1405} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 62, 'TRANS': 1339} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 8861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1114, 8861 Classifications: {'peptide': 1114} Link IDs: {'CIS': 3, 'PTRANS': 50, 'TRANS': 1060} Chain breaks: 8 Chain: "C" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2095 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain: "E" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1752 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain: "F" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 688 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 77} Chain: "H" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1068 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain breaks: 1 Chain: "I" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 971 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} 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: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 919 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "L" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 363 Classifications: {'peptide': 46} Link IDs: {'TRANS': 45} Chain: "3" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 361 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'TRANS': 71} Unresolved non-hydrogen bonds: 257 Unresolved non-hydrogen angles: 328 Unresolved non-hydrogen dihedrals: 206 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 5, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 153 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: "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: "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: "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: "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: "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: "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: "X" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 921 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 6, 'TRANS': 142} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 330 Unresolved non-hydrogen angles: 418 Unresolved non-hydrogen dihedrals: 285 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'TYR:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 6, 'HIS:plan': 2} 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: "N" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 791 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "T" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 968 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Chain breaks: 1 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: "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: "P" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 110 Classifications: {'RNA': 5} Modifications used: {'5*END': 1, 'rna3p_pur': 5} Link IDs: {'rna3p': 4} 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: "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: "0" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 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: "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: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4794 SG CYS M 24 58.028 100.395 129.695 1.00110.50 S ATOM 4816 SG CYS M 27 54.128 100.591 129.928 1.00115.03 S ATOM 4956 SG CYS M 45 55.889 102.109 127.205 1.00109.04 S ATOM 4975 SG CYS M 48 56.307 103.661 130.592 1.00 92.60 S ATOM 7391 SG CYS A 107 126.662 117.400 110.991 1.00 23.17 S ATOM 7415 SG CYS A 110 127.562 116.948 114.506 1.00 23.38 S ATOM 7720 SG CYS A 148 129.266 119.454 112.197 1.00 24.08 S ATOM 7810 SG CYS A 167 130.035 115.715 111.858 1.00 25.98 S ATOM 7086 SG CYS A 67 83.357 101.068 119.837 1.00 20.38 S ATOM 7108 SG CYS A 70 84.372 100.258 123.442 1.00 20.45 S ATOM 7161 SG CYS A 77 83.031 104.128 121.710 1.00 18.80 S ATOM 25985 SG CYS B1163 96.335 106.674 131.442 1.00 15.39 S ATOM 26003 SG CYS B1166 96.359 108.013 128.230 1.00 15.37 S ATOM 26128 SG CYS B1182 95.459 104.365 128.596 1.00 18.55 S ATOM 26147 SG CYS B1185 99.120 105.531 129.152 1.00 18.12 S ATOM 27134 SG CYS C 86 18.863 126.378 121.485 1.00 9.53 S ATOM 27151 SG CYS C 88 20.618 124.231 119.346 1.00 8.80 S ATOM 27184 SG CYS C 92 17.259 126.105 118.366 1.00 10.47 S ATOM 27207 SG CYS C 95 20.770 127.868 118.484 1.00 9.60 S ATOM 32134 SG CYS I 7 123.629 164.058 63.110 1.00 14.23 S ATOM 32159 SG CYS I 10 123.847 160.048 63.086 1.00 14.85 S ATOM 32325 SG CYS I 29 124.528 161.768 66.107 1.00 14.43 S ATOM 32349 SG CYS I 32 126.761 162.391 63.009 1.00 15.54 S ATOM 32676 SG CYS I 75 89.635 192.317 74.083 1.00 10.20 S ATOM 32698 SG CYS I 78 86.957 193.086 71.054 1.00 11.15 S ATOM 32914 SG CYS I 103 87.264 189.811 72.222 1.00 11.45 S ATOM 32934 SG CYS I 106 90.334 190.902 70.953 1.00 11.36 S ATOM 33106 SG CYS J 7 34.416 153.498 106.504 1.00 8.02 S ATOM 33129 SG CYS J 10 31.081 154.893 108.428 1.00 7.76 S ATOM 33409 SG CYS J 45 34.103 157.071 107.594 1.00 7.48 S ATOM 33415 SG CYS J 46 31.861 156.027 105.261 1.00 8.35 S ATOM 34558 SG CYS L 31 42.150 119.261 80.687 1.00 15.39 S ATOM 34682 SG CYS L 48 42.063 116.165 78.295 1.00 15.92 S ATOM 36165 SG CYS 0 115 135.778 33.058 79.355 1.00117.61 S ATOM 36307 SG CYS 0 133 132.160 30.768 81.628 1.00 46.59 S ATOM 36492 SG CYS 0 156 130.333 29.235 79.373 1.00 90.79 S ATOM 36793 SG CYS 0 191 136.102 26.541 79.405 1.00115.32 S ATOM 43171 SG CYS 4 289 197.682 26.792 49.225 1.00 0.00 S ATOM 43190 SG CYS 4 292 200.151 25.706 51.708 1.00 0.00 S ATOM 43275 SG CYS 4 305 199.325 23.464 48.465 1.00 0.00 S ATOM 43291 SG CYS 4 308 197.092 23.645 51.468 1.00 0.00 S ATOM 45589 SG CYS 6 403 219.443 35.762 76.697 1.00 0.00 S ATOM 45611 SG CYS 6 406 219.624 39.150 75.134 1.00 0.00 S ATOM 45779 SG CYS 6 437 217.369 38.561 78.113 1.00 0.00 S ATOM 45795 SG CYS 6 440 216.506 37.105 74.574 1.00 0.00 S ATOM 45737 SG CYS 6 429 211.125 27.836 72.024 1.00 0.00 S ATOM 45753 SG CYS 6 432 214.811 27.307 72.555 1.00 0.00 S ATOM 45873 SG CYS 6 451 213.752 30.309 70.643 1.00 0.00 S ATOM 45888 SG CYS 6 454 213.298 26.896 69.028 1.00 0.00 S ATOM 45234 SG CYS 6 349 201.272 42.722 35.784 1.00 0.00 S ATOM 45255 SG CYS 6 352 200.091 45.701 33.955 1.00 0.00 S ATOM 45324 SG CYS 6 363 198.512 44.831 37.368 1.00 0.00 S ATOM 45342 SG CYS 6 366 197.790 42.661 34.328 1.00 0.00 S ATOM 45151 SG CYS 6 336 202.771 57.246 38.043 1.00 30.00 S ATOM 45162 SG CYS 6 338 200.753 54.413 39.663 1.00 30.00 S ATOM 45289 SG CYS 6 357 203.553 56.142 41.620 1.00 30.00 S ATOM 62031 SG CYS W 124 84.143 82.171 122.446 1.00 0.00 S ATOM 62052 SG CYS W 127 84.288 84.184 122.183 1.00 0.00 S ATOM 62257 SG CYS W 152 80.110 83.129 120.844 1.00 0.00 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" P DG N 27 " occ=0.00 ... (20 atoms not shown) pdb=" C4 DG N 27 " occ=0.00 residue: pdb=" P DG N 33 " occ=0.00 ... (20 atoms not shown) pdb=" C4 DG N 33 " occ=0.00 residue: pdb=" P DC T 133 " occ=0.00 ... (17 atoms not shown) pdb=" C6 DC T 133 " occ=0.00 residue: pdb=" P DC T 139 " occ=0.00 ... (17 atoms not shown) pdb=" C6 DC T 139 " occ=0.00 Time building chain proxies: 24.32, per 1000 atoms: 0.39 Number of scatterers: 62733 At special positions: 0 Unit cell: (268.18, 208.82, 186.56, 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 15 29.99 Fe 4 26.01 S 347 16.00 P 90 15.00 Mg 1 11.99 O 11992 8.00 N 11015 7.00 C 39269 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: 12.32 Conformation dependent library (CDL) restraints added in 5.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 0 801 " pdb="FE3 SF4 0 801 " - pdb=" SG CYS 0 133 " pdb="FE3 SF4 0 801 " - pdb=" SG CYS 0 156 " pdb="FE1 SF4 0 801 " - pdb=" SG CYS 0 115 " pdb="FE4 SF4 0 801 " - pdb=" SG CYS 0 191 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN 4 401 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 308 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 289 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 292 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 305 " pdb=" ZN 6 501 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 406 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 403 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 437 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 440 " pdb=" ZN 6 502 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 432 " 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 6 454 " pdb=" ZN 6 503 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 349 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 352 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 366 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 363 " pdb=" ZN 6 504 " pdb="ZN ZN 6 504 " - pdb=" ND1 HIS 6 339 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 357 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 338 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 336 " pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1802 " - pdb=" NE2 GLN A 68 " 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 B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " 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 I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 45 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 48 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 24 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 27 " pdb=" ZN W 501 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 124 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 127 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 152 " Number of angles added : 72 15518 Ramachandran restraints generated. 7759 Oldfield, 0 Emsley, 7759 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14630 Finding SS restraints... Secondary structure from input PDB file: 311 helices and 77 sheets defined 45.2% alpha, 12.6% beta 30 base pairs and 54 stacking pairs defined. Time for finding SS restraints: 17.78 Creating SS restraints... Processing helix chain 'Q' and resid 26 through 35 Processing helix chain 'Q' and resid 107 through 114 removed outlier: 3.590A pdb=" N LEU Q 111 " --> pdb=" O PRO Q 107 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN Q 113 " --> pdb=" O GLU Q 109 " (cutoff:3.500A) Processing helix chain 'Q' and resid 337 through 345 Processing helix chain 'Q' and resid 407 through 415 removed outlier: 4.089A pdb=" N ASP Q 414 " --> pdb=" O GLU Q 410 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS Q 415 " --> pdb=" O LYS Q 411 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 79 Processing helix chain 'R' and resid 80 through 82 No H-bonds generated for 'chain 'R' and resid 80 through 82' Processing helix chain 'R' and resid 234 through 242 Processing helix chain 'R' and resid 295 through 311 Processing helix chain 'R' and resid 314 through 323 removed outlier: 3.594A pdb=" N LYS R 319 " --> pdb=" O LEU R 315 " (cutoff:3.500A) Processing helix chain 'R' and resid 325 through 336 removed outlier: 3.953A pdb=" N LEU R 329 " --> pdb=" O PRO R 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 34 Processing helix chain 'D' and resid 54 through 76 removed outlier: 4.141A pdb=" N GLU D 61 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN D 74 " --> pdb=" O PHE D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 134 removed outlier: 4.037A pdb=" N ILE D 126 " --> pdb=" O GLU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 152 Processing helix chain 'D' and resid 157 through 170 Processing helix chain 'D' and resid 173 through 183 Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.844A pdb=" N TYR G 25 " --> pdb=" O ARG G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'M' and resid 122 through 141 removed outlier: 4.088A pdb=" N VAL M 126 " --> pdb=" O LYS M 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 143 through 158 Processing helix chain 'M' and resid 169 through 183 Processing helix chain 'M' and resid 188 through 196 Processing helix chain 'M' and resid 200 through 218 Processing helix chain 'M' and resid 237 through 247 removed outlier: 4.438A pdb=" N ARG M 241 " --> pdb=" O THR M 237 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE M 242 " --> pdb=" O TYR M 238 " (cutoff:3.500A) Processing helix chain 'M' and resid 249 through 266 removed outlier: 3.677A pdb=" N LYS M 264 " --> pdb=" O ALA M 260 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU M 265 " --> pdb=" O LYS M 261 " (cutoff:3.500A) Processing helix chain 'M' and resid 274 through 289 Processing helix chain 'M' and resid 294 through 303 removed outlier: 4.022A pdb=" N VAL M 298 " --> pdb=" O THR M 294 " (cutoff:3.500A) Processing helix chain 'M' and resid 307 through 320 removed outlier: 3.967A pdb=" N ILE M 315 " --> pdb=" O SER M 311 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU M 318 " --> pdb=" O LYS M 314 " (cutoff:3.500A) Processing helix chain 'M' and resid 321 through 324 removed outlier: 4.447A pdb=" N VAL M 324 " --> pdb=" O ASP M 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 321 through 324' Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 95 through 104 Processing helix chain 'A' and resid 119 through 128 removed outlier: 3.604A pdb=" N ALA A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 203 through 213 removed outlier: 3.982A pdb=" N ILE A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 222 Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 260 through 282 Processing helix chain 'A' and resid 288 through 305 removed outlier: 3.690A pdb=" N LEU A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 367 through 372 Processing helix chain 'A' and resid 384 through 394 Processing helix chain 'A' and resid 416 through 418 No H-bonds generated for 'chain 'A' and resid 416 through 418' Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.658A pdb=" N TYR A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 507 through 511 Processing helix chain 'A' and resid 524 through 536 removed outlier: 3.564A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 Processing helix chain 'A' and resid 574 through 582 removed outlier: 4.009A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.732A 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 Proline residue: A 639 - end of helix Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 672 through 699 Processing helix chain 'A' and resid 709 through 737 Processing helix chain 'A' and resid 741 through 749 Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 809 through 845 removed outlier: 3.584A pdb=" N ALA A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 874 through 878 Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 909 through 913 removed outlier: 3.694A pdb=" N LEU A 912 " --> pdb=" O ASP A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 920 removed outlier: 3.546A pdb=" N ILE A 919 " --> pdb=" O SER A 915 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU A 920 " --> pdb=" O GLY A 916 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 915 through 920' Processing helix chain 'A' and resid 925 through 947 Processing helix chain 'A' and resid 959 through 972 removed outlier: 3.641A pdb=" N ILE A 963 " --> pdb=" O ASN A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 996 Processing helix chain 'A' and resid 1004 through 1026 removed outlier: 4.619A pdb=" N LEU A1017 " --> pdb=" O ASP A1013 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N PHE A1018 " --> pdb=" O ALA A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1034 Processing helix chain 'A' and resid 1038 through 1056 Processing helix chain 'A' and resid 1063 through 1079 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1089 through 1093 Processing helix chain 'A' and resid 1096 through 1106 Processing helix chain 'A' and resid 1127 through 1139 Processing helix chain 'A' and resid 1165 through 1171 removed outlier: 3.786A pdb=" N ILE A1169 " --> pdb=" O GLU A1165 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1205 Processing helix chain 'A' and resid 1208 through 1220 Processing helix chain 'A' and resid 1258 through 1270 Processing helix chain 'A' and resid 1312 through 1318 removed outlier: 3.883A pdb=" N THR A1318 " --> pdb=" O SER A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1359 removed outlier: 7.514A pdb=" N ILE A1341 " --> pdb=" O GLU A1337 " (cutoff:3.500A) removed outlier: 9.033A pdb=" N GLU A1342 " --> pdb=" O VAL A1338 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA A1343 " --> pdb=" O LEU A1339 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP A1359 " --> pdb=" O VAL A1355 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1376 removed outlier: 3.903A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1392 Processing helix chain 'A' and resid 1395 through 1401 Processing helix chain 'A' and resid 1404 through 1415 Processing helix chain 'A' and resid 1423 through 1431 removed outlier: 3.604A pdb=" N ASN A1427 " --> pdb=" O GLY A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1440 Processing helix chain 'B' and resid 29 through 37 removed outlier: 3.784A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 57 Processing helix chain 'B' and resid 57 through 64 Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 179 through 183 removed outlier: 4.364A 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 300 Processing helix chain 'B' and resid 307 through 322 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 334 removed outlier: 3.728A pdb=" N ILE B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 360 removed outlier: 3.660A pdb=" N PHE B 360 " --> pdb=" O LEU B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 390 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 435 Processing helix chain 'B' and resid 449 through 464 removed outlier: 4.238A pdb=" N ILE B 453 " --> pdb=" O ASN B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 570 through 574 Processing helix chain 'B' and resid 592 through 605 removed outlier: 3.834A pdb=" N LEU B 596 " --> pdb=" O ASN B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 667 Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 695 through 699 removed outlier: 3.729A 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 749 removed outlier: 3.574A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 756 Processing helix chain 'B' and resid 758 through 762 Processing helix chain 'B' and resid 763 through 774 removed outlier: 3.525A pdb=" N ASN B 767 " --> pdb=" O GLN B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 811 Processing helix chain 'B' and resid 813 through 817 Processing helix chain 'B' and resid 843 through 849 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.580A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.703A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1062 