Starting phenix.real_space_refine (version: dev) on Mon Dec 19 07:31:22 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c0f_7324/12_2022/6c0f_7324_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c0f_7324/12_2022/6c0f_7324.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c0f_7324/12_2022/6c0f_7324.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c0f_7324/12_2022/6c0f_7324.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c0f_7324/12_2022/6c0f_7324_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c0f_7324/12_2022/6c0f_7324_neut.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 49": "NH1" <-> "NH2" Residue "A ARG 275": "NH1" <-> "NH2" Residue "A ARG 288": "NH1" <-> "NH2" Residue "A ARG 350": "NH1" <-> "NH2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "C ARG 107": "NH1" <-> "NH2" Residue "C TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 246": "NH1" <-> "NH2" Residue "C ARG 326": "NH1" <-> "NH2" Residue "D ARG 18": "NH1" <-> "NH2" Residue "D PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 29": "NH1" <-> "NH2" Residue "D ARG 79": "NH1" <-> "NH2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D ARG 150": "NH1" <-> "NH2" Residue "E PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 30": "NH1" <-> "NH2" Residue "F ARG 88": "NH1" <-> "NH2" Residue "F ARG 100": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 57": "NH1" <-> "NH2" Residue "G ARG 68": "NH1" <-> "NH2" Residue "G PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 204": "NH1" <-> "NH2" Residue "I ARG 34": "NH1" <-> "NH2" Residue "I ARG 48": "NH1" <-> "NH2" Residue "I ARG 126": "NH1" <-> "NH2" Residue "I ARG 189": "NH1" <-> "NH2" Residue "I ARG 205": "NH1" <-> "NH2" Residue "I ARG 245": "NH1" <-> "NH2" Residue "I TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 34": "NH1" <-> "NH2" Residue "K ARG 170": "NH1" <-> "NH2" Residue "K ARG 240": "NH1" <-> "NH2" Residue "K ARG 277": "NH1" <-> "NH2" Residue "K ARG 285": "NH1" <-> "NH2" Residue "L ARG 42": "NH1" <-> "NH2" Residue "L ARG 49": "NH1" <-> "NH2" Residue "L ARG 73": "NH1" <-> "NH2" Residue "L PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 19": "NH1" <-> "NH2" Residue "M ARG 108": "NH1" <-> "NH2" Residue "N ARG 20": "NH1" <-> "NH2" Residue "N ARG 144": "NH1" <-> "NH2" Residue "N ARG 188": "NH1" <-> "NH2" Residue "O TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 18": "NH1" <-> "NH2" Residue "P ARG 56": "NH1" <-> "NH2" Residue "P ARG 126": "NH1" <-> "NH2" Residue "Q ARG 92": "NH1" <-> "NH2" Residue "S ARG 28": "NH1" <-> "NH2" Residue "S ARG 117": "NH1" <-> "NH2" Residue "V ARG 32": "NH1" <-> "NH2" Residue "V ARG 70": "NH1" <-> "NH2" Residue "V ARG 88": "NH1" <-> "NH2" Residue "W ARG 400": "NH1" <-> "NH2" Residue "W TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 121": "NH1" <-> "NH2" Residue "7 ARG 7": "NH1" <-> "NH2" Residue "7 ARG 11": "NH1" <-> "NH2" Residue "7 ARG 56": "NH1" <-> "NH2" Residue "7 ARG 172": "NH1" <-> "NH2" Residue "7 ARG 175": "NH1" <-> "NH2" Residue "7 ARG 221": "NH1" <-> "NH2" Residue "7 ARG 225": "NH1" <-> "NH2" Residue "b ARG 60": "NH1" <-> "NH2" Residue "b ARG 263": "NH1" <-> "NH2" Residue "b ARG 274": "NH1" <-> "NH2" Residue "b ARG 275": "NH1" <-> "NH2" Residue "e ARG 24": "NH1" <-> "NH2" Residue "e TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 48": "NH1" <-> "NH2" Residue "f ARG 60": "NH1" <-> "NH2" Residue "h TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 105": "NH1" <-> "NH2" Residue "h TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 99": "NH1" <-> "NH2" Residue "j ARG 56": "NH1" <-> "NH2" Residue "j ARG 63": "NH1" <-> "NH2" Residue "n ARG 13": "NH1" <-> "NH2" Residue "n ARG 18": "NH1" <-> "NH2" Residue "n ARG 23": "NH1" <-> "NH2" Residue "n ARG 34": "NH1" <-> "NH2" Residue "n ARG 88": "NH1" <-> "NH2" Residue "n ARG 92": "NH1" <-> "NH2" Residue "n ARG 104": "NH1" <-> "NH2" Residue "n ARG 109": "NH1" <-> "NH2" Residue "n ARG 369": "NH1" <-> "NH2" Residue "n ARG 414": "NH1" <-> "NH2" Residue "n ARG 424": "NH1" <-> "NH2" Residue "o ARG 97": "NH1" <-> "NH2" Residue "o ARG 121": "NH1" <-> "NH2" Residue "o ARG 182": "NH1" <-> "NH2" Residue "o ARG 207": "NH1" <-> "NH2" Residue "p ARG 71": "NH1" <-> "NH2" Residue "p ARG 80": "NH1" <-> "NH2" Residue "p ARG 112": "NH1" <-> "NH2" Residue "p ARG 135": "NH1" <-> "NH2" Residue "p PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 200": "NH1" <-> "NH2" Residue "p ARG 244": "NH1" <-> "NH2" Residue "p ARG 286": "NH1" <-> "NH2" Residue "p ARG 340": "NH1" <-> "NH2" Residue "p ARG 376": "NH1" <-> "NH2" Residue "s ARG 265": "NH1" <-> "NH2" Residue "s ARG 275": "NH1" <-> "NH2" Residue "s ARG 281": "NH1" <-> "NH2" Residue "s ARG 287": "NH1" <-> "NH2" Residue "s ARG 375": "NH1" <-> "NH2" Residue "s ARG 387": "NH1" <-> "NH2" Residue "t ARG 74": "NH1" <-> "NH2" Residue "t ARG 130": "NH1" <-> "NH2" Residue "t ARG 148": "NH1" <-> "NH2" Residue "t ARG 205": "NH1" <-> "NH2" Residue "t ARG 211": "NH1" <-> "NH2" Residue "t ARG 299": "NH1" <-> "NH2" Residue "u ARG 2": "NH1" <-> "NH2" Residue "u ARG 23": "NH1" <-> "NH2" Residue "u ARG 33": "NH1" <-> "NH2" Residue "u ARG 43": "NH1" <-> "NH2" Residue "u ARG 44": "NH1" <-> "NH2" Residue "u ARG 56": "NH1" <-> "NH2" Residue "u PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 75": "NH1" <-> "NH2" Residue "u ARG 105": "NH1" <-> "NH2" Residue "u ARG 113": "NH1" <-> "NH2" Residue "u ARG 122": "NH1" <-> "NH2" Residue "v ARG 62": "NH1" <-> "NH2" Residue "v ARG 126": "NH1" <-> "NH2" Residue "w ARG 187": "NH1" <-> "NH2" Residue "y TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 85": "NH1" <-> "NH2" Residue "y ARG 100": "NH1" <-> "NH2" Residue "y TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 223": "NH1" <-> "NH2" Residue "z ARG 15": "NH1" <-> "NH2" Residue "z ARG 60": "NH1" <-> "NH2" Residue "z ARG 115": "NH1" <-> "NH2" Residue "z ARG 117": "NH1" <-> "NH2" Residue "z ARG 127": "NH1" <-> "NH2" Residue "z ARG 235": "NH1" <-> "NH2" Residue "z ARG 247": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 91742 Number of models: 1 Model: "" Number of chains: 46 Chain: "1" Number of atoms: 29055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1357, 29055 Classifications: {'RNA': 1357} Modifications used: {'rna2p_pur': 128, 'rna2p_pyr': 87, 'rna3p_pur': 629, 'rna3p_pyr': 513} Link IDs: {'rna2p': 214, 'rna3p': 1142} Chain breaks: 13 Chain: "2" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3353 Classifications: {'RNA': 158} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 17, 'rna3p_pur': 61, 'rna3p_pyr': 63} Link IDs: {'rna2p': 33, 'rna3p': 124} Chain: "6" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1838 Classifications: {'RNA': 87} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 19, 'rna3p_pur': 32, 'rna3p_pyr': 28} Link IDs: {'rna2p': 26, 'rna3p': 60} Chain breaks: 1 Chain: "A" Number of atoms: 3126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3126 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 12, 'TRANS': 381} Chain breaks: 1 Chain: "B" Number of atoms: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2577 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 11, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2418 Classifications: {'peptide': 314} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 298} Chain breaks: 1 Chain: "D" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1578 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 6, 'TRANS': 183} Chain: "E" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1366 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 161} Chain: "F" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1941 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain: "G" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1453 Classifications: {'peptide': 187} Link IDs: {'CIS': 2, 'PTRANS': 8, 'TRANS': 176} Chain: "I" Number of atoms: 2429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2429 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 12, 'TRANS': 275} Chain: "K" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2099 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 10, 'TRANS': 249} Chain breaks: 1 Chain: "L" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 845 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "M" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 997 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "N" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1509 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 4, 'TRANS': 171} Chain breaks: 1 Chain: "O" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1451 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 176} Chain breaks: 1 Chain: "P" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 975 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain breaks: 2 Chain: "Q" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1015 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 7, 'TRANS': 124} Chain: "S" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1437 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "V" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 903 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "W" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 806 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 6, 'TRANS': 91} Chain: "Y" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 993 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "7" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1295 