removed outlier: 3.585A pdb=" N ILE B1055 " --> pdb=" O THR B1051 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1121 through 1125 Processing helix chain 'B' and resid 1131 through 1141 Processing helix chain 'B' and resid 1143 through 1153 Processing helix chain 'B' and resid 1198 through 1210 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 204 through 210 removed outlier: 3.912A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 268 Processing helix chain 'E' and resid 3 through 27 Processing helix chain 'E' and resid 31 through 36 removed outlier: 3.696A pdb=" N GLU E 36 " --> pdb=" O GLN E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 47 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 102 removed outlier: 3.836A pdb=" N GLN E 101 " --> pdb=" O VAL E 97 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU E 102 " --> pdb=" O ILE E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 123 removed outlier: 3.604A pdb=" N LEU E 123 " --> pdb=" O SER E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 127 removed outlier: 4.435A pdb=" N ILE E 127 " --> pdb=" O VAL E 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 124 through 127' Processing helix chain 'E' and resid 138 through 141 Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'H' and resid 130 through 134 removed outlier: 4.089A pdb=" N ASN H 133 " --> pdb=" O ARG H 130 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN H 134 " --> pdb=" O ASN H 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 130 through 134' Processing helix chain 'I' and resid 61 through 65 Processing helix chain 'J' and resid 16 through 29 removed outlier: 4.644A pdb=" N SER J 20 " --> pdb=" O ASP J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 40 Processing helix chain 'J' and resid 43 through 52 removed outlier: 4.016A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 53 removed outlier: 3.934A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP K 53 " --> pdb=" O GLU K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 111 Processing helix chain '3' and resid 75 through 91 removed outlier: 3.504A pdb=" N LYS 3 80 " --> pdb=" O VAL 3 76 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU 3 81 " --> pdb=" O GLU 3 77 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL 3 82 " --> pdb=" O VAL 3 78 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP 3 83 " --> pdb=" O GLU 3 79 " (cutoff:3.500A) Processing helix chain '3' and resid 92 through 95 Processing helix chain '3' and resid 102 through 123 removed outlier: 3.882A pdb=" N LYS 3 119 " --> pdb=" O ASP 3 115 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS 3 122 " --> pdb=" O TYR 3 118 " (cutoff:3.500A) Processing helix chain '3' and resid 128 through 145 Processing helix chain '0' and resid 18 through 34 removed outlier: 3.815A pdb=" N LYS 0 30 " --> pdb=" O CYS 0 26 " (cutoff:3.500A) Processing helix chain '0' and resid 47 through 63 removed outlier: 3.844A pdb=" N SER 0 51 " --> pdb=" O GLY 0 47 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR 0 56 " --> pdb=" O LEU 0 52 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN 0 60 " --> pdb=" O THR 0 56 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N MET 0 61 " --> pdb=" O ILE 0 57 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS 0 62 " --> pdb=" O ALA 0 58 " (cutoff:3.500A) Processing helix chain '0' and resid 75 through 98 removed outlier: 3.906A pdb=" N ASN 0 88 " --> pdb=" O VAL 0 84 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU 0 89 " --> pdb=" O GLU 0 85 " (cutoff:3.500A) Processing helix chain '0' and resid 117 through 122 removed outlier: 3.638A pdb=" N LYS 0 122 " --> pdb=" O PRO 0 118 " (cutoff:3.500A) Processing helix chain '0' and resid 125 through 137 Processing helix chain '0' and resid 142 through 147 removed outlier: 3.683A pdb=" N GLU 0 146 " --> pdb=" O LYS 0 142 " (cutoff:3.500A) Processing helix chain '0' and resid 158 through 165 Processing helix chain '0' and resid 177 through 188 removed outlier: 3.738A pdb=" N GLU 0 187 " --> pdb=" O LYS 0 183 " (cutoff:3.500A) Processing helix chain '0' and resid 191 through 199 removed outlier: 3.815A pdb=" N ILE 0 195 " --> pdb=" O CYS 0 191 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG 0 198 " --> pdb=" O PHE 0 194 " (cutoff:3.500A) Processing helix chain '0' and resid 200 through 202 No H-bonds generated for 'chain '0' and resid 200 through 202' Processing helix chain '0' and resid 210 through 215 Processing helix chain '0' and resid 223 through 227 Processing helix chain '0' and resid 237 through 239 No H-bonds generated for 'chain '0' and resid 237 through 239' Processing helix chain '0' and resid 240 through 248 removed outlier: 3.515A pdb=" N CYS 0 244 " --> pdb=" O ILE 0 240 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU 0 246 " --> pdb=" O ASN 0 242 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU 0 248 " --> pdb=" O CYS 0 244 " (cutoff:3.500A) Processing helix chain '0' and resid 253 through 278 removed outlier: 3.585A pdb=" N ARG 0 258 " --> pdb=" O THR 0 254 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG 0 275 " --> pdb=" O ILE 0 271 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS 0 276 " --> pdb=" O SER 0 272 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL 0 277 " --> pdb=" O GLU 0 273 " (cutoff:3.500A) Processing helix chain '0' and resid 278 through 285 removed outlier: 3.570A pdb=" N LEU 0 282 " --> pdb=" O ASP 0 278 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU 0 285 " --> pdb=" O LYS 0 281 " (cutoff:3.500A) Processing helix chain '0' and resid 286 through 292 removed outlier: 3.525A pdb=" N VAL 0 290 " --> pdb=" O TYR 0 286 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN 0 291 " --> pdb=" O GLU 0 287 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY 0 292 " --> pdb=" O LYS 0 288 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 286 through 292' Processing helix chain '0' and resid 294 through 299 removed outlier: 3.690A pdb=" N LEU 0 299 " --> pdb=" O SER 0 295 " (cutoff:3.500A) Processing helix chain '0' and resid 327 through 345 removed outlier: 3.680A pdb=" N PHE 0 334 " --> pdb=" O HIS 0 330 " (cutoff:3.500A) Processing helix chain '0' and resid 355 through 367 Processing helix chain '0' and resid 370 through 375 Processing helix chain '0' and resid 376 through 386 removed outlier: 3.673A pdb=" N SER 0 382 " --> pdb=" O SER 0 378 " (cutoff:3.500A) Processing helix chain '0' and resid 387 through 389 No H-bonds generated for 'chain '0' and resid 387 through 389' Processing helix chain '0' and resid 396 through 410 removed outlier: 3.708A pdb=" N LYS 0 400 " --> pdb=" O PHE 0 396 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP 0 401 " --> pdb=" O THR 0 397 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER 0 410 " --> pdb=" O ALA 0 406 " (cutoff:3.500A) Processing helix chain '0' and resid 424 through 428 removed outlier: 3.622A pdb=" N ALA 0 428 " --> pdb=" O ILE 0 425 " (cutoff:3.500A) Processing helix chain '0' and resid 442 through 453 Proline residue: 0 448 - end of helix removed outlier: 3.646A pdb=" N ARG 0 452 " --> pdb=" O PRO 0 448 " (cutoff:3.500A) Processing helix chain '0' and resid 467 through 474 removed outlier: 4.235A pdb=" N ARG 0 471 " --> pdb=" O ASP 0 467 " (cutoff:3.500A) Processing helix chain '0' and resid 515 through 533 removed outlier: 3.834A pdb=" N ARG 0 520 " --> pdb=" O PRO 0 516 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ASN 0 521 " --> pdb=" O SER 0 517 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE 0 532 " --> pdb=" O GLU 0 528 " (cutoff:3.500A) Processing helix chain '0' and resid 543 through 557 removed outlier: 3.860A pdb=" N SER 0 549 " --> pdb=" O LEU 0 545 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET 0 557 " --> pdb=" O MET 0 553 " (cutoff:3.500A) Processing helix chain '0' and resid 558 through 567 removed outlier: 4.321A pdb=" N GLU 0 562 " --> pdb=" O GLY 0 558 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL 0 563 " --> pdb=" O ILE 0 559 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS 0 565 " --> pdb=" O ASP 0 561 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS 0 567 " --> pdb=" O VAL 0 563 " (cutoff:3.500A) Processing helix chain '0' and resid 575 through 592 removed outlier: 3.745A pdb=" N LYS 0 588 " --> pdb=" O GLU 0 584 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA 0 589 " --> pdb=" O THR 0 585 " (cutoff:3.500A) Processing helix chain '0' and resid 605 through 610 removed outlier: 4.182A pdb=" N GLY 0 609 " --> pdb=" O LYS 0 605 " (cutoff:3.500A) Processing helix chain '0' and resid 633 through 646 removed outlier: 3.842A pdb=" N PHE 0 641 " --> pdb=" O ALA 0 637 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET 0 642 " --> pdb=" O ARG 0 638 " (cutoff:3.500A) Processing helix chain '0' and resid 649 through 667 removed outlier: 3.649A 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 691 removed outlier: 3.589A pdb=" N LYS 0 689 " --> pdb=" O PHE 0 686 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG 0 690 " --> pdb=" O SER 0 687 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER 0 691 " --> pdb=" O ARG 0 688 " (cutoff:3.500A) Processing helix chain '0' and resid 694 through 701 removed outlier: 3.637A pdb=" N GLY 0 700 " --> pdb=" O TRP 0 696 " (cutoff:3.500A) Processing helix chain '0' and resid 702 through 706 removed outlier: 3.768A pdb=" N LEU 0 706 " --> pdb=" O ASP 0 703 " (cutoff:3.500A) Processing helix chain '0' and resid 709 through 725 removed outlier: 3.691A pdb=" N ALA 0 725 " --> pdb=" O LEU 0 721 " (cutoff:3.500A) Processing helix chain '0' and resid 743 through 753 removed outlier: 4.131A pdb=" N SER 0 750 " --> pdb=" O LYS 0 746 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ARG 0 751 " --> pdb=" O HIS 0 747 " (cutoff:3.500A) Processing helix chain '4' and resid 33 through 38 removed outlier: 3.605A pdb=" N THR 4 38 " --> pdb=" O PRO 4 34 " (cutoff:3.500A) Processing helix chain '4' and resid 38 through 43 removed outlier: 4.115A pdb=" N GLU 4 42 " --> pdb=" O THR 4 38 " (cutoff:3.500A) Processing helix chain '4' and resid 50 through 68 removed outlier: 3.570A pdb=" N LEU 4 57 " --> pdb=" O VAL 4 53 " (cutoff:3.500A) removed outlier: 3.811A 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: 4.314A 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: 3.759A pdb=" N ILE 4 200 " --> pdb=" O ILE 4 196 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N PHE 4 201 " --> pdb=" O MET 4 197 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER 4 202 " --> pdb=" O ASN 4 198 " (cutoff:3.500A) Processing helix chain '4' and resid 221 through 232 removed outlier: 3.583A pdb=" N THR 4 228 " --> pdb=" O LEU 4 224 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ASP 4 229 " --> pdb=" O GLN 4 225 " (cutoff:3.500A) Processing helix chain '4' and resid 243 through 252 removed outlier: 4.124A pdb=" N TYR 4 247 " --> pdb=" O GLY 4 243 " (cutoff:3.500A) Processing helix chain '4' and resid 313 through 323 removed outlier: 3.955A pdb=" N LYS 4 323 " --> pdb=" O LYS 4 319 " (cutoff:3.500A) Processing helix chain '6' and resid 133 through 138 Processing helix chain '6' and resid 144 through 164 removed outlier: 3.651A pdb=" N MET 6 148 " --> pdb=" O ASN 6 144 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN 6 151 " --> pdb=" O ALA 6 147 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N HIS 6 158 " --> pdb=" O ILE 6 154 " (cutoff:3.500A) Processing helix chain '6' and resid 188 through 202 removed outlier: 3.516A pdb=" N HIS 6 192 " --> pdb=" O ASN 6 188 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER 6 198 " --> pdb=" O ASP 6 194 " (cutoff:3.500A) Processing helix chain '6' and resid 209 through 221 removed outlier: 3.519A pdb=" N GLY 6 219 " --> pdb=" O GLU 6 215 " (cutoff:3.500A) Processing helix chain '6' and resid 246 through 257 removed outlier: 3.740A pdb=" N THR 6 250 " --> pdb=" O ASP 6 246 " (cutoff:3.500A) Processing helix chain '6' and resid 270 through 281 Processing helix chain '6' and resid 293 through 306 removed outlier: 3.778A pdb=" N LYS 6 298 " --> pdb=" O GLU 6 294 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU 6 300 " --> pdb=" O HIS 6 296 " (cutoff:3.500A) Processing helix chain '6' and resid 373 through 384 removed outlier: 3.509A pdb=" N SER 6 379 " --> pdb=" O HIS 6 375 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N HIS 6 382 " --> pdb=" O ARG 6 378 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET 6 384 " --> pdb=" O TYR 6 380 " (cutoff:3.500A) Processing helix chain '6' and resid 437 through 445 removed outlier: 3.526A pdb=" N PHE 6 443 " --> pdb=" O ASP 6 439 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS 6 445 " --> pdb=" O ASP 6 441 " (cutoff:3.500A) Processing helix chain '6' and resid 451 through 456 Processing helix chain '1' and resid 170 through 177 Processing helix chain '1' and resid 177 through 188 Processing helix chain '1' and resid 188 through 197 removed outlier: 3.631A pdb=" N MET 1 192 " --> pdb=" O ASN 1 188 " (cutoff:3.500A) Processing helix chain '1' and resid 205 through 213 removed outlier: 3.876A pdb=" N PHE 1 209 " --> pdb=" O PRO 1 205 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TRP 1 210 " --> pdb=" O PRO 1 206 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER 1 211 " --> pdb=" O SER 1 207 " (cutoff:3.500A) Processing helix chain '1' and resid 213 through 226 Processing helix chain '1' and resid 251 through 263 removed outlier: 3.599A pdb=" N ILE 1 256 " --> pdb=" O SER 1 252 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN 1 258 " --> pdb=" O GLU 1 254 " (cutoff:3.500A) Processing helix chain '1' and resid 263 through 273 removed outlier: 4.083A pdb=" N LYS 1 267 " --> pdb=" O TYR 1 263 " (cutoff:3.500A) Processing helix chain '1' and resid 279 through 295 removed outlier: 5.233A pdb=" N ALA 1 285 " --> pdb=" O PRO 1 281 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER 1 289 " --> pdb=" O ALA 1 285 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER 1 290 " --> pdb=" O ARG 1 286 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU 1 292 " --> pdb=" O PHE 1 288 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE 1 293 " --> pdb=" O SER 1 289 " (cutoff:3.500A) Processing helix chain '1' and resid 314 through 319 removed outlier: 3.582A pdb=" N UNK 1 319 " --> pdb=" O LEU 1 315 " (cutoff:3.500A) Processing helix chain '1' and resid 371 through 389 removed outlier: 3.507A pdb=" N LYS 1 376 " --> pdb=" O VAL 1 372 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY 1 377 " --> pdb=" O ASP 1 373 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET 1 385 " --> pdb=" O LEU 1 381 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET 1 387 " --> pdb=" O GLU 1 383 " (cutoff:3.500A) Processing helix chain '1' and resid 467 through 483 Processing helix chain '1' and resid 496 through 516 removed outlier: 3.785A pdb=" N UNK 1 501 " --> pdb=" O UNK 1 497 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG 1 502 " --> pdb=" O UNK 1 498 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ILE 1 509 " --> pdb=" O THR 1 505 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ASN 1 510 " --> pdb=" O UNK 1 506 " (cutoff:3.500A) Processing helix chain '1' and resid 540 through 567 removed outlier: 3.798A pdb=" N CYS 1 557 " --> pdb=" O LEU 1 553 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE 1 560 " --> pdb=" O THR 1 556 " (cutoff:3.500A) Processing helix chain '1' and resid 575 through 605 removed outlier: 3.587A pdb=" N VAL 1 579 " --> pdb=" O GLN 1 575 " (cutoff:3.500A) Processing helix chain '1' and resid 606 through 639 removed outlier: 3.980A pdb=" N THR 1 611 " --> pdb=" O SER 1 607 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA 1 614 " --> pdb=" O ASN 1 610 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR 1 615 " --> pdb=" O THR 1 611 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU 1 616 " --> pdb=" O CYS 1 612 " (cutoff:3.500A) Proline residue: 1 618 - end of helix Processing helix chain '7' and resid 104 through 109 removed outlier: 3.519A pdb=" N ASP 7 107 " --> pdb=" O PHE 7 104 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL 7 109 " --> pdb=" O PRO 7 106 " (cutoff:3.500A) Processing helix chain '7' and resid 124 through 128 removed outlier: 3.934A 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 178 through 187 removed outlier: 3.525A pdb=" N GLY 7 187 " --> pdb=" O ALA 7 183 " (cutoff:3.500A) Processing helix chain '7' and resid 189 through 201 removed outlier: 3.913A pdb=" N ILE 7 194 " --> pdb=" O THR 7 190 " (cutoff:3.500A) Processing helix chain '7' and resid 206 through 218 Processing helix chain '7' and resid 238 through 248 Processing helix chain '7' and resid 262 through 268 Processing helix chain '7' and resid 322 through 333 removed outlier: 3.747A pdb=" N GLN 7 331 " --> pdb=" O LYS 7 327 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE 7 333 " --> pdb=" O ARG 7 329 " (cutoff:3.500A) Processing helix chain '7' and resid 363 through 375 removed outlier: 4.398A pdb=" N LYS 7 368 " --> pdb=" O PRO 7 364 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER 7 369 " --> pdb=" O TYR 7 365 " (cutoff:3.500A) Processing helix chain '7' and resid 391 through 404 removed outlier: 4.316A pdb=" N VAL 7 395 " --> pdb=" O GLY 7 391 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLY 7 396 " --> pdb=" O LYS 7 392 " (cutoff:3.500A) Processing helix chain '7' and resid 413 through 424 removed outlier: 3.787A pdb=" N MET 7 418 " --> pdb=" O SER 7 414 " (cutoff:3.500A) Processing helix chain '7' and resid 457 through 461 Processing helix chain '7' and resid 467 through 480 removed outlier: 4.550A pdb=" N GLN 7 471 " --> pdb=" O SER 7 467 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR 7 478 " --> pdb=" O MET 7 474 " (cutoff:3.500A) Processing helix chain '7' and resid 490 through 494 Proline residue: 7 494 - end of helix Processing helix chain '7' and resid 495 through 506 removed outlier: 3.778A pdb=" N THR 7 504 " --> pdb=" O ARG 7 500 " (cutoff:3.500A) Processing helix chain '7' and resid 526 through 532 Processing helix chain '7' and resid 539 through 544 removed outlier: 3.552A pdb=" N LEU 7 543 " --> pdb=" O ASN 7 539 " (cutoff:3.500A) Processing helix chain '7' and resid 562 through 572 Processing helix chain '7' and resid 574 through 580 removed outlier: 4.038A pdb=" N LEU 7 579 " --> pdb=" O LYS 7 576 " (cutoff:3.500A) Processing helix chain '7' and resid 584 through 601 removed outlier: 3.518A pdb=" N LEU 7 594 " --> pdb=" O ALA 7 590 " (cutoff:3.500A) Processing helix chain '7' and resid 612 through 621 removed outlier: 3.972A pdb=" N ALA 7 619 " --> pdb=" O LEU 7 615 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU 7 620 " --> pdb=" O GLN 7 616 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LYS 7 621 " --> pdb=" O GLU 7 617 " (cutoff:3.500A) Processing helix chain '7' and resid 632 through 645 removed outlier: 3.564A pdb=" N TYR 7 645 " --> pdb=" O GLN 7 641 " (cutoff:3.500A) Processing helix chain '7' and resid 655 through 659 removed outlier: 3.517A pdb=" N ASP 7 659 " --> pdb=" O LYS 7 656 " (cutoff:3.500A) Processing helix chain '7' and resid 679 through 691 removed outlier: 3.656A pdb=" N LEU 7 691 " --> pdb=" O LEU 7 687 " (cutoff:3.500A) Processing helix chain '7' and resid 714 through 729 removed outlier: 4.558A pdb=" N TYR 7 718 " --> pdb=" O GLN 7 714 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL 7 727 " --> pdb=" O GLN 7 723 " (cutoff:3.500A) Processing helix chain '7' and resid 741 through 745 removed outlier: 3.641A pdb=" N ILE 7 745 " --> pdb=" O MET 7 742 " (cutoff:3.500A) Processing helix chain '7' and resid 752 through 764 removed outlier: 3.541A pdb=" N ARG 7 757 " --> pdb=" O PRO 7 753 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU 7 758 " --> pdb=" O ARG 7 754 " (cutoff:3.500A) Processing helix chain '5' and resid 13 through 26 Processing helix chain '5' and resid 46 through 63 Processing helix chain '2' and resid 9 through 14 Processing helix chain '2' and resid 18 through 27 removed outlier: 3.518A pdb=" N THR 2 27 " --> pdb=" O ASN 2 23 " (cutoff:3.500A) Processing helix chain '2' and resid 28 through 39 removed outlier: 3.791A pdb=" N ILE 2 38 " --> pdb=" O ALA 2 34 " (cutoff:3.500A) Processing helix chain '2' and resid 40 through 53 removed outlier: 3.566A pdb=" N ASN 2 53 " --> pdb=" O ALA 2 49 " (cutoff:3.500A) Processing helix chain '2' and resid 58 through 66 removed outlier: 3.691A pdb=" N LEU 2 62 " --> pdb=" O PRO 2 58 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL 2 66 " --> pdb=" O LEU 2 62 " (cutoff:3.500A) Processing helix chain '2' and resid 70 through 84 removed outlier: 4.010A pdb=" N PHE 2 74 " --> pdb=" O GLY 2 70 " (cutoff:3.500A) Processing helix chain '2' and resid 101 through 113 removed outlier: 3.589A pdb=" N LEU 2 108 " --> pdb=" O PHE 2 104 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG 2 109 " --> pdb=" O LYS 2 105 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASN 2 110 " --> pdb=" O ILE 2 106 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA 2 111 " --> pdb=" O SER 2 107 " (cutoff:3.500A) Processing helix chain '2' and resid 135 through 151 Processing helix chain '2' and resid 160 through 170 Processing helix chain '2' and resid 185 through 194 Processing helix chain '2' and resid 196 through 211 removed outlier: 3.822A pdb=" N GLN 2 206 " --> pdb=" O THR 2 202 " (cutoff:3.500A) Processing helix chain '2' and resid 217 through 231 removed outlier: 3.580A pdb=" N GLY 2 229 " --> pdb=" O ILE 2 225 " (cutoff:3.500A) Processing helix chain '2' and resid 243 through 257 Processing helix chain '2' and resid 262 through 266 removed outlier: 3.939A pdb=" N ASN 2 265 " --> pdb=" O LYS 2 262 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP 2 266 " --> pdb=" O HIS 2 263 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 262 through 266' Processing helix chain '2' and resid 272 through 280 removed outlier: 4.394A pdb=" N LEU 2 276 " --> pdb=" O THR 2 272 " (cutoff:3.500A) Processing helix chain '2' and resid 353 through 362 removed outlier: 3.883A pdb=" N ALA 2 358 " --> pdb=" O PRO 2 354 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU 2 362 " --> pdb=" O ALA 2 358 " (cutoff:3.500A) Processing helix chain '2' and resid 379 through 389 removed outlier: 3.541A pdb=" N ILE 2 383 " --> pdb=" O THR 2 379 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG 2 385 " --> pdb=" O GLU 2 381 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ALA 2 386 " --> pdb=" O SER 2 382 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ASN 2 389 " --> pdb=" O ARG 2 385 " (cutoff:3.500A) Processing helix chain '2' and resid 394 through 403 removed outlier: 3.981A pdb=" N ALA 2 398 " --> pdb=" O ASP 2 394 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU 2 401 " --> pdb=" O ILE 2 397 " (cutoff:3.500A) Processing helix chain '2' and resid 404 through 407 removed outlier: 3.708A pdb=" N GLN 2 407 " --> pdb=" O ALA 2 404 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 404 through 407' Processing helix chain '2' and resid 408 through 414 removed outlier: 3.533A pdb=" N GLU 2 414 " --> pdb=" O ARG 2 410 " (cutoff:3.500A) Processing helix chain '2' and resid 434 through 450 removed outlier: 3.504A pdb=" N VAL 2 438 " --> pdb=" O PRO 2 434 " (cutoff:3.500A) Processing helix chain '2' and resid 464 through 479 removed outlier: 4.048A pdb=" N TYR 2 468 " --> pdb=" O THR 2 464 " (cutoff:3.500A) Processing helix chain '2' and resid 494 through 507 removed outlier: 4.499A pdb=" N ASN 2 498 " --> pdb=" O SER 2 494 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL 2 501 " --> pdb=" O GLY 2 497 " (cutoff:3.500A) Processing helix chain 'X' and resid 124 through 139 removed outlier: 3.990A pdb=" N GLN X 136 " --> pdb=" O THR X 132 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY X 139 " --> pdb=" O ILE X 135 " (cutoff:3.500A) Processing helix chain 'X' and resid 143 through 152 removed outlier: 4.182A pdb=" N LEU X 148 " --> pdb=" O VAL X 144 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU X 151 " --> pdb=" O LEU X 147 " (cutoff:3.500A) Processing helix chain 'X' and resid 156 through 166 removed outlier: 4.000A 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 213 Processing helix chain 'X' and resid 216 through 224 removed outlier: 3.760A pdb=" N THR X 220 " --> pdb=" O GLN X 216 " (cutoff:3.500A) Processing helix chain 'X' and resid 256 through 264 removed outlier: 3.608A pdb=" N GLU X 264 " --> pdb=" O VAL X 260 " (cutoff:3.500A) Processing helix chain 'O' and resid 81 through 89 Processing helix chain 'O' and resid 128 through 146 removed outlier: 3.930A pdb=" N SER O 136 " --> pdb=" O SER O 132 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 179 Processing helix chain 'O' and resid 219 through 229 removed outlier: 3.633A pdb=" N ILE O 223 " --> pdb=" O GLN O 219 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR O 224 " --> pdb=" O ARG O 220 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE O 227 " --> pdb=" O ILE O 223 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA O 229 " --> pdb=" O GLN O 225 " (cutoff:3.500A) Processing helix chain 'O' and resid 230 through 237 Processing helix chain 'W' and resid 5 through 21 removed outlier: 4.222A pdb=" N LYS W 14 " --> pdb=" O LYS W 10 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE W 15 " --> pdb=" O ASN W 11 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL W 16 " --> pdb=" O LEU W 12 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR W 21 " --> pdb=" O VAL W 17 " (cutoff:3.500A) Processing helix chain 'W' and resid 23 through 35 removed outlier: 3.950A pdb=" N LEU W 27 " --> pdb=" O GLY W 23 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA W 31 " --> pdb=" O LEU W 27 " (cutoff:3.500A) Processing helix chain 'W' and resid 39 through 47 removed outlier: 3.535A pdb=" N GLN W 45 " --> pdb=" O ASP W 41 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU W 47 " --> pdb=" O LEU W 43 " (cutoff:3.500A) Processing helix chain 'W' and resid 50 through 64 Proline residue: W 56 - end of helix removed outlier: 3.574A pdb=" N ALA W 59 " --> pdb=" O GLY W 55 " (cutoff:3.500A) Processing helix chain 'W' and resid 90 through 116 removed outlier: 3.623A pdb=" N TRP W 100 " --> pdb=" O ASP W 96 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL W 105 " --> pdb=" O LYS W 101 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL W 106 " --> pdb=" O VAL W 102 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLN W 107 " --> pdb=" O HIS W 103 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP W 112 " --> pdb=" O ARG W 108 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU W 113 " --> pdb=" O LEU W 109 " (cutoff:3.500A) Processing helix chain 'W' and resid 132 through 137 Processing helix chain 'W' and resid 164 through 191 removed outlier: 3.740A pdb=" N LYS W 168 " --> pdb=" O LYS W 164 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN W 169 " --> pdb=" O ASN W 165 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASP W 170 " --> pdb=" O LYS W 166 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS W 171 " --> pdb=" O GLU W 167 " (cutoff:3.500A) Proline residue: W 181 - end of helix removed outlier: 4.275A pdb=" N ASP W 184 " --> pdb=" O GLN W 180 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER W 185 " --> pdb=" O PRO W 181 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Q' and resid 98 through 102 removed outlier: 3.633A pdb=" N PHE Q 101 " --> pdb=" O ILE R 95 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Q' and resid 115 through 118 removed outlier: 3.719A pdb=" N PHE R 135 " --> pdb=" O HIS Q 117 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N THR R 136 " --> pdb=" O ILE R 214 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ILE R 214 " --> pdb=" O THR R 136 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N VAL R 68 " --> pdb=" O HIS R 220 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N CYS R 222 " --> pdb=" O VAL R 68 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU R 70 " --> pdb=" O CYS R 222 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N VAL R 224 " --> pdb=" O LEU R 70 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ARG R 72 " --> pdb=" O VAL R 224 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Q' and resid 115 through 118 removed outlier: 3.719A pdb=" N PHE R 135 " --> pdb=" O HIS Q 117 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N THR R 136 " --> pdb=" O ILE R 214 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ILE R 214 " --> pdb=" O THR R 136 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N GLU R 221 " --> pdb=" O THR R 125 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR R 125 " --> pdb=" O GLU R 221 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE R 104 " --> pdb=" O LEU R 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Q' and resid 393 through 396 removed outlier: 3.630A pdb=" N TRP Q 361 " --> pdb=" O MET Q 352 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N TRP Q 350 " --> pdb=" O GLY Q 363 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N HIS Q 140 " --> pdb=" O VAL Q 351 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 49 through 50 removed outlier: 4.488A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 85 through 87 removed outlier: 3.690A pdb=" N LYS G 146 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ILE G 160 " --> pdb=" O GLU G 148 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LYS G 107 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N GLY G 161 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N PHE G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 85 through 87 removed outlier: 3.764A pdb=" N GLY G 169 " --> pdb=" O ARG G 144 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 120 through 121 Processing sheet with id=AA9, first strand: chain 'M' and resid 34 through 37 removed outlier: 6.461A pdb=" N VAL M 43 " --> pdb=" O LEU M 52 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AB2, first strand: chain 'A' and resid 82 through 90 removed outlier: 6.833A pdb=" N THR A 237 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 151 through 152 Processing sheet with id=AB4, first strand: chain 'A' and resid 173 through 177 removed outlier: 4.464A pdb=" N LEU A 181 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 343 through 345 removed outlier: 3.562A pdb=" N LYS A 343 " --> pdb=" O PHE B1130 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU B1128 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.550A pdb=" N ARG A 469 " --> pdb=" O GLY A 365 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N PHE A 468 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL A 352 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N LEU A 470 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N SER A 354 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 375 through 379 removed outlier: 4.193A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG A 407 " --> pdb=" O ASP A 411 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP A 411 " --> pdb=" O ARG A 407 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AB9, first strand: chain 'A' and resid 606 through 607 removed outlier: 6.747A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 766 through 767 removed outlier: 3.526A pdb=" N VAL A 800 " --> pdb=" O GLY A 766 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 849 through 851 removed outlier: 3.549A pdb=" N THR A 855 " --> pdb=" O HIS A 851 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR A 856 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 879 through 882 Processing sheet with id=AC4, first strand: chain 'A' and resid 1281 through 1288 removed outlier: 4.019A pdb=" N ARG A1281 " --> pdb=" O ASP A1309 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A1308 " --> pdb=" O LEU A1116 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1141 through 1142 Processing sheet with id=AC6, first strand: chain 'A' and resid 1225 through 1228 removed outlier: 4.167A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ARG A1194 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N SER A1150 " --> pdb=" O ARG A1194 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLU A1196 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N SER A1150 " --> pdb=" O ARG I 45 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG I 45 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE A1152 " --> pdb=" O VAL I 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 1291 through 1292 Processing sheet with id=AC8, first strand: chain 'B' and resid 90 through 97 removed outlier: 5.717A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B 128 " --> pdb=" O GLY B 168 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AD1, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AD2, first strand: chain 'B' and resid 404 through 407 removed outlier: 6.685A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 223 through 227 removed outlier: 3.723A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 544 through 547 removed outlier: 4.509A pdb=" N ARG B 632 " --> pdb=" O SER B 546 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 649 through 651 Processing sheet with id=AD6, first strand: chain 'B' and resid 564 through 565 removed outlier: 7.067A pdb=" N ARG B 579 " --> pdb=" O LEU B 624 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 614 through 615 Processing sheet with id=AD8, first strand: chain 'B' and resid 793 through 796 removed outlier: 5.869A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 793 through 796 removed outlier: 5.869A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AE2, first strand: chain 'B' and resid 987 through 989 removed outlier: 4.352A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B1010 " --> pdb=" O ILE B 824 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 987 through 989 Processing sheet with id=AE4, first strand: chain 'B' and resid 873 through 874 Processing sheet with id=AE5, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AE6, first strand: chain 'B' and resid 1157 through 1163 Processing sheet with id=AE7, first strand: chain 'C' and resid 7 through 13 removed outlier: 5.504A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.876A pdb=" N GLU C 152 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N THR C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LYS C 154 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N VAL C 51 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR C 156 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL C 49 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL C 158 " --> pdb=" O ASP C 47 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 72 through 74 removed outlier: 4.374A pdb=" N GLN C 73 " --> pdb=" O GLY C 130 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 111 through 114 Processing sheet with id=AF2, first strand: chain 'E' and resid 61 through 62 removed outlier: 6.481A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 152 through 155 Processing sheet with id=AF4, first strand: chain 'H' and resid 10 through 16 removed outlier: 5.450A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL H 114 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N TYR H 115 " --> pdb=" O TYR H 102 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 58 through 60 Processing sheet with id=AF6, first strand: chain 'H' and resid 106 through 108 Processing sheet with id=AF7, first strand: chain 'I' and resid 14 through 15 Processing sheet with id=AF8, first strand: chain 'I' and resid 83 through 87 Processing sheet with id=AF9, first strand: chain 'K' and resid 21 through 23 removed outlier: 6.696A pdb=" N LYS K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TYR K 61 " --> pdb=" O LYS K 72 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLN K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain '0' and resid 2 through 4 Processing sheet with id=AG2, first strand: chain '0' and resid 40 through 41 Processing sheet with id=AG3, first strand: chain '0' and resid 105 through 108 removed outlier: 4.132A pdb=" N LEU 0 106 " --> pdb=" O ILE 0 205 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N SER 0 209 " --> pdb=" O LEU 0 108 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER 0 73 " --> pdb=" O TYR 0 208 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE 0 70 " --> pdb=" O ILE 0 233 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ASP 0 235 " --> pdb=" O ILE 0 70 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N CYS 0 72 " --> pdb=" O ASP 0 235 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL 0 232 " --> pdb=" O ILE 0 457 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N THR 0 459 " --> pdb=" O VAL 0 232 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N PHE 0 234 " --> pdb=" O THR 0 459 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain '0' and resid 417 through 419 removed outlier: 4.565A pdb=" N LEU 0 417 " --> pdb=" O THR 0 438 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N THR 0 438 " --> pdb=" O LEU 0 417 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain '0' and resid 492 through 494 removed outlier: 5.597A pdb=" N LEU 0 493 " --> pdb=" O MET 0 679 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain '0' and resid 537 through 541 removed outlier: 5.939A pdb=" N MET 0 537 " --> pdb=" O LEU 0 598 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N SER 0 600 " --> pdb=" O MET 0 537 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N VAL 0 539 " --> pdb=" O SER 0 600 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N LEU 0 568 " --> pdb=" O ILE 0 597 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LEU 0 599 " --> pdb=" O LEU 0 568 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU 0 570 " --> pdb=" O LEU 0 599 " (cutoff:3.500A) removed outlier: 9.351A pdb=" N VAL 0 601 " --> pdb=" O LEU 0 570 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain '4' and resid 83 through 85 removed outlier: 3.721A pdb=" N ALA 4 78 " --> pdb=" O ILE 4 30 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR 4 27 " --> pdb=" O ARG 4 175 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU 4 177 " --> pdb=" O THR 4 27 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU 4 31 " --> pdb=" O LEU 4 179 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N CYS 4 181 " --> pdb=" O GLU 4 31 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU 4 176 " --> pdb=" O ASP 4 211 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N VAL 4 213 " --> pdb=" O LEU 4 176 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL 4 178 " --> pdb=" O VAL 4 213 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE 4 215 " --> pdb=" O VAL 4 178 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N THR 4 180 " --> pdb=" O ILE 4 215 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL 4 234 " --> pdb=" O ILE 4 210 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain '4' and resid 287 through 288 Processing sheet with id=AG9, first strand: chain '6' and resid 178 through 186 removed outlier: 6.491A pdb=" N GLN 6 180 " --> pdb=" O ARG 6 175 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARG 6 175 " --> pdb=" O GLN 6 180 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL 6 182 " --> pdb=" O ILE 6 173 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N ILE 6 173 " --> pdb=" O VAL 6 182 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N GLN 6 184 " --> pdb=" O ILE 6 171 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ILE 6 171 " --> pdb=" O GLN 6 184 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ARG 6 124 " --> pdb=" O GLN 6 168 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N GLY 6 170 " --> pdb=" O ARG 6 124 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU 6 126 " --> pdb=" O GLY 6 170 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N ILE 6 172 " --> pdb=" O LEU 6 126 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU 6 128 " --> pdb=" O ILE 6 172 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N MET 6 174 " --> pdb=" O LEU 6 128 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU 6 231 " --> pdb=" O SER 6 125 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ARG 6 230 " --> pdb=" O ARG 6 260 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N LYS 6 262 " --> pdb=" O ARG 6 230 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N VAL 6 232 " --> pdb=" O LYS 6 262 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain '6' and resid 322 through 323 Processing sheet with id=AH2, first strand: chain '6' and resid 326 through 327 Processing sheet with id=AH3, first strand: chain '6' and resid 390 through 391 removed outlier: 3.514A pdb=" N ALA 6 390 " --> pdb=" O ARG 6 428 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain '7' and resid 162 through 165 removed outlier: 4.061A pdb=" N GLU 7 162 " --> pdb=" O LYS 7 174 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N GLU 7 172 " --> pdb=" O ILE 7 164 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain '7' and resid 382 through 383 removed outlier: 7.203A pdb=" N GLY 7 382 " --> pdb=" O GLY 7 512 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL 7 407 " --> pdb=" O VAL 7 453 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N SER 7 455 " --> pdb=" O VAL 7 407 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N VAL 7 409 " --> pdb=" O SER 7 455 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain '7' and resid 552 through 559 removed outlier: 6.080A pdb=" N GLN 7 553 " --> pdb=" O PHE 7 705 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N SER 7 707 " --> pdb=" O GLN 7 553 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ALA 7 555 " --> pdb=" O SER 7 707 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N VAL 7 709 " --> pdb=" O ALA 7 555 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N VAL 7 557 " --> pdb=" O VAL 7 709 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU 7 670 " --> pdb=" O TYR 7 706 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LEU 7 708 " --> pdb=" O LEU 7 670 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLN 7 672 " --> pdb=" O LEU 7 708 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N SER 7 710 " --> pdb=" O GLN 7 672 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE 7 606 " --> pdb=" O ILE 7 671 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain '5' and resid 5 through 6 Processing sheet with id=AH8, first strand: chain '5' and resid 31 through 34 removed outlier: 3.944A pdb=" N LEU 5 9 " --> pdb=" O TYR 2 454 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR 2 454 " --> pdb=" O LEU 5 9 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN 5 11 " --> pdb=" O ILE 2 452 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE 2 452 " --> pdb=" O GLN 5 11 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain '2' and resid 87 through 88 removed outlier: 4.417A pdb=" N ASN 2 99 " --> pdb=" O ILE 2 88 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'U' and resid 273 through 275 removed outlier: 3.557A pdb=" N LEU V 60 " --> pdb=" O LYS U 278 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL V 62 " --> pdb=" O GLN U 280 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N THR V 61 " --> pdb=" O VAL V 85 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL V 85 " --> pdb=" O THR V 61 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LYS V 63 " --> pdb=" O CYS V 83 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N CYS V 83 " --> pdb=" O LYS V 63 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ILE V 79 " --> pdb=" O ASP V 67 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N TYR V 69 " --> pdb=" O THR V 77 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N THR V 77 " --> pdb=" O TYR V 69 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE V 71 " --> pdb=" O VAL V 75 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL V 75 " --> pdb=" O PHE V 71 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL V 75 " --> pdb=" O CYS V 116 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N CYS V 116 " --> pdb=" O VAL V 75 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N THR V 77 " --> pdb=" O VAL V 114 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL V 114 " --> pdb=" O THR V 77 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE V 79 " --> pdb=" O ARG V 112 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ARG V 112 " --> pdb=" O ILE V 79 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LYS V 81 " --> pdb=" O LYS V 110 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LYS V 110 " --> pdb=" O LYS V 81 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS U 246 " --> pdb=" O VAL V 114 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS V 116 " --> pdb=" O CYS U 246 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N MET U 244 " --> pdb=" O VAL U 267 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL U 267 " --> pdb=" O MET U 244 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N CYS U 246 " --> pdb=" O GLY U 265 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N GLY U 265 " --> pdb=" O CYS U 246 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N TYR U 248 " --> pdb=" O LYS U 263 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS U 263 " --> pdb=" O TYR U 248 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS U 250 " --> pdb=" O SER U 261 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'O' and resid 92 through 95 removed outlier: 4.439A pdb=" N ASN O 95 " --> pdb=" O ALA O 101 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ALA O 101 " --> pdb=" O ASN O 95 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE O 106 " --> pdb=" O THR O 111 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR O 111 " --> pdb=" O ILE O 106 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LYS O 120 " --> pdb=" O PHE O 116 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY O 125 " --> pdb=" O ILE O 70 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ILE O 70 " --> pdb=" O GLY O 125 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU O 67 " --> pdb=" O SER O 163 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N SER O 163 " --> pdb=" O LEU O 67 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N THR O 73 " --> pdb=" O ILE O 157 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ILE O 157 " --> pdb=" O THR O 73 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N THR O 75 " --> pdb=" O PHE O 155 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N PHE O 155 " --> pdb=" O THR O 75 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'O' and resid 185 through 186 removed outlier: 3.658A pdb=" N GLU O 186 " --> pdb=" O PHE O 190 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL O 203 " --> pdb=" O THR O 215 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR O 215 " --> pdb=" O VAL O 203 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'W' and resid 68 through 74 removed outlier: 3.799A pdb=" N GLU W 74 " --> pdb=" O VAL W 82 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N VAL W 82 " --> pdb=" O GLU W 74 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'W' and resid 122 through 123 2593 hydrogen bonds defined for protein. 7305 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 67 hydrogen bonds 118 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 54 stacking parallelities Total time for adding SS restraints: 30.24 Time building geometry restraints manager: 14.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 26216 1.42 - 1.64: 37198 1.64 - 1.85: 532 1.85 - 2.07: 0 2.07 - 2.29: 12 Bond restraints: 63958 Sorted by residual: bond pdb=" CA GLU B 687 " pdb=" C GLU B 687 " ideal model delta sigma weight residual 1.523 1.396 0.127 1.41e-02 5.03e+03 8.08e+01 bond pdb=" CA HIS A 786 " pdb=" C HIS A 786 " ideal model delta sigma weight residual 1.523 1.374 0.150 1.80e-02 3.09e+03 6.90e+01 bond pdb=" C VAL A 512 " pdb=" N SER A 513 " ideal model delta sigma weight residual 1.331 1.213 0.118 2.07e-02 2.33e+03 3.24e+01 bond pdb=" CA HIS A 118 " pdb=" C HIS A 118 " ideal model delta sigma weight residual 1.522 1.456 0.066 1.43e-02 4.89e+03 2.12e+01 bond pdb=" CA ILE B 992 " pdb=" CB ILE B 992 " ideal model delta sigma weight residual 1.553 1.520 0.033 7.40e-03 1.83e+04 2.03e+01 ... (remaining 63953 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 84237 2.94 - 5.87: 2243 5.87 - 8.81: 182 8.81 - 11.74: 52 11.74 - 14.68: 9 Bond angle restraints: 86723 Sorted by residual: angle pdb=" C2' G P 9 " pdb=" C1' G P 9 " pdb=" N9 G P 9 " ideal model delta sigma weight residual 112.00 121.54 -9.54 1.50e+00 4.44e-01 4.04e+01 angle pdb=" C GLY A1123 " pdb=" N HIS A1124 " pdb=" CA HIS A1124 " ideal model delta sigma weight residual 121.70 133.01 -11.31 1.80e+00 3.09e-01 3.95e+01 angle pdb=" C GLU M 268 " pdb=" N ILE M 269 " pdb=" CA ILE M 269 " ideal model delta sigma weight residual 121.97 133.27 -11.30 1.80e+00 3.09e-01 3.94e+01 angle pdb=" C MET A1444 " pdb=" N ILE A1445 " pdb=" CA ILE A1445 " ideal model delta sigma weight residual 121.70 132.76 -11.06 1.80e+00 3.09e-01 3.77e+01 angle pdb=" N VAL H 57 " pdb=" CA VAL H 57 " pdb=" C VAL H 57 " ideal model delta sigma weight residual 107.75 116.54 -8.79 1.46e+00 4.69e-01 3.62e+01 ... (remaining 86718 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.75: 36684 32.75 - 65.51: 1694 65.51 - 98.26: 100 98.26 - 131.02: 0 131.02 - 163.77: 1 Dihedral angle restraints: 38479 sinusoidal: 15660 harmonic: 22819 Sorted by residual: dihedral pdb=" CA SER B 838 " pdb=" C SER B 838 " pdb=" N MET B 839 " pdb=" CA MET B 839 " ideal model delta harmonic sigma weight residual -180.00 -105.65 -74.35 0 5.00e+00 4.00e-02 2.21e+02 dihedral pdb=" CA ASP B 837 " pdb=" C ASP B 837 " pdb=" N SER B 838 " pdb=" CA SER B 838 " ideal model delta harmonic sigma weight residual -180.00 -115.48 -64.52 0 5.00e+00 4.00e-02 1.67e+02 dihedral pdb=" CA ALA M 270 " pdb=" C ALA M 270 " pdb=" N GLY M 271 " pdb=" CA GLY M 271 " ideal model delta harmonic sigma weight residual -180.00 -117.46 -62.54 0 5.00e+00 4.00e-02 1.56e+02 ... (remaining 38476 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 7653 0.064 - 0.128: 1900 0.128 - 0.192: 208 0.192 - 0.257: 17 0.257 - 0.321: 6 Chirality restraints: 9784 Sorted by residual: chirality pdb=" CA HIS A 786 " pdb=" N HIS A 786 " pdb=" C HIS A 786 " pdb=" CB HIS A 786 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CA MET A1444 " pdb=" N MET A1444 " pdb=" C MET A1444 " pdb=" CB MET A1444 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CA GLU B 687 " pdb=" N GLU B 687 " pdb=" C GLU B 687 " pdb=" CB GLU B 687 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 9781 not shown) Planarity restraints: 10970 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR M 200 " 0.018 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C THR M 200 " -0.061 2.00e-02 2.50e+03 pdb=" O THR M 200 " 0.023 2.00e-02 2.50e+03 pdb=" N LYS M 201 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 567 " 0.058 5.00e-02 4.00e+02 8.66e-02 1.20e+01 pdb=" N PRO A 568 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 568 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 568 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 410 " -0.057 5.00e-02 4.00e+02 8.61e-02 1.19e+01 pdb=" N PRO B 411 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO B 411 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 411 " -0.047 5.00e-02 4.00e+02 ... (remaining 10967 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.39: 698 2.39 - 3.02: 43078 3.02 - 3.65: 102499 3.65 - 4.27: 149333 4.27 - 4.90: 238852 Nonbonded interactions: 534460 Sorted by model distance: nonbonded pdb=" CB CYS 0 156 " pdb=" S1 SF4 0 801 " model vdw 1.769 3.040 nonbonded pdb=" NE2 GLN A 68 " pdb=" ND1 HIS A 80 " model vdw 1.921 3.200 nonbonded pdb=" O SER G 95 " pdb=" OH TYR G 130 " model vdw 1.993 3.040 nonbonded pdb=" O GLY A1423 " pdb=" ND2 ASN A1427 " model vdw 1.994 3.120 nonbonded pdb=" N ASP B 188 " pdb=" OD1 ASP B 188 " model vdw 1.999 3.120 ... (remaining 534455 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: 12.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.730 Check model and map are aligned: 0.340 Set scattering table: 0.420 Process input model: 143.890 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 160.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5119 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 : 0.015 0.150 63958 Z= 1.007 Angle : 1.087 14.680 86723 Z= 0.598 Chirality : 0.054 0.321 9784 Planarity : 0.005 0.087 10958 Dihedral : 17.007 163.775 23813 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 29.17 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.63 % Favored : 89.14 % Rotamer: Outliers : 12.47 % Allowed : 13.20 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.15 % Twisted Proline : 0.30 % Twisted General : 0.29 % 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: -2.14 (0.09), residues: 7759 helix: -0.50 (0.09), residues: 2926 sheet: -1.51 (0.17), residues: 937 loop : -2.14 (0.09), residues: 3896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 146 HIS 0.016 0.002 HIS A 587 PHE 0.031 0.002 PHE B 963 TYR 0.027 0.002 TYR A 303 ARG 0.013 0.001 ARG H 146 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15518 Ramachandran restraints generated. 7759 Oldfield, 0 Emsley, 7759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15518 Ramachandran restraints generated. 7759 Oldfield, 0 Emsley, 7759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1014 residues out of total 7065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 783 poor density : 231 time to evaluate : 5.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 98 TYR cc_start: 0.9533 (OUTLIER) cc_final: 0.9057 (p90) REVERT: Q 106 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7615 (tp) REVERT: Q 122 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.8074 (mm110) REVERT: G 97 HIS cc_start: 0.2747 (OUTLIER) cc_final: 0.2203 (p-80) REVERT: M 291 ILE cc_start: -0.0145 (OUTLIER) cc_final: -0.0497 (mm) REVERT: A 862 ASN cc_start: 0.7449 (OUTLIER) cc_final: 0.7183 (m-40) REVERT: A 1362 TYR cc_start: 0.7861 (OUTLIER) cc_final: 0.7172 (t80) REVERT: A 1444 MET cc_start: 0.3647 (mtt) cc_final: 0.3256 (mtt) REVERT: B 137 TYR cc_start: 0.7160 (OUTLIER) cc_final: 0.5950 (m-10) REVERT: B 199 MET cc_start: 0.7104 (OUTLIER) cc_final: 0.6588 (pmm) REVERT: B 466 TRP cc_start: 0.8723 (OUTLIER) cc_final: 0.8357 (m-90) REVERT: B 733 HIS cc_start: 0.4147 (OUTLIER) cc_final: 0.3711 (p90) REVERT: B 789 MET cc_start: 0.7125 (OUTLIER) cc_final: 0.6783 (ttt) REVERT: B 962 LYS cc_start: 0.7330 (OUTLIER) cc_final: 0.7115 (ttpt) REVERT: B 995 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7621 (mpp80) REVERT: C 163 ILE cc_start: 0.7213 (OUTLIER) cc_final: 0.6954 (pt) REVERT: F 112 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6691 (mm-30) REVERT: I 118 ARG cc_start: 0.1196 (OUTLIER) cc_final: -0.0930 (tmt-80) REVERT: K 82 ASP cc_start: 0.7435 (OUTLIER) cc_final: 0.6653 (t0) REVERT: L 34 CYS cc_start: 0.6569 (OUTLIER) cc_final: 0.5879 (p) REVERT: 0 115 CYS cc_start: 0.4650 (OUTLIER) cc_final: 0.4434 (t) REVERT: 0 485 MET cc_start: -0.2656 (ttt) cc_final: -0.3882 (mtt) REVERT: 0 572 GLU cc_start: -0.1507 (OUTLIER) cc_final: -0.2136 (tt0) REVERT: 0 584 GLU cc_start: 0.0631 (OUTLIER) cc_final: 0.0263 (tt0) REVERT: 1 385 MET cc_start: -0.2656 (mtm) cc_final: -0.2924 (ppp) REVERT: 7 435 CYS cc_start: -0.0466 (OUTLIER) cc_final: -0.0683 (m) REVERT: 7 541 MET cc_start: -0.0653 (tpt) cc_final: -0.0882 (ttt) REVERT: 7 622 MET cc_start: 0.1201 (ppp) cc_final: -0.0281 (ptt) REVERT: 5 27 MET cc_start: -0.2446 (ptt) cc_final: -0.3169 (ptp) REVERT: 2 92 SER cc_start: -0.0240 (OUTLIER) cc_final: -0.0587 (p) REVERT: X 262 MET cc_start: 0.0223 (mtt) cc_final: -0.0381 (mtp) REVERT: W 58 ILE cc_start: -0.2771 (OUTLIER) cc_final: -0.3244 (mm) outliers start: 783 outliers final: 376 residues processed: 997 average time/residue: 0.5715 time to fit residues: 996.7653 Evaluate side-chains 618 residues out of total 7065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 401 poor density : 217 time to evaluate : 5.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 98 TYR Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain Q residue 106 ILE Chi-restraints excluded: chain Q residue 118 LEU Chi-restraints excluded: chain Q residue 122 GLN Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 132 ASP Chi-restraints excluded: chain Q residue 336 ASP Chi-restraints excluded: chain Q residue 359 ASN Chi-restraints excluded: chain Q residue 380 ASP Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 83 ASP Chi-restraints excluded: chain R residue 94 LYS Chi-restraints excluded: chain R residue 95 ILE Chi-restraints excluded: chain R residue 121 ASP Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 127 LYS Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 130 GLU Chi-restraints excluded: chain R residue 138 GLN Chi-restraints excluded: chain R residue 217 THR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 65 ASP Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain G residue 97 HIS Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 58 ASP Chi-restraints excluded: chain M residue 160 GLU Chi-restraints excluded: chain M residue 170 SER Chi-restraints excluded: chain M residue 175 SER Chi-restraints excluded: chain M residue 187 ARG Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 291 ILE Chi-restraints excluded: chain M residue 305 THR Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 419 LYS Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 488 ASN Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 567 LYS Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 862 ASN Chi-restraints excluded: chain A residue 879 GLU Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 889 SER Chi-restraints excluded: chain A residue 903 ASN Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 909 ASP Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1043 ASP Chi-restraints excluded: chain A residue 1056 SER Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1078 GLN Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1107 VAL Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1138 ILE Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1160 SER Chi-restraints excluded: chain A residue 1172 LEU Chi-restraints excluded: chain A residue 1174 PHE Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1204 ASP Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1211 GLN Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1223 ASP Chi-restraints excluded: chain A residue 1237 ILE Chi-restraints excluded: chain A residue 1240 CYS Chi-restraints excluded: chain A residue 1257 ASP Chi-restraints excluded: chain A residue 1263 ILE Chi-restraints excluded: chain A residue 1265 ASN Chi-restraints excluded: chain A residue 1278 ASN Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1299 VAL Chi-restraints excluded: chain A residue 1327 ILE Chi-restraints excluded: chain A residue 1329 THR Chi-restraints excluded: chain A residue 1334 ASP Chi-restraints excluded: chain A residue 1358 SER Chi-restraints excluded: chain A residue 1362 TYR Chi-restraints excluded: chain A residue 1372 VAL Chi-restraints excluded: chain A residue 1382 THR Chi-restraints excluded: chain A residue 1383 SER Chi-restraints excluded: chain A residue 1386 ARG Chi-restraints excluded: chain A residue 1392 SER Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1441 PHE Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 137 TYR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 195 CYS Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 466 TRP Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 516 ASN Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 625 LYS Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 642 ASP Chi-restraints excluded: chain B residue 668 ASP Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 685 LEU Chi-restraints excluded: chain B residue 708 GLU Chi-restraints excluded: chain B residue 722 ASP Chi-restraints excluded: chain B residue 733 HIS Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 783 THR Chi-restraints excluded: chain B residue 789 MET Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 864 LYS Chi-restraints excluded: chain B residue 875 GLU Chi-restraints excluded: chain B residue 879 ARG Chi-restraints excluded: chain B residue 887 HIS Chi-restraints excluded: chain B residue 894 ASP Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 909 ASP Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 951 GLN Chi-restraints excluded: chain B residue 962 LYS Chi-restraints excluded: chain B residue 963 PHE Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 996 ARG Chi-restraints excluded: chain B residue 1002 THR Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1032 SER Chi-restraints excluded: chain B residue 1048 THR Chi-restraints excluded: chain B residue 1051 THR Chi-restraints excluded: chain B residue 1101 ASP Chi-restraints excluded: chain B residue 1111 MET Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1129 ARG Chi-restraints excluded: chain B residue 1162 ILE Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain B residue 1183 LYS Chi-restraints excluded: chain B residue 1191 ILE Chi-restraints excluded: chain B residue 1218 THR Chi-restraints excluded: chain B residue 1222 ARG Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 123 ASN Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 67 GLU Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 128 LYS Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 145 ARG Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain I residue 9 ASP Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 60 GLN Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain I residue 78 CYS Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain I residue 118 ARG Chi-restraints excluded: chain I residue 120 GLN Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain K residue 14 GLU Chi-restraints excluded: chain K residue 20 LYS Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 82 ASP Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 31 CYS Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 44 ASP Chi-restraints excluded: chain L residue 48 CYS Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 55 ILE Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain 0 residue 109 THR Chi-restraints excluded: chain 0 residue 115 CYS Chi-restraints excluded: chain 0 residue 162 LEU Chi-restraints excluded: chain 0 residue 287 GLU Chi-restraints excluded: chain 0 residue 344 THR Chi-restraints excluded: chain 0 residue 393 VAL Chi-restraints excluded: chain 0 residue 572 GLU Chi-restraints excluded: chain 0 residue 584 GLU Chi-restraints excluded: chain 4 residue 128 GLU Chi-restraints excluded: chain 4 residue 180 THR Chi-restraints excluded: chain 4 residue 210 ILE Chi-restraints excluded: chain 4 residue 212 VAL Chi-restraints excluded: chain 4 residue 228 THR Chi-restraints excluded: chain 4 residue 263 VAL Chi-restraints excluded: chain 6 residue 440 CYS Chi-restraints excluded: chain 1 residue 381 LEU Chi-restraints excluded: chain 7 residue 408 ILE Chi-restraints excluded: chain 7 residue 435 CYS Chi-restraints excluded: chain 7 residue 453 VAL Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 92 SER Chi-restraints excluded: chain U residue 264 ASP Chi-restraints excluded: chain V residue 57 GLN Chi-restraints excluded: chain O residue 91 ASN Chi-restraints excluded: chain O residue 183 SER Chi-restraints excluded: chain O residue 205 LEU Chi-restraints excluded: chain O residue 213 VAL Chi-restraints excluded: chain W residue 15 PHE Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain W residue 126 ILE Chi-restraints excluded: chain W residue 149 CYS Chi-restraints excluded: chain W residue 156 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 771 random chunks: chunk 651 optimal weight: 8.9990 chunk 584 optimal weight: 30.0000 chunk 324 optimal weight: 6.9990 chunk 199 optimal weight: 7.9990 chunk 394 optimal weight: 6.9990 chunk 312 optimal weight: 3.9990 chunk 604 optimal weight: 50.0000 chunk 233 optimal weight: 6.9990 chunk 367 optimal weight: 10.0000 chunk 449 optimal weight: 10.0000 chunk 700 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN G 71 ASN G 153 GLN ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN A 548 ASN A 700 ASN ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 742 ASN A 903 ASN A1048 ASN ** A1173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 GLN ** B 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1112 GLN B1177 HIS B1193 GLN E 99 HIS ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 128 ASN ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 104 ASN 0 66 HIS ** 0 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 503 GLN ** 0 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 302 ASN ** 7 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 702 ASN 2 352 ASN 2 500 GLN O 68 GLN ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 107 GLN ** W 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4984 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 63958 Z= 0.389 Angle : 0.773 13.980 86723 Z= 0.410 Chirality : 0.047 0.354 9784 Planarity : 0.005 0.091 10958 Dihedral : 14.590 163.362 10350 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.45 % Favored : 91.39 % Rotamer: Outliers : 6.07 % Allowed : 17.30 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.13 % Twisted Proline : 0.30 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.09), residues: 7759 helix: -0.08 (0.09), residues: 3098 sheet: -1.36 (0.17), residues: 861 loop : -2.02 (0.10), residues: 3800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 109 HIS 0.014 0.002 HIS 6 381 PHE 0.033 0.002 PHE 0 656 TYR 0.024 0.002 TYR A 852 ARG 0.010 0.001 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15518 Ramachandran restraints generated. 7759 Oldfield, 0 Emsley, 7759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15518 Ramachandran restraints generated. 7759 Oldfield, 0 Emsley, 7759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 7065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 381 poor density : 223 time to evaluate : 5.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 98 TYR cc_start: 0.9538 (OUTLIER) cc_final: 0.8914 (p90) REVERT: Q 114 MET cc_start: 0.9055 (mmm) cc_final: 0.8433 (mmm) REVERT: Q 122 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.8078 (mm110) REVERT: B 466 TRP cc_start: 0.8629 (OUTLIER) cc_final: 0.8400 (m-90) REVERT: B 848 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.7232 (mmt90) REVERT: B 995 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.7359 (mpp80) REVERT: B 996 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.7026 (ttt-90) REVERT: B 1129 ARG cc_start: 0.7119 (OUTLIER) cc_final: 0.6728 (ttm110) REVERT: F 112 GLU cc_start: 0.6445 (OUTLIER) cc_final: 0.5957 (mm-30) REVERT: I 118 ARG cc_start: 0.0949 (OUTLIER) cc_final: 0.0667 (tpt90) REVERT: 0 115 CYS cc_start: 0.4946 (OUTLIER) cc_final: 0.4680 (t) REVERT: 0 485 MET cc_start: -0.2685 (ttt) cc_final: -0.3820 (mtt) REVERT: 0 584 GLU cc_start: 0.0348 (OUTLIER) cc_final: -0.0051 (tt0) REVERT: 4 206 MET cc_start: 0.0738 (mpp) cc_final: -0.0037 (mtm) REVERT: 6 322 MET cc_start: 0.2493 (ppp) cc_final: 0.1764 (ppp) REVERT: 6 384 MET cc_start: 0.7017 (OUTLIER) cc_final: 0.6689 (pmm) REVERT: 1 385 MET cc_start: -0.3095 (mtm) cc_final: -0.3523 (ppp) REVERT: 1 387 MET cc_start: -0.1006 (mmt) cc_final: -0.1236 (mmt) REVERT: 7 541 MET cc_start: -0.0581 (tpt) cc_final: -0.0988 (ttt) REVERT: 7 622 MET cc_start: 0.1304 (ppp) cc_final: 0.0352 (ptt) REVERT: 5 27 MET cc_start: -0.2248 (ptt) cc_final: -0.2953 (ptp) REVERT: 2 92 SER cc_start: -0.0333 (OUTLIER) cc_final: -0.0547 (p) REVERT: 2 97 MET cc_start: 0.2117 (mmt) cc_final: 0.1663 (mmt) REVERT: X 262 MET cc_start: -0.0018 (mtt) cc_final: -0.0579 (mtp) REVERT: W 58 ILE cc_start: -0.2828 (OUTLIER) cc_final: -0.3314 (mm) outliers start: 381 outliers final: 233 residues processed: 586 average time/residue: 0.5562 time to fit residues: 566.1503 Evaluate side-chains 462 residues out of total 7065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 247 poor density : 215 time to evaluate : 5.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 98 TYR Chi-restraints excluded: chain Q residue 122 GLN Chi-restraints excluded: chain Q residue 351 VAL Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 83 ASP Chi-restraints excluded: chain R residue 94 LYS Chi-restraints excluded: chain R residue 97 ILE Chi-restraints excluded: chain R residue 121 ASP Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 127 LYS Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 217 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 83 LYS Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain M residue 58 ASP Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 187 ARG Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 305 THR Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 419 LYS Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 567 LYS Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 879 GLU Chi-restraints excluded: chain A residue 889 SER Chi-restraints excluded: chain A residue 903 ASN Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 909 ASP Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1038 THR 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 1089 VAL Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1138 ILE Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1172 LEU Chi-restraints excluded: chain A residue 1174 PHE Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1204 ASP Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1211 GLN Chi-restraints excluded: chain A residue 1223 ASP Chi-restraints excluded: chain A residue 1240 CYS Chi-restraints excluded: chain A residue 1265 ASN Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1299 VAL Chi-restraints excluded: chain A residue 1327 ILE Chi-restraints excluded: chain A residue 1329 THR Chi-restraints excluded: chain A residue 1372 VAL Chi-restraints excluded: chain A residue 1382 THR Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 195 CYS Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 466 TRP Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 685 LEU Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain B residue 848 ARG Chi-restraints excluded: chain B residue 863 GLU Chi-restraints excluded: chain B residue 864 LYS Chi-restraints excluded: chain B residue 884 ARG Chi-restraints excluded: chain B residue 887 HIS Chi-restraints excluded: chain B residue 894 ASP Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 963 PHE Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain B residue 996 ARG Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1051 THR Chi-restraints excluded: chain B residue 1129 ARG Chi-restraints excluded: chain B residue 1183 LYS Chi-restraints excluded: chain B residue 1218 THR Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 128 LYS Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 145 ARG Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain I residue 118 ARG Chi-restraints excluded: chain I residue 120 GLN Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain K residue 20 LYS Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 104 ASN Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 44 ASP Chi-restraints excluded: chain L residue 48 CYS Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain 0 residue 115 CYS Chi-restraints excluded: chain 0 residue 162 LEU Chi-restraints excluded: chain 0 residue 175 VAL Chi-restraints excluded: chain 0 residue 287 GLU Chi-restraints excluded: chain 0 residue 344 THR Chi-restraints excluded: chain 0 residue 393 VAL Chi-restraints excluded: chain 0 residue 584 GLU Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 4 residue 128 GLU Chi-restraints excluded: chain 4 residue 210 ILE Chi-restraints excluded: chain 4 residue 212 VAL Chi-restraints excluded: chain 4 residue 228 THR Chi-restraints excluded: chain 4 residue 263 VAL Chi-restraints excluded: chain 6 residue 169 MET Chi-restraints excluded: chain 6 residue 310 VAL Chi-restraints excluded: chain 6 residue 384 MET Chi-restraints excluded: chain 6 residue 440 CYS Chi-restraints excluded: chain 1 residue 381 LEU Chi-restraints excluded: chain 7 residue 445 MET Chi-restraints excluded: chain 7 residue 474 MET Chi-restraints excluded: chain 7 residue 742 MET Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 92 SER Chi-restraints excluded: chain 2 residue 480 VAL Chi-restraints excluded: chain U residue 264 ASP Chi-restraints excluded: chain V residue 57 GLN Chi-restraints excluded: chain O residue 91 ASN Chi-restraints excluded: chain O residue 205 LEU Chi-restraints excluded: chain O residue 213 VAL Chi-restraints excluded: chain W residue 15 PHE Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain W residue 63 SER Chi-restraints excluded: chain W residue 113 LEU Chi-restraints excluded: chain W residue 126 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 771 random chunks: chunk 389 optimal weight: 2.9990 chunk 217 optimal weight: 0.7980 chunk 582 optimal weight: 50.0000 chunk 476 optimal weight: 4.9990 chunk 193 optimal weight: 7.9990 chunk 701 optimal weight: 20.0000 chunk 757 optimal weight: 0.9980 chunk 624 optimal weight: 50.0000 chunk 695 optimal weight: 50.0000 chunk 239 optimal weight: 0.9980 chunk 562 optimal weight: 4.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 ASN ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 ASN ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 HIS ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1390 ASN B1093 GLN ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 12 ASN ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 108 HIS L 53 HIS ** 0 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 707 ASN ** 0 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 349 ASN ** 7 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 405 HIS ** U 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 91 ASN ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4899 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 63958 Z= 0.210 Angle : 0.657 12.554 86723 Z= 0.347 Chirality : 0.045 0.251 9784 Planarity : 0.004 0.082 10958 Dihedral : 13.468 153.837 9991 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.66 % Favored : 92.24 % Rotamer: Outliers : 4.78 % Allowed : 17.79 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.15 % Twisted Proline : 0.30 % 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: -1.32 (0.09), residues: 7759 helix: 0.36 (0.09), residues: 3095 sheet: -1.36 (0.17), residues: 862 loop : -1.83 (0.10), residues: 3802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP Q 350 HIS 0.012 0.001 HIS A 587 PHE 0.043 0.001 PHE 0 656 TYR 0.021 0.001 TYR A 852 ARG 0.010 0.000 ARG I 5 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15518 Ramachandran restraints generated. 7759 Oldfield, 0 Emsley, 7759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15518 Ramachandran restraints generated. 7759 Oldfield, 0 Emsley, 7759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 7065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 300 poor density : 221 time to evaluate : 5.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 98 TYR cc_start: 0.9525 (OUTLIER) cc_final: 0.8909 (p90) REVERT: Q 352 MET cc_start: 0.6644 (mpp) cc_final: 0.6350 (mtm) REVERT: R 121 ASP cc_start: 0.8906 (OUTLIER) cc_final: 0.8664 (p0) REVERT: M 291 ILE cc_start: -0.0334 (OUTLIER) cc_final: -0.0536 (mt) REVERT: A 66 LYS cc_start: 0.3420 (OUTLIER) cc_final: 0.3065 (mptt) REVERT: A 1284 MET cc_start: 0.5492 (mtm) cc_final: 0.5141 (mtm) REVERT: A 1345 ARG cc_start: 0.6894 (OUTLIER) cc_final: 0.6608 (tmt-80) REVERT: F 112 GLU cc_start: 0.6397 (OUTLIER) cc_final: 0.5827 (mm-30) REVERT: I 80 SER cc_start: 0.5409 (OUTLIER) cc_final: 0.2766 (p) REVERT: 0 115 CYS cc_start: 0.4872 (OUTLIER) cc_final: 0.4577 (t) REVERT: 0 468 MET cc_start: -0.5189 (OUTLIER) cc_final: -0.6678 (ptt) REVERT: 0 485 MET cc_start: -0.2708 (ttt) cc_final: -0.3873 (mtt) REVERT: 0 584 GLU cc_start: 0.0107 (OUTLIER) cc_final: -0.0366 (pt0) REVERT: 4 206 MET cc_start: 0.0725 (mpp) cc_final: -0.0168 (mtm) REVERT: 6 384 MET cc_start: 0.6820 (OUTLIER) cc_final: 0.6539 (pmm) REVERT: 1 385 MET cc_start: -0.3080 (mtm) cc_final: -0.3709 (ppp) REVERT: 1 387 MET cc_start: -0.0544 (mmt) cc_final: -0.0783 (mmt) REVERT: 7 497 MET cc_start: -0.1595 (ptm) cc_final: -0.1864 (ptt) REVERT: 7 499 ARG cc_start: -0.1865 (OUTLIER) cc_final: -0.3120 (mpt180) REVERT: 7 541 MET cc_start: -0.0492 (tpt) cc_final: -0.1000 (ttt) REVERT: 7 561 MET cc_start: 0.1818 (OUTLIER) cc_final: 0.0745 (tpt) REVERT: 7 622 MET cc_start: 0.0965 (ppp) cc_final: -0.0002 (ptt) REVERT: X 262 MET cc_start: 0.0512 (mtt) cc_final: -0.0246 (mtp) REVERT: O 123 VAL cc_start: -0.1835 (OUTLIER) cc_final: -0.2075 (t) REVERT: W 58 ILE cc_start: -0.2921 (OUTLIER) cc_final: -0.3361 (mm) outliers start: 300 outliers final: 172 residues processed: 504 average time/residue: 0.5509 time to fit residues: 488.4219 Evaluate side-chains 401 residues out of total 7065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 214 time to evaluate : 5.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 98 TYR Chi-restraints excluded: chain Q residue 133 PHE Chi-restraints excluded: chain Q residue 351 VAL Chi-restraints excluded: chain Q residue 359 ASN Chi-restraints excluded: chain Q residue 379 GLU Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 83 ASP Chi-restraints excluded: chain R residue 94 LYS Chi-restraints excluded: chain R residue 121 ASP Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 127 LYS Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 217 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain M residue 58 ASP Chi-restraints excluded: chain M residue 187 ARG Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 291 ILE Chi-restraints excluded: chain M residue 305 THR Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 903 ASN Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 909 ASP Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1172 LEU Chi-restraints excluded: chain A residue 1174 PHE Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1204 ASP Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1223 ASP Chi-restraints excluded: chain A residue 1257 ASP Chi-restraints excluded: chain A residue 1265 ASN Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1345 ARG Chi-restraints excluded: chain A residue 1372 VAL Chi-restraints excluded: chain A residue 1382 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 864 LYS Chi-restraints excluded: chain B residue 884 ARG Chi-restraints excluded: chain B residue 887 HIS Chi-restraints excluded: chain B residue 894 ASP Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 963 PHE Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1051 THR Chi-restraints excluded: chain B residue 1218 THR Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain F residue 85 MET Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 128 LYS Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 145 ARG Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain I residue 120 GLN Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 48 CYS Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain 0 residue 115 CYS Chi-restraints excluded: chain 0 residue 162 LEU Chi-restraints excluded: chain 0 residue 175 VAL Chi-restraints excluded: chain 0 residue 240 ILE Chi-restraints excluded: chain 0 residue 287 GLU Chi-restraints excluded: chain 0 residue 335 LEU Chi-restraints excluded: chain 0 residue 393 VAL Chi-restraints excluded: chain 0 residue 468 MET Chi-restraints excluded: chain 0 residue 554 TRP Chi-restraints excluded: chain 0 residue 584 GLU Chi-restraints excluded: chain 4 residue 128 GLU Chi-restraints excluded: chain 4 residue 210 ILE Chi-restraints excluded: chain 4 residue 212 VAL Chi-restraints excluded: chain 4 residue 228 THR Chi-restraints excluded: chain 4 residue 263 VAL Chi-restraints excluded: chain 6 residue 166 ILE Chi-restraints excluded: chain 6 residue 169 MET Chi-restraints excluded: chain 6 residue 310 VAL Chi-restraints excluded: chain 6 residue 384 MET Chi-restraints excluded: chain 6 residue 440 CYS Chi-restraints excluded: chain 7 residue 445 MET Chi-restraints excluded: chain 7 residue 474 MET Chi-restraints excluded: chain 7 residue 499 ARG Chi-restraints excluded: chain 7 residue 561 MET Chi-restraints excluded: chain 7 residue 742 MET Chi-restraints excluded: chain 2 residue 11 THR Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 219 VAL Chi-restraints excluded: chain 2 residue 480 VAL Chi-restraints excluded: chain O residue 123 VAL Chi-restraints excluded: chain O residue 205 LEU Chi-restraints excluded: chain W residue 15 PHE Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain W residue 113 LEU Chi-restraints excluded: chain W residue 126 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 771 random chunks: chunk 693 optimal weight: 0.8980 chunk 527 optimal weight: 0.3980 chunk 364 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 334 optimal weight: 3.9990 chunk 470 optimal weight: 20.0000 chunk 703 optimal weight: 40.0000 chunk 745 optimal weight: 10.0000 chunk 367 optimal weight: 8.9990 chunk 667 optimal weight: 40.0000 chunk 200 optimal weight: 10.0000 overall best weight: 4.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 223 GLN ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 193 GLN ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1130 GLN ** A1173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 951 GLN ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 ASN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 93 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4951 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 63958 Z= 0.300 Angle : 0.666 12.475 86723 Z= 0.348 Chirality : 0.044 0.247 9784 Planarity : 0.004 0.087 10958 Dihedral : 12.957 150.864 9842 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.99 % Favored : 91.91 % Rotamer: Outliers : 4.19 % Allowed : 18.14 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.15 % Twisted Proline : 0.30 % Twisted General : 0.19 % 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: -1.18 (0.09), residues: 7759 helix: 0.51 (0.09), residues: 3105 sheet: -1.29 (0.17), residues: 872 loop : -1.80 (0.10), residues: 3782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP Q 350 HIS 0.010 0.001 HIS A 587 PHE 0.040 0.001 PHE 0 720 TYR 0.020 0.001 TYR 1 630 ARG 0.006 0.000 ARG R 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15518 Ramachandran restraints generated. 7759 Oldfield, 0 Emsley, 7759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15518 Ramachandran restraints generated. 7759 Oldfield, 0 Emsley, 7759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 7065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 263 poor density : 219 time to evaluate : 5.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 98 TYR cc_start: 0.9539 (OUTLIER) cc_final: 0.8926 (p90) REVERT: A 66 LYS cc_start: 0.3582 (OUTLIER) cc_final: 0.3153 (mptt) REVERT: A 1345 ARG cc_start: 0.6988 (OUTLIER) cc_final: 0.6483 (ttt-90) REVERT: F 112 GLU cc_start: 0.6390 (OUTLIER) cc_final: 0.5774 (mm-30) REVERT: H 123 MET cc_start: 0.6328 (tmm) cc_final: 0.5736 (ttp) REVERT: J 49 MET cc_start: 0.5691 (mmm) cc_final: 0.5372 (mmm) REVERT: 0 115 CYS cc_start: 0.5339 (OUTLIER) cc_final: 0.5087 (t) REVERT: 0 485 MET cc_start: -0.2574 (ttt) cc_final: -0.3867 (mtt) REVERT: 0 584 GLU cc_start: 0.0199 (OUTLIER) cc_final: -0.0309 (pt0) REVERT: 4 206 MET cc_start: 0.0507 (mpp) cc_final: -0.0093 (mtm) REVERT: 6 384 MET cc_start: 0.7081 (OUTLIER) cc_final: 0.6696 (pmm) REVERT: 1 385 MET cc_start: -0.3197 (mtm) cc_final: -0.3876 (ppp) REVERT: 1 387 MET cc_start: -0.0599 (mmt) cc_final: -0.0813 (mmt) REVERT: 7 474 MET cc_start: 0.4107 (OUTLIER) cc_final: 0.3769 (tpt) REVERT: 7 497 MET cc_start: -0.1448 (ptm) cc_final: -0.1852 (ptt) REVERT: 7 499 ARG cc_start: -0.1943 (OUTLIER) cc_final: -0.3031 (mpt180) REVERT: 7 561 MET cc_start: 0.2145 (mmm) cc_final: 0.1176 (tpt) REVERT: 7 622 MET cc_start: 0.0660 (ppp) cc_final: -0.1132 (ptt) REVERT: 5 27 MET cc_start: -0.1882 (ptp) cc_final: -0.2169 (ptp) REVERT: 2 97 MET cc_start: 0.1860 (mmt) cc_final: 0.1658 (mmt) REVERT: X 262 MET cc_start: 0.0443 (mtt) cc_final: -0.0299 (mtp) REVERT: W 58 ILE cc_start: -0.2660 (OUTLIER) cc_final: -0.3072 (mm) outliers start: 263 outliers final: 180 residues processed: 466 average time/residue: 0.5513 time to fit residues: 453.0994 Evaluate side-chains 405 residues out of total 7065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 215 time to evaluate : 5.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 98 TYR Chi-restraints excluded: chain Q residue 350 TRP Chi-restraints excluded: chain Q residue 359 ASN Chi-restraints excluded: chain Q residue 379 GLU Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 83 ASP Chi-restraints excluded: chain R residue 94 LYS Chi-restraints excluded: chain R residue 121 ASP Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 127 LYS Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 217 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain M residue 58 ASP Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 168 MET Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 305 THR Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 903 ASN Chi-restraints excluded: chain A residue 909 ASP Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1034 GLU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1172 LEU Chi-restraints excluded: chain A residue 1174 PHE Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1204 ASP Chi-restraints excluded: chain A residue 1223 ASP Chi-restraints excluded: chain A residue 1265 ASN Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1345 ARG Chi-restraints excluded: chain A residue 1372 VAL Chi-restraints excluded: chain A residue 1382 THR Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 863 GLU Chi-restraints excluded: chain B residue 864 LYS Chi-restraints excluded: chain B residue 884 ARG Chi-restraints excluded: chain B residue 887 HIS Chi-restraints excluded: chain B residue 894 ASP Chi-restraints excluded: chain B residue 963 PHE Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1051 THR Chi-restraints excluded: chain B residue 1218 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain F residue 85 MET Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 128 LYS Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 145 ARG Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain I residue 120 GLN Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 113 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain 0 residue 39 ILE Chi-restraints excluded: chain 0 residue 115 CYS Chi-restraints excluded: chain 0 residue 136 MET Chi-restraints excluded: chain 0 residue 162 LEU Chi-restraints excluded: chain 0 residue 175 VAL Chi-restraints excluded: chain 0 residue 240 ILE Chi-restraints excluded: chain 0 residue 287 GLU Chi-restraints excluded: chain 0 residue 335 LEU Chi-restraints excluded: chain 0 residue 393 VAL Chi-restraints excluded: chain 0 residue 554 TRP Chi-restraints excluded: chain 0 residue 584 GLU Chi-restraints excluded: chain 4 residue 28 VAL Chi-restraints excluded: chain 4 residue 128 GLU Chi-restraints excluded: chain 4 residue 210 ILE Chi-restraints excluded: chain 4 residue 212 VAL Chi-restraints excluded: chain 4 residue 228 THR Chi-restraints excluded: chain 4 residue 263 VAL Chi-restraints excluded: chain 6 residue 166 ILE Chi-restraints excluded: chain 6 residue 169 MET Chi-restraints excluded: chain 6 residue 310 VAL Chi-restraints excluded: chain 6 residue 384 MET Chi-restraints excluded: chain 6 residue 440 CYS Chi-restraints excluded: chain 1 residue 381 LEU Chi-restraints excluded: chain 1 residue 386 ILE Chi-restraints excluded: chain 7 residue 445 MET Chi-restraints excluded: chain 7 residue 474 MET Chi-restraints excluded: chain 7 residue 499 ARG Chi-restraints excluded: chain 7 residue 502 VAL Chi-restraints excluded: chain 7 residue 701 PHE Chi-restraints excluded: chain 7 residue 742 MET Chi-restraints excluded: chain 2 residue 11 THR Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 219 VAL Chi-restraints excluded: chain 2 residue 480 VAL Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain W residue 15 PHE Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain W residue 113 LEU Chi-restraints excluded: chain W residue 126 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 771 random chunks: chunk 620 optimal weight: 3.9990 chunk 423 optimal weight: 9.9990 chunk 10 optimal weight: 30.0000 chunk 554 optimal weight: 3.9990 chunk 307 optimal weight: 1.9990 chunk 635 optimal weight: 20.0000 chunk 515 optimal weight: 0.0040 chunk 0 optimal weight: 80.0000 chunk 380 optimal weight: 7.9990 chunk 668 optimal weight: 50.0000 chunk 188 optimal weight: 1.9990 overall best weight: 2.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 ASN ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 ASN ** A1173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 HIS ** 0 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4894 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 63958 Z= 0.198 Angle : 0.624 13.065 86723 Z= 0.326 Chirality : 0.043 0.241 9784 Planarity : 0.004 0.083 10958 Dihedral : 12.763 145.158 9824 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.72 % Favored : 92.18 % Rotamer: Outliers : 3.65 % Allowed : 18.86 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.01 (0.10), residues: 7759 helix: 0.69 (0.09), residues: 3127 sheet: -1.23 (0.17), residues: 869 loop : -1.73 (0.10), residues: 3763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP Q 350 HIS 0.010 0.001 HIS A 587 PHE 0.036 0.001 PHE 0 720 TYR 0.020 0.001 TYR A 852 ARG 0.012 0.000 ARG A 407 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15518 Ramachandran restraints generated. 7759 Oldfield, 0 Emsley, 7759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15518 Ramachandran restraints generated. 7759 Oldfield, 0 Emsley, 7759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 7065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 229 poor density : 217 time to evaluate : 5.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 98 TYR cc_start: 0.9527 (OUTLIER) cc_final: 0.8922 (p90) REVERT: Q 352 MET cc_start: 0.6448 (mpp) cc_final: 0.6185 (mtm) REVERT: G 95 SER cc_start: 0.2367 (OUTLIER) cc_final: 0.2042 (p) REVERT: A 66 LYS cc_start: 0.3579 (OUTLIER) cc_final: 0.2975 (mptt) REVERT: A 985 ASP cc_start: 0.4878 (OUTLIER) cc_final: 0.4379 (p0) REVERT: A 1345 ARG cc_start: 0.6871 (OUTLIER) cc_final: 0.6416 (ttt-90) REVERT: B 797 TYR cc_start: 0.7636 (OUTLIER) cc_final: 0.7357 (t80) REVERT: F 112 GLU cc_start: 0.6200 (OUTLIER) cc_final: 0.5573 (mm-30) REVERT: H 123 MET cc_start: 0.6264 (tmm) cc_final: 0.5716 (ttp) REVERT: 0 115 CYS cc_start: 0.4941 (OUTLIER) cc_final: 0.4694 (t) REVERT: 0 485 MET cc_start: -0.2536 (ttt) cc_final: -0.3764 (mtt) REVERT: 0 584 GLU cc_start: 0.0176 (OUTLIER) cc_final: -0.0461 (pt0) REVERT: 4 206 MET cc_start: 0.0479 (mpp) cc_final: -0.0066 (mtm) REVERT: 1 385 MET cc_start: -0.3212 (mtm) cc_final: -0.3940 (ppp) REVERT: 1 387 MET cc_start: -0.0720 (mmt) cc_final: -0.0921 (mmt) REVERT: 7 497 MET cc_start: -0.1308 (ptm) cc_final: -0.1795 (ptt) REVERT: 7 499 ARG cc_start: -0.2091 (OUTLIER) cc_final: -0.2385 (mtt180) REVERT: 7 561 MET cc_start: 0.2094 (mmm) cc_final: 0.1211 (tpt) REVERT: 7 622 MET cc_start: 0.0829 (ppp) cc_final: -0.0959 (ptt) REVERT: X 262 MET cc_start: 0.0515 (mtt) cc_final: 0.0259 (mtp) REVERT: W 58 ILE cc_start: -0.2904 (OUTLIER) cc_final: -0.3244 (mm) outliers start: 229 outliers final: 167 residues processed: 434 average time/residue: 0.6045 time to fit residues: 461.3973 Evaluate side-chains 393 residues out of total 7065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 215 time to evaluate : 5.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 98 TYR Chi-restraints excluded: chain Q residue 350 TRP Chi-restraints excluded: chain Q residue 351 VAL Chi-restraints excluded: chain Q residue 359 ASN Chi-restraints excluded: chain Q residue 379 GLU Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 79 GLU Chi-restraints excluded: chain R residue 83 ASP Chi-restraints excluded: chain R residue 94 LYS Chi-restraints excluded: chain R residue 121 ASP Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 127 LYS Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 217 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 65 ASP Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain M residue 58 ASP Chi-restraints excluded: chain M residue 187 ARG Chi-restraints excluded: chain M residue 305 THR Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 903 ASN Chi-restraints excluded: chain A residue 909 ASP Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1034 GLU Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1172 LEU Chi-restraints excluded: chain A residue 1174 PHE Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1204 ASP Chi-restraints excluded: chain A residue 1265 ASN Chi-restraints excluded: chain A residue 1345 ARG Chi-restraints excluded: chain A residue 1382 THR Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 797 TYR Chi-restraints excluded: chain B residue 864 LYS Chi-restraints excluded: chain B residue 884 ARG Chi-restraints excluded: chain B residue 887 HIS Chi-restraints excluded: chain B residue 935 ARG Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 963 PHE Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1051 THR Chi-restraints excluded: chain B residue 1060 ARG Chi-restraints excluded: chain B residue 1218 THR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain F residue 85 MET Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 128 LYS Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 145 ARG Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain I residue 120 GLN Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 113 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 62 LYS Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain 0 residue 39 ILE Chi-restraints excluded: chain 0 residue 115 CYS Chi-restraints excluded: chain 0 residue 136 MET Chi-restraints excluded: chain 0 residue 162 LEU Chi-restraints excluded: chain 0 residue 175 VAL Chi-restraints excluded: chain 0 residue 231 ILE Chi-restraints excluded: chain 0 residue 240 ILE Chi-restraints excluded: chain 0 residue 287 GLU Chi-restraints excluded: chain 0 residue 312 LEU Chi-restraints excluded: chain 0 residue 335 LEU Chi-restraints excluded: chain 0 residue 393 VAL Chi-restraints excluded: chain 0 residue 554 TRP Chi-restraints excluded: chain 0 residue 584 GLU Chi-restraints excluded: chain 4 residue 28 VAL Chi-restraints excluded: chain 4 residue 148 THR Chi-restraints excluded: chain 4 residue 210 ILE Chi-restraints excluded: chain 4 residue 212 VAL Chi-restraints excluded: chain 4 residue 228 THR Chi-restraints excluded: chain 4 residue 263 VAL Chi-restraints excluded: chain 6 residue 169 MET Chi-restraints excluded: chain 6 residue 310 VAL Chi-restraints excluded: chain 6 residue 440 CYS Chi-restraints excluded: chain 1 residue 381 LEU Chi-restraints excluded: chain 1 residue 386 ILE Chi-restraints excluded: chain 7 residue 445 MET Chi-restraints excluded: chain 7 residue 499 ARG Chi-restraints excluded: chain 7 residue 668 THR Chi-restraints excluded: chain 7 residue 701 PHE Chi-restraints excluded: chain 7 residue 742 MET Chi-restraints excluded: chain 2 residue 11 THR Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 87 LEU Chi-restraints excluded: chain 2 residue 219 VAL Chi-restraints excluded: chain 2 residue 480 VAL Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain W residue 15 PHE Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain W residue 113 LEU Chi-restraints excluded: chain W residue 126 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 771 random chunks: chunk 250 optimal weight: 0.0770 chunk 671 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 chunk 437 optimal weight: 40.0000 chunk 183 optimal weight: 0.9980 chunk 745 optimal weight: 30.0000 chunk 619 optimal weight: 30.0000 chunk 345 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 246 optimal weight: 0.0170 chunk 391 optimal weight: 0.0870 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 ASN ** A1173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 ASN B 761 HIS ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 GLN ** 0 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 650 ASN ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4836 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 63958 Z= 0.160 Angle : 0.607 13.180 86723 Z= 0.314 Chirality : 0.043 0.279 9784 Planarity : 0.004 0.086 10958 Dihedral : 12.470 140.594 9786 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.11 % Favored : 92.80 % Rotamer: Outliers : 3.30 % Allowed : 19.54 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.83 (0.10), residues: 7759 helix: 0.87 (0.09), residues: 3122 sheet: -1.23 (0.17), residues: 882 loop : -1.65 (0.10), residues: 3755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP Q 350 HIS 0.006 0.001 HIS C 91 PHE 0.040 0.001 PHE 0 656 TYR 0.018 0.001 TYR A 852 ARG 0.010 0.000 ARG A 57 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15518 Ramachandran restraints generated. 7759 Oldfield, 0 Emsley, 7759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15518 Ramachandran restraints generated. 7759 Oldfield, 0 Emsley, 7759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 7065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 221 time to evaluate : 5.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 98 TYR cc_start: 0.9500 (OUTLIER) cc_final: 0.8884 (p90) REVERT: A 66 LYS cc_start: 0.3648 (OUTLIER) cc_final: 0.3394 (mptt) REVERT: B 797 TYR cc_start: 0.7612 (OUTLIER) cc_final: 0.7229 (t80) REVERT: H 123 MET cc_start: 0.6233 (tmm) cc_final: 0.5751 (ttp) REVERT: 0 115 CYS cc_start: 0.4973 (OUTLIER) cc_final: 0.4765 (t) REVERT: 0 485 MET cc_start: -0.2792 (ttt) cc_final: -0.4071 (mtt) REVERT: 0 664 GLN cc_start: -0.2520 (OUTLIER) cc_final: -0.3162 (pt0) REVERT: 1 387 MET cc_start: -0.0764 (mmt) cc_final: -0.0975 (mmt) REVERT: 7 497 MET cc_start: -0.1221 (ptm) cc_final: -0.2190 (ptt) REVERT: 7 499 ARG cc_start: -0.2266 (OUTLIER) cc_final: -0.2557 (mtt180) REVERT: 7 561 MET cc_start: 0.2144 (OUTLIER) cc_final: 0.1378 (tpt) REVERT: 7 622 MET cc_start: 0.0880 (ppp) cc_final: -0.0028 (ptt) REVERT: X 262 MET cc_start: 0.0276 (mtt) cc_final: -0.0083 (mtp) REVERT: W 58 ILE cc_start: -0.2823 (OUTLIER) cc_final: -0.3337 (mm) outliers start: 207 outliers final: 134 residues processed: 416 average time/residue: 0.5773 time to fit residues: 423.2542 Evaluate side-chains 358 residues out of total 7065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 216 time to evaluate : 5.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 98 TYR Chi-restraints excluded: chain Q residue 103 LEU Chi-restraints excluded: chain Q residue 350 TRP Chi-restraints excluded: chain Q residue 396 THR Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 79 GLU Chi-restraints excluded: chain R residue 121 ASP Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 217 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain M residue 58 ASP Chi-restraints excluded: chain M residue 305 THR Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 644 LYS Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 909 ASP Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1172 LEU Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1204 ASP Chi-restraints excluded: chain A residue 1265 ASN Chi-restraints excluded: chain A residue 1382 THR Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 466 TRP Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 797 TYR Chi-restraints excluded: chain B residue 864 LYS Chi-restraints excluded: chain B residue 884 ARG Chi-restraints excluded: chain B residue 887 HIS Chi-restraints excluded: chain B residue 935 ARG Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 963 PHE Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1051 THR Chi-restraints excluded: chain B residue 1060 ARG Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 145 ARG Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain I residue 120 GLN Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 113 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 62 LYS Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain 0 residue 39 ILE Chi-restraints excluded: chain 0 residue 115 CYS Chi-restraints excluded: chain 0 residue 136 MET Chi-restraints excluded: chain 0 residue 162 LEU Chi-restraints excluded: chain 0 residue 175 VAL Chi-restraints excluded: chain 0 residue 207 ILE Chi-restraints excluded: chain 0 residue 240 ILE Chi-restraints excluded: chain 0 residue 253 THR Chi-restraints excluded: chain 0 residue 287 GLU Chi-restraints excluded: chain 0 residue 312 LEU Chi-restraints excluded: chain 0 residue 335 LEU Chi-restraints excluded: chain 0 residue 393 VAL Chi-restraints excluded: chain 0 residue 554 TRP Chi-restraints excluded: chain 0 residue 584 GLU Chi-restraints excluded: chain 0 residue 664 GLN Chi-restraints excluded: chain 4 residue 28 VAL Chi-restraints excluded: chain 4 residue 210 ILE Chi-restraints excluded: chain 4 residue 212 VAL Chi-restraints excluded: chain 4 residue 228 THR Chi-restraints excluded: chain 4 residue 263 VAL Chi-restraints excluded: chain 6 residue 169 MET Chi-restraints excluded: chain 6 residue 310 VAL Chi-restraints excluded: chain 6 residue 440 CYS Chi-restraints excluded: chain 1 residue 381 LEU Chi-restraints excluded: chain 1 residue 386 ILE Chi-restraints excluded: chain 7 residue 445 MET Chi-restraints excluded: chain 7 residue 499 ARG Chi-restraints excluded: chain 7 residue 561 MET Chi-restraints excluded: chain 7 residue 668 THR Chi-restraints excluded: chain 7 residue 742 MET Chi-restraints excluded: chain 5 residue 27 MET Chi-restraints excluded: chain 2 residue 11 THR Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 87 LEU Chi-restraints excluded: chain 2 residue 219 VAL Chi-restraints excluded: chain 2 residue 480 VAL Chi-restraints excluded: chain O residue 136 SER Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain W residue 15 PHE Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain W residue 113 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 771 random chunks: chunk 719 optimal weight: 20.0000 chunk 84 optimal weight: 4.9990 chunk 425 optimal weight: 9.9990 chunk 544 optimal weight: 50.0000 chunk 422 optimal weight: 2.9990 chunk 627 optimal weight: 50.0000 chunk 416 optimal weight: 6.9990 chunk 743 optimal weight: 5.9990 chunk 465 optimal weight: 10.0000 chunk 453 optimal weight: 50.0000 chunk 343 optimal weight: 0.0870 overall best weight: 4.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 770 GLN B1112 GLN ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 75 GLN ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4922 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 63958 Z= 0.273 Angle : 0.636 13.010 86723 Z= 0.329 Chirality : 0.043 0.367 9784 Planarity : 0.004 0.084 10958 Dihedral : 12.421 143.663 9746 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.48 % Favored : 92.43 % Rotamer: Outliers : 3.23 % Allowed : 19.65 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.76 (0.10), residues: 7759 helix: 0.94 (0.09), residues: 3123 sheet: -1.23 (0.17), residues: 901 loop : -1.60 (0.10), residues: 3735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP Q 350 HIS 0.009 0.001 HIS 6 381 PHE 0.035 0.001 PHE 0 656 TYR 0.021 0.001 TYR F 137 ARG 0.016 0.000 ARG C 127 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15518 Ramachandran restraints generated. 7759 Oldfield, 0 Emsley, 7759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15518 Ramachandran restraints generated. 7759 Oldfield, 0 Emsley, 7759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 7065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 219 time to evaluate : 6.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 98 TYR cc_start: 0.9515 (OUTLIER) cc_final: 0.8895 (p90) REVERT: G 95 SER cc_start: 0.2144 (OUTLIER) cc_final: 0.1837 (p) REVERT: G 106 MET cc_start: 0.3620 (pmm) cc_final: 0.3187 (pmm) REVERT: 0 115 CYS cc_start: 0.4818 (OUTLIER) cc_final: 0.4556 (t) REVERT: 0 485 MET cc_start: -0.2798 (ttt) cc_final: -0.4186 (mtt) REVERT: 0 584 GLU cc_start: -0.0089 (OUTLIER) cc_final: -0.0562 (pt0) REVERT: 4 206 MET cc_start: 0.0628 (mpp) cc_final: -0.0261 (mtm) REVERT: 1 385 MET cc_start: -0.2328 (mtt) cc_final: -0.2758 (ptp) REVERT: 7 497 MET cc_start: -0.1440 (ptm) cc_final: -0.1952 (ptt) REVERT: 7 499 ARG cc_start: -0.2218 (OUTLIER) cc_final: -0.2556 (mtt180) REVERT: 7 561 MET cc_start: 0.2162 (OUTLIER) cc_final: 0.1352 (tpt) REVERT: 7 622 MET cc_start: 0.0763 (ppp) cc_final: -0.1010 (ptt) REVERT: X 262 MET cc_start: 0.0615 (mtt) cc_final: 0.0162 (mtp) REVERT: W 58 ILE cc_start: -0.2825 (OUTLIER) cc_final: -0.3191 (mm) outliers start: 203 outliers final: 154 residues processed: 410 average time/residue: 0.5515 time to fit residues: 397.6290 Evaluate side-chains 378 residues out of total 7065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 217 time to evaluate : 5.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 98 TYR Chi-restraints excluded: chain Q residue 103 LEU Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 350 TRP Chi-restraints excluded: chain Q residue 396 THR Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 79 GLU Chi-restraints excluded: chain R residue 121 ASP Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 211 LYS Chi-restraints excluded: chain R residue 217 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 153 ARG Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain M residue 187 ARG Chi-restraints excluded: chain M residue 305 THR Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 644 LYS Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 903 ASN Chi-restraints excluded: chain A residue 909 ASP Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1034 GLU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1172 LEU Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1204 ASP Chi-restraints excluded: chain A residue 1265 ASN Chi-restraints excluded: chain A residue 1382 THR Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain A residue 1441 PHE Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 864 LYS Chi-restraints excluded: chain B residue 884 ARG Chi-restraints excluded: chain B residue 887 HIS Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1051 THR Chi-restraints excluded: chain B residue 1060 ARG Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain F residue 85 MET Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 145 ARG Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain I residue 120 GLN Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 113 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 62 LYS Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain 0 residue 39 ILE Chi-restraints excluded: chain 0 residue 76 MET Chi-restraints excluded: chain 0 residue 115 CYS Chi-restraints excluded: chain 0 residue 136 MET Chi-restraints excluded: chain 0 residue 162 LEU Chi-restraints excluded: chain 0 residue 175 VAL Chi-restraints excluded: chain 0 residue 240 ILE Chi-restraints excluded: chain 0 residue 253 THR Chi-restraints excluded: chain 0 residue 287 GLU Chi-restraints excluded: chain 0 residue 312 LEU Chi-restraints excluded: chain 0 residue 335 LEU Chi-restraints excluded: chain 0 residue 393 VAL Chi-restraints excluded: chain 0 residue 554 TRP Chi-restraints excluded: chain 0 residue 584 GLU Chi-restraints excluded: chain 4 residue 28 VAL Chi-restraints excluded: chain 4 residue 210 ILE Chi-restraints excluded: chain 4 residue 212 VAL Chi-restraints excluded: chain 4 residue 228 THR Chi-restraints excluded: chain 4 residue 263 VAL Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 6 residue 169 MET Chi-restraints excluded: chain 6 residue 310 VAL Chi-restraints excluded: chain 6 residue 440 CYS Chi-restraints excluded: chain 1 residue 386 ILE Chi-restraints excluded: chain 7 residue 445 MET Chi-restraints excluded: chain 7 residue 499 ARG Chi-restraints excluded: chain 7 residue 561 MET Chi-restraints excluded: chain 7 residue 668 THR Chi-restraints excluded: chain 7 residue 701 PHE Chi-restraints excluded: chain 7 residue 742 MET Chi-restraints excluded: chain 5 residue 27 MET Chi-restraints excluded: chain 2 residue 11 THR Chi-restraints excluded: chain 2 residue 21 VAL Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 87 LEU Chi-restraints excluded: chain 2 residue 219 VAL Chi-restraints excluded: chain 2 residue 378 ILE Chi-restraints excluded: chain 2 residue 480 VAL Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain W residue 15 PHE Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain W residue 113 LEU Chi-restraints excluded: chain W residue 126 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 771 random chunks: chunk 459 optimal weight: 8.9990 chunk 296 optimal weight: 8.9990 chunk 443 optimal weight: 40.0000 chunk 223 optimal weight: 0.9980 chunk 146 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 472 optimal weight: 0.0030 chunk 506 optimal weight: 40.0000 chunk 367 optimal weight: 3.9990 chunk 69 optimal weight: 30.0000 chunk 584 optimal weight: 30.0000 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 HIS ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4871 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 63958 Z= 0.175 Angle : 0.614 13.448 86723 Z= 0.316 Chirality : 0.043 0.362 9784 Planarity : 0.004 0.085 10958 Dihedral : 12.367 141.718 9740 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.15 % Favored : 92.76 % Rotamer: Outliers : 2.64 % Allowed : 20.13 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.70 (0.10), residues: 7759 helix: 1.00 (0.09), residues: 3128 sheet: -1.16 (0.17), residues: 896 loop : -1.59 (0.10), residues: 3735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP Q 350 HIS 0.007 0.001 HIS 6 381 PHE 0.035 0.001 PHE 0 656 TYR 0.019 0.001 TYR A 852 ARG 0.005 0.000 ARG F 90 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15518 Ramachandran restraints generated. 7759 Oldfield, 0 Emsley, 7759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15518 Ramachandran restraints generated. 7759 Oldfield, 0 Emsley, 7759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 7065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 217 time to evaluate : 5.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 98 TYR cc_start: 0.9495 (OUTLIER) cc_final: 0.8862 (p90) REVERT: G 95 SER cc_start: 0.2078 (OUTLIER) cc_final: 0.1816 (p) REVERT: G 106 MET cc_start: 0.3769 (pmm) cc_final: 0.3138 (pmm) REVERT: H 123 MET cc_start: 0.6103 (tmm) cc_final: 0.5608 (ttp) REVERT: 0 115 CYS cc_start: 0.5110 (OUTLIER) cc_final: 0.4880 (t) REVERT: 0 485 MET cc_start: -0.2907 (ttt) cc_final: -0.4344 (mtt) REVERT: 0 664 GLN cc_start: -0.2510 (OUTLIER) cc_final: -0.3127 (pt0) REVERT: 4 179 LEU cc_start: -0.3507 (OUTLIER) cc_final: -0.3726 (tp) REVERT: 4 206 MET cc_start: 0.0731 (mpp) cc_final: -0.0055 (mtm) REVERT: 1 385 MET cc_start: -0.2562 (mtt) cc_final: -0.3002 (ptp) REVERT: 7 497 MET cc_start: -0.1445 (ptm) cc_final: -0.2451 (ptt) REVERT: 7 499 ARG cc_start: -0.2288 (OUTLIER) cc_final: -0.3407 (mpt180) REVERT: 7 561 MET cc_start: 0.2030 (OUTLIER) cc_final: 0.1266 (tpt) REVERT: 7 583 MET cc_start: 0.0692 (pmm) cc_final: 0.0406 (mtt) REVERT: 7 622 MET cc_start: 0.0726 (ppp) cc_final: -0.1056 (ptt) REVERT: X 262 MET cc_start: 0.0465 (mtt) cc_final: 0.0091 (mtp) REVERT: W 58 ILE cc_start: -0.2955 (OUTLIER) cc_final: -0.3340 (mm) outliers start: 166 outliers final: 137 residues processed: 375 average time/residue: 0.5557 time to fit residues: 370.8541 Evaluate side-chains 359 residues out of total 7065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 214 time to evaluate : 5.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 98 TYR Chi-restraints excluded: chain Q residue 103 LEU Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 350 TRP Chi-restraints excluded: chain Q residue 396 THR Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 79 GLU Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 211 LYS Chi-restraints excluded: chain R residue 217 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 153 ARG Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain M residue 187 ARG Chi-restraints excluded: chain M residue 305 THR Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 644 LYS Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 909 ASP Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1034 GLU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1172 LEU Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1204 ASP Chi-restraints excluded: chain A residue 1265 ASN Chi-restraints excluded: chain A residue 1382 THR Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 797 TYR Chi-restraints excluded: chain B residue 864 LYS Chi-restraints excluded: chain B residue 884 ARG Chi-restraints excluded: chain B residue 887 HIS Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1060 ARG Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 145 ARG Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain I residue 120 GLN Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 113 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 62 LYS Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain 0 residue 39 ILE Chi-restraints excluded: chain 0 residue 115 CYS Chi-restraints excluded: chain 0 residue 136 MET Chi-restraints excluded: chain 0 residue 162 LEU Chi-restraints excluded: chain 0 residue 175 VAL Chi-restraints excluded: chain 0 residue 240 ILE Chi-restraints excluded: chain 0 residue 287 GLU Chi-restraints excluded: chain 0 residue 312 LEU Chi-restraints excluded: chain 0 residue 335 LEU Chi-restraints excluded: chain 0 residue 393 VAL Chi-restraints excluded: chain 0 residue 554 TRP Chi-restraints excluded: chain 0 residue 584 GLU Chi-restraints excluded: chain 0 residue 664 GLN Chi-restraints excluded: chain 4 residue 28 VAL Chi-restraints excluded: chain 4 residue 179 LEU Chi-restraints excluded: chain 4 residue 210 ILE Chi-restraints excluded: chain 4 residue 212 VAL Chi-restraints excluded: chain 4 residue 228 THR Chi-restraints excluded: chain 4 residue 263 VAL Chi-restraints excluded: chain 6 residue 169 MET Chi-restraints excluded: chain 6 residue 310 VAL Chi-restraints excluded: chain 6 residue 440 CYS Chi-restraints excluded: chain 1 residue 386 ILE Chi-restraints excluded: chain 7 residue 445 MET Chi-restraints excluded: chain 7 residue 499 ARG Chi-restraints excluded: chain 7 residue 561 MET Chi-restraints excluded: chain 7 residue 668 THR Chi-restraints excluded: chain 7 residue 701 PHE Chi-restraints excluded: chain 7 residue 742 MET Chi-restraints excluded: chain 5 residue 27 MET Chi-restraints excluded: chain 2 residue 11 THR Chi-restraints excluded: chain 2 residue 21 VAL Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 87 LEU Chi-restraints excluded: chain 2 residue 219 VAL Chi-restraints excluded: chain 2 residue 480 VAL Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain W residue 15 PHE Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain W residue 113 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 771 random chunks: chunk 675 optimal weight: 30.0000 chunk 711 optimal weight: 50.0000 chunk 649 optimal weight: 50.0000 chunk 692 optimal weight: 0.7980 chunk 416 optimal weight: 4.9990 chunk 301 optimal weight: 20.0000 chunk 543 optimal weight: 30.0000 chunk 212 optimal weight: 3.9990 chunk 625 optimal weight: 50.0000 chunk 654 optimal weight: 5.9990 chunk 690 optimal weight: 20.0000 overall best weight: 7.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1128 GLN ** A1173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 686 ASN B 761 HIS ** B 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 GLN ** 0 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 133 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5008 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 63958 Z= 0.422 Angle : 0.727 13.073 86723 Z= 0.374 Chirality : 0.045 0.321 9784 Planarity : 0.004 0.085 10958 Dihedral : 12.588 147.673 9733 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.12 % Favored : 91.78 % Rotamer: Outliers : 2.85 % Allowed : 20.04 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.15 % Twisted Proline : 0.00 % 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: -0.89 (0.10), residues: 7759 helix: 0.82 (0.09), residues: 3132 sheet: -1.30 (0.17), residues: 876 loop : -1.66 (0.10), residues: 3751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP K 109 HIS 0.013 0.002 HIS A 399 PHE 0.034 0.002 PHE 0 656 TYR 0.026 0.002 TYR F 137 ARG 0.020 0.001 ARG 0 380 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15518 Ramachandran restraints generated. 7759 Oldfield, 0 Emsley, 7759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15518 Ramachandran restraints generated. 7759 Oldfield, 0 Emsley, 7759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 7065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 216 time to evaluate : 5.532 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: Q 98 TYR cc_start: 0.9540 (OUTLIER) cc_final: 0.8970 (p90) REVERT: G 95 SER cc_start: 0.2316 (OUTLIER) cc_final: 0.2071 (p) REVERT: G 106 MET cc_start: 0.3864 (pmm) cc_final: 0.3300 (pmm) REVERT: A 257 ARG cc_start: 0.5041 (OUTLIER) cc_final: 0.4004 (mtm-85) REVERT: 0 115 CYS cc_start: 0.5166 (OUTLIER) cc_final: 0.4932 (t) REVERT: 0 485 MET cc_start: -0.2721 (ttt) cc_final: -0.4260 (mtt) REVERT: 0 584 GLU cc_start: 0.0061 (OUTLIER) cc_final: -0.0307 (pt0) REVERT: 0 664 GLN cc_start: -0.2723 (OUTLIER) cc_final: -0.3367 (pt0) REVERT: 4 179 LEU cc_start: -0.3462 (OUTLIER) cc_final: -0.3671 (tp) REVERT: 4 206 MET cc_start: 0.0901 (mpp) cc_final: 0.0102 (mtm) REVERT: 1 385 MET cc_start: -0.2686 (mtt) cc_final: -0.3042 (ptp) REVERT: 7 497 MET cc_start: -0.1332 (ptm) cc_final: -0.2307 (ptt) REVERT: 7 499 ARG cc_start: -0.2093 (OUTLIER) cc_final: -0.2491 (mtt180) REVERT: 7 561 MET cc_start: 0.1991 (mmm) cc_final: 0.1142 (tpt) REVERT: 7 583 MET cc_start: 0.0833 (pmm) cc_final: 0.0509 (mtt) REVERT: 7 622 MET cc_start: 0.0505 (ppp) cc_final: -0.1332 (ptt) REVERT: W 58 ILE cc_start: -0.3075 (OUTLIER) cc_final: -0.3382 (mm) outliers start: 179 outliers final: 145 residues processed: 383 average time/residue: 0.5698 time to fit residues: 387.9674 Evaluate side-chains 368 residues out of total 7065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 214 time to evaluate : 5.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 98 TYR Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 350 TRP Chi-restraints excluded: chain Q residue 396 THR Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 79 GLU Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 211 LYS Chi-restraints excluded: chain R residue 217 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 153 ARG Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain M residue 187 ARG Chi-restraints excluded: chain M residue 305 THR Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 644 LYS Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 903 ASN Chi-restraints excluded: chain A residue 909 ASP Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1034 GLU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1172 LEU Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1204 ASP Chi-restraints excluded: chain A residue 1265 ASN Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1382 THR Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 864 LYS Chi-restraints excluded: chain B residue 884 ARG Chi-restraints excluded: chain B residue 887 HIS Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 145 ARG Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain I residue 120 GLN Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 113 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain 0 residue 39 ILE Chi-restraints excluded: chain 0 residue 115 CYS Chi-restraints excluded: chain 0 residue 136 MET Chi-restraints excluded: chain 0 residue 162 LEU Chi-restraints excluded: chain 0 residue 175 VAL Chi-restraints excluded: chain 0 residue 231 ILE Chi-restraints excluded: chain 0 residue 240 ILE Chi-restraints excluded: chain 0 residue 287 GLU Chi-restraints excluded: chain 0 residue 312 LEU Chi-restraints excluded: chain 0 residue 335 LEU Chi-restraints excluded: chain 0 residue 393 VAL Chi-restraints excluded: chain 0 residue 462 THR Chi-restraints excluded: chain 0 residue 584 GLU Chi-restraints excluded: chain 0 residue 664 GLN Chi-restraints excluded: chain 4 residue 28 VAL Chi-restraints excluded: chain 4 residue 179 LEU Chi-restraints excluded: chain 4 residue 210 ILE Chi-restraints excluded: chain 4 residue 212 VAL Chi-restraints excluded: chain 4 residue 228 THR Chi-restraints excluded: chain 4 residue 263 VAL Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 6 residue 169 MET Chi-restraints excluded: chain 6 residue 310 VAL Chi-restraints excluded: chain 6 residue 440 CYS Chi-restraints excluded: chain 7 residue 445 MET Chi-restraints excluded: chain 7 residue 499 ARG Chi-restraints excluded: chain 7 residue 668 THR Chi-restraints excluded: chain 7 residue 701 PHE Chi-restraints excluded: chain 7 residue 742 MET Chi-restraints excluded: chain 5 residue 27 MET Chi-restraints excluded: chain 2 residue 11 THR Chi-restraints excluded: chain 2 residue 21 VAL Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 87 LEU Chi-restraints excluded: chain 2 residue 219 VAL Chi-restraints excluded: chain 2 residue 371 VAL Chi-restraints excluded: chain 2 residue 480 VAL Chi-restraints excluded: chain X residue 190 SER Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain W residue 113 LEU Chi-restraints excluded: chain W residue 126 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 771 random chunks: chunk 454 optimal weight: 30.0000 chunk 732 optimal weight: 8.9990 chunk 446 optimal weight: 6.9990 chunk 347 optimal weight: 3.9990 chunk 509 optimal weight: 4.9990 chunk 768 optimal weight: 7.9990 chunk 706 optimal weight: 2.9990 chunk 611 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 472 optimal weight: 0.6980 chunk 375 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 ASN ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1128 GLN ** A1173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4922 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 63958 Z= 0.209 Angle : 0.648 14.209 86723 Z= 0.332 Chirality : 0.043 0.354 9784 Planarity : 0.004 0.220 10958 Dihedral : 12.510 143.798 9731 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.35 % Favored : 92.56 % Rotamer: Outliers : 2.40 % Allowed : 20.53 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.77 (0.10), residues: 7759 helix: 0.94 (0.09), residues: 3121 sheet: -1.23 (0.17), residues: 881 loop : -1.61 (0.10), residues: 3757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP 0 554 HIS 0.007 0.001 HIS 6 381 PHE 0.036 0.001 PHE 0 656 TYR 0.019 0.001 TYR 1 630 ARG 0.018 0.000 ARG W 60 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15518 Ramachandran restraints generated. 7759 Oldfield, 0 Emsley, 7759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15518 Ramachandran restraints generated. 7759 Oldfield, 0 Emsley, 7759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 7065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 215 time to evaluate : 5.542 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: Q 98 TYR cc_start: 0.9540 (OUTLIER) cc_final: 0.8950 (p90) REVERT: G 95 SER cc_start: 0.2179 (OUTLIER) cc_final: 0.1891 (p) REVERT: G 106 MET cc_start: 0.3758 (pmm) cc_final: 0.3148 (pmm) REVERT: A 257 ARG cc_start: 0.4959 (OUTLIER) cc_final: 0.4140 (mtm-85) REVERT: 0 61 MET cc_start: 0.7449 (ppp) cc_final: 0.7075 (ppp) REVERT: 0 485 MET cc_start: -0.2707 (ttt) cc_final: -0.4336 (mtt) REVERT: 0 584 GLU cc_start: 0.0039 (OUTLIER) cc_final: -0.0313 (pt0) REVERT: 0 664 GLN cc_start: -0.2653 (OUTLIER) cc_final: -0.3302 (pt0) REVERT: 4 206 MET cc_start: 0.0816 (mpp) cc_final: 0.0057 (mtm) REVERT: 1 385 MET cc_start: -0.2852 (mtt) cc_final: -0.3058 (ptp) REVERT: 7 497 MET cc_start: -0.1165 (ptm) cc_final: -0.2055 (ptt) REVERT: 7 499 ARG cc_start: -0.2222 (OUTLIER) cc_final: -0.2609 (mtt180) REVERT: 7 561 MET cc_start: 0.2097 (mmm) cc_final: 0.1289 (tpt) REVERT: 7 583 MET cc_start: 0.0672 (pmm) cc_final: 0.0390 (mtt) REVERT: 7 622 MET cc_start: 0.0522 (ppp) cc_final: -0.0622 (ptt) REVERT: X 262 MET cc_start: -0.0211 (mtp) cc_final: -0.1034 (ptp) outliers start: 151 outliers final: 134 residues processed: 355 average time/residue: 0.5551 time to fit residues: 350.3759 Evaluate side-chains 353 residues out of total 7065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 213 time to evaluate : 5.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 98 TYR Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 350 TRP Chi-restraints excluded: chain Q residue 396 THR Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 121 ASP Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 211 LYS Chi-restraints excluded: chain R residue 217 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 153 ARG Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain M residue 187 ARG Chi-restraints excluded: chain M residue 305 THR Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 644 LYS Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 909 ASP Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1034 GLU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1172 LEU Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1204 ASP Chi-restraints excluded: chain A residue 1265 ASN Chi-restraints excluded: chain A residue 1382 THR Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1428 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 863 GLU Chi-restraints excluded: chain B residue 864 LYS Chi-restraints excluded: chain B residue 884 ARG Chi-restraints excluded: chain B residue 887 HIS Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 145 ARG Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain I residue 120 GLN Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 113 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain 0 residue 39 ILE Chi-restraints excluded: chain 0 residue 136 MET Chi-restraints excluded: chain 0 residue 162 LEU Chi-restraints excluded: chain 0 residue 175 VAL Chi-restraints excluded: chain 0 residue 231 ILE Chi-restraints excluded: chain 0 residue 240 ILE Chi-restraints excluded: chain 0 residue 287 GLU Chi-restraints excluded: chain 0 residue 312 LEU Chi-restraints excluded: chain 0 residue 335 LEU Chi-restraints excluded: chain 0 residue 393 VAL Chi-restraints excluded: chain 0 residue 584 GLU Chi-restraints excluded: chain 0 residue 664 GLN Chi-restraints excluded: chain 4 residue 28 VAL Chi-restraints excluded: chain 4 residue 179 LEU Chi-restraints excluded: chain 4 residue 210 ILE Chi-restraints excluded: chain 4 residue 212 VAL Chi-restraints excluded: chain 4 residue 228 THR Chi-restraints excluded: chain 4 residue 263 VAL Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 6 residue 169 MET Chi-restraints excluded: chain 6 residue 310 VAL Chi-restraints excluded: chain 6 residue 440 CYS Chi-restraints excluded: chain 7 residue 445 MET Chi-restraints excluded: chain 7 residue 499 ARG Chi-restraints excluded: chain 7 residue 668 THR Chi-restraints excluded: chain 7 residue 701 PHE Chi-restraints excluded: chain 7 residue 742 MET Chi-restraints excluded: chain 5 residue 27 MET Chi-restraints excluded: chain 2 residue 11 THR Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 87 LEU Chi-restraints excluded: chain 2 residue 219 VAL Chi-restraints excluded: chain 2 residue 480 VAL Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 204 LEU Chi-restraints excluded: chain W residue 46 LEU Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain W residue 113 LEU Chi-restraints excluded: chain W residue 126 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 771 random chunks: chunk 485 optimal weight: 50.0000 chunk 651 optimal weight: 20.0000 chunk 187 optimal weight: 0.9980 chunk 563 optimal weight: 30.0000 chunk 90 optimal weight: 0.9990 chunk 169 optimal weight: 0.8980 chunk 612 optimal weight: 4.9990 chunk 256 optimal weight: 0.0770 chunk 629 optimal weight: 50.0000 chunk 77 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 994 GLN ** A1173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 179 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.057763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.044636 restraints weight = 672537.744| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 5.90 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3619 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3619 r_free = 0.3619 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 333 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3618 r_free = 0.3618 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 338 | |-----------------------------------------------------------------------------| r_final: 0.3618 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 63958 Z= 0.156 Angle : 0.627 13.193 86723 Z= 0.320 Chirality : 0.043 0.327 9784 Planarity : 0.004 0.208 10958 Dihedral : 12.233 137.892 9730 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.04 % Favored : 92.89 % Rotamer: Outliers : 2.09 % Allowed : 20.90 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.61 (0.10), residues: 7759 helix: 1.08 (0.10), residues: 3108 sheet: -1.03 (0.17), residues: 861 loop : -1.56 (0.10), residues: 3790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP 0 554 HIS 0.007 0.001 HIS 6 381 PHE 0.033 0.001 PHE 0 656 TYR 0.018 0.001 TYR 1 630 ARG 0.010 0.000 ARG W 60 =============================================================================== Job complete usr+sys time: 11278.82 seconds wall clock time: 201 minutes 12.94 seconds (12072.94 seconds total)