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain breaks: 1 Chain: "8" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 836 Classifications: {'peptide': 98} Link IDs: {'TRANS': 97} Chain: "b" Number of atoms: 1919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1919 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 228} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "e" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 914 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain breaks: 1 Chain: "f" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 850 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "h" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 969 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "i" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 665 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain: "j" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 575 Classifications: {'peptide': 72} Link IDs: {'PCIS': 1, 'TRANS': 70} Chain: "x" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 140 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'TRANS': 27} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'UNK:plan-1': 28} Unresolved non-hydrogen planarities: 28 Chain: "m" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 370 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'TRANS': 73} Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 222 Unresolved non-hydrogen dihedrals: 74 Planarities with less than four sites: {'UNK:plan-1': 74} Unresolved non-hydrogen planarities: 74 Chain: "n" Number of atoms: 2794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2794 Classifications: {'peptide': 341} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 320} Chain breaks: 3 Chain: "o" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1107 Classifications: {'peptide': 133} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 128} Chain: "p" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3486 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 21, 'TRANS': 415} Chain breaks: 1 Chain: "q" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 1409 Classifications: {'peptide': 285} Incomplete info: {'backbone_only': 16, 'truncation_to_alanine': 269} Link IDs: {'TRANS': 284} Chain breaks: 5 Unresolved non-hydrogen bonds: 586 Unresolved non-hydrogen angles: 887 Unresolved non-hydrogen dihedrals: 285 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'UNK:plan-1': 285} Unresolved non-hydrogen planarities: 285 Chain: "s" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1069 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 8, 'TRANS': 148} Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 73 Planarities with less than four sites: {'UNK:plan-1': 73} Unresolved non-hydrogen planarities: 73 Chain: "t" Number of atoms: 1965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1965 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 9, 'TRANS': 238} Chain breaks: 1 Chain: "u" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1088 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "v" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1795 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 11, 'TRANS': 213} Chain breaks: 1 Chain: "w" Number of atoms: 562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 562 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain: "y" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1709 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "z" Number of atoms: 2058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2058 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 7, 'TRANS': 235} Chain breaks: 1 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "u" 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 42483 SG CYS D 15 194.310 105.763 129.296 1.00 48.84 S ATOM 42585 SG CYS D 28 194.871 107.518 126.205 1.00 48.96 S ATOM 42665 SG CYS D 38 194.712 104.487 125.925 1.00 41.05 S ATOM 42704 SG CYS D 43 197.337 105.725 127.106 1.00 41.34 S ATOM 71658 SG CYS j 19 130.007 90.737 174.531 1.00 76.24 S ATOM 71683 SG CYS j 22 132.452 91.435 171.901 1.00 80.69 S ATOM 71783 SG CYS j 34 131.110 88.059 172.311 1.00 77.17 S ATOM 71801 SG CYS j 37 133.332 89.398 174.734 1.00 76.14 S ATOM 84573 SG CYS u 6 57.787 76.209 82.607 1.00182.25 S ATOM 84600 SG CYS u 9 57.416 79.472 84.196 1.00191.89 S ATOM 84785 SG CYS u 32 60.398 78.631 82.871 1.00189.48 S ATOM 84817 SG CYS u 36 58.751 77.568 85.711 1.00178.40 S Time building chain proxies: 36.82, per 1000 atoms: 0.40 Number of scatterers: 91742 At special positions: 0 Unit cell: (269.1, 201.5, 323.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 137 16.00 P 1602 15.00 O 21513 8.00 N 16655 7.00 C 51832 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 36.41 Conformation dependent library (CDL) restraints added in 6.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 401 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 38 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 28 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 43 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 15 " pdb=" ZN j 101 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 37 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 34 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 22 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 19 " pdb=" ZN u 300 " pdb="ZN ZN u 300 " - pdb=" SG CYS u 36 " pdb="ZN ZN u 300 " - pdb=" SG CYS u 9 " pdb="ZN ZN u 300 " - pdb=" SG CYS u 32 " pdb="ZN ZN u 300 " - pdb=" SG CYS u 6 " Number of angles added : 18 13458 Ramachandran restraints generated. 6729 Oldfield, 0 Emsley, 6729 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13926 Finding SS restraints... Secondary structure from input PDB file: 253 helices and 73 sheets defined 45.2% alpha, 17.6% beta 501 base pairs and 845 stacking pairs defined. Time for finding SS restraints: 23.58 Creating SS restraints... Processing helix chain 'A' and resid 42 through 46 removed outlier: 4.005A pdb=" N TYR A 46 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 327 through 331 Processing helix chain 'B' and resid 111 through 119 removed outlier: 3.679A pdb=" N TYR B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 135 removed outlier: 3.645A pdb=" N ALA B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 154 Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 187 through 198 Processing helix chain 'B' and resid 204 through 208 Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'C' and resid 31 through 44 removed outlier: 3.682A pdb=" N SER C 41 " --> pdb=" O THR C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 132 removed outlier: 3.924A pdb=" N ALA C 130 " --> pdb=" O ILE C 126 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL C 131 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA C 132 " --> pdb=" O ALA C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 139 Processing helix chain 'C' and resid 153 through 159 Processing helix chain 'C' and resid 161 through 173 Processing helix chain 'C' and resid 174 through 184 Processing helix chain 'C' and resid 190 through 195 removed outlier: 3.775A pdb=" N LYS C 193 " --> pdb=" O GLY C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 219 Processing helix chain 'C' and resid 234 through 239 Processing helix chain 'C' and resid 240 through 243 Processing helix chain 'C' and resid 252 through 263 removed outlier: 4.259A pdb=" N ASP C 259 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN C 260 " --> pdb=" O THR C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 291 removed outlier: 3.670A pdb=" N ILE C 289 " --> pdb=" O ASP C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 299 Processing helix chain 'C' and resid 320 through 327 removed outlier: 3.524A pdb=" N LEU C 327 " --> pdb=" O VAL C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 338 removed outlier: 4.377A pdb=" N VAL C 333 " --> pdb=" O PRO C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 342 Processing helix chain 'D' and resid 3 through 13 Processing helix chain 'D' and resid 66 through 70 Processing helix chain 'D' and resid 85 through 97 Processing helix chain 'D' and resid 101 through 128 removed outlier: 3.614A pdb=" N ARG D 105 " --> pdb=" O SER D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 156 Processing helix chain 'D' and resid 157 through 173 removed outlier: 3.528A pdb=" N ALA D 161 " --> pdb=" O LYS D 157 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY D 173 " --> pdb=" O ARG D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 191 Processing helix chain 'E' and resid 68 through 73 Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.669A pdb=" N LYS E 100 " --> pdb=" O ASN E 97 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE E 101 " --> pdb=" O VAL E 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 97 through 101' Processing helix chain 'E' and resid 103 through 107 Processing helix chain 'E' and resid 112 through 122 removed outlier: 3.861A pdb=" N GLU E 118 " --> pdb=" O LYS E 114 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA E 119 " --> pdb=" O GLU E 115 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASN E 120 " --> pdb=" O LYS E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 150 removed outlier: 3.743A pdb=" N VAL E 135 " --> pdb=" O LYS E 131 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA E 144 " --> pdb=" O VAL E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 161 Processing helix chain 'F' and resid 9 through 73 removed outlier: 3.653A pdb=" N ALA F 35 " --> pdb=" O ALA F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 106 Processing helix chain 'F' and resid 120 through 131 Processing helix chain 'F' and resid 140 through 151 Processing helix chain 'F' and resid 165 through 174 removed outlier: 3.640A pdb=" N ILE F 169 " --> pdb=" O ASP F 165 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN F 172 " --> pdb=" O ILE F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 190 removed outlier: 3.509A pdb=" N LEU F 184 " --> pdb=" O SER F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 202 Processing helix chain 'F' and resid 234 through 244 removed outlier: 3.866A pdb=" N LYS F 238 " --> pdb=" O GLU F 234 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS F 241 " --> pdb=" O ASN F 237 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 62 Processing helix chain 'G' and resid 63 through 69 removed outlier: 3.728A pdb=" N ILE G 67 " --> pdb=" O LYS G 63 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 95 Processing helix chain 'G' and resid 101 through 119 Processing helix chain 'G' and resid 135 through 143 Processing helix chain 'G' and resid 159 through 163 Processing helix chain 'G' and resid 164 through 173 removed outlier: 4.659A pdb=" N ALA G 168 " --> pdb=" O VAL G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 189 removed outlier: 3.518A pdb=" N LEU G 189 " --> pdb=" O ARG G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 222 Processing helix chain 'G' and resid 226 through 231 removed outlier: 3.839A pdb=" N LYS G 231 " --> pdb=" O ASP G 227 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 44 Processing helix chain 'I' and resid 44 through 55 removed outlier: 4.317A pdb=" N ARG I 48 " --> pdb=" O ASN I 44 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU I 49 " --> pdb=" O PRO I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 84 Processing helix chain 'I' and resid 104 through 118 removed outlier: 3.862A pdb=" N TYR I 108 " --> pdb=" O LYS I 104 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU I 116 " --> pdb=" O ASN I 112 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE I 117 " --> pdb=" O ILE I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 131 through 142 Processing helix chain 'I' and resid 204 through 218 Processing helix chain 'I' and resid 283 through 288 Processing helix chain 'K' and resid 33 through 49 Processing helix chain 'K' and resid 70 through 76 Processing helix chain 'K' and resid 106 through 117 removed outlier: 4.026A pdb=" N THR K 116 " --> pdb=" O GLU K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 135 Processing helix chain 'K' and resid 136 through 148 removed outlier: 3.517A pdb=" N LEU K 140 " --> pdb=" O SER K 136 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN K 143 " --> pdb=" O ASP K 139 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER K 146 " --> pdb=" O ASP K 142 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU K 147 " --> pdb=" O GLN K 143 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 163 Processing helix chain 'K' and resid 166 through 176 removed outlier: 3.548A pdb=" N GLN K 176 " --> pdb=" O ALA K 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 188 removed outlier: 3.928A pdb=" N THR K 188 " --> pdb=" O ASP K 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 184 through 188' Processing helix chain 'K' and resid 190 through 195 removed outlier: 3.983A pdb=" N GLY K 195 " --> pdb=" O PRO K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 201 removed outlier: 3.506A pdb=" N TYR K 199 " --> pdb=" O GLY K 195 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS K 201 " --> pdb=" O LYS K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 218 through 232 removed outlier: 3.627A pdb=" N LYS K 227 " --> pdb=" O THR K 223 " (cutoff:3.500A) Processing helix chain 'K' and resid 255 through 274 Processing helix chain 'K' and resid 296 through 302 removed outlier: 4.162A pdb=" N GLU K 302 " --> pdb=" O LEU K 298 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 46 removed outlier: 3.755A pdb=" N LYS L 32 " --> pdb=" O GLN L 28 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL L 33 " --> pdb=" O ALA L 29 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA L 43 " --> pdb=" O ARG L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 84 removed outlier: 3.520A pdb=" N VAL L 80 " --> pdb=" O THR L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 91 Processing helix chain 'L' and resid 105 through 123 removed outlier: 3.520A pdb=" N ILE L 123 " --> pdb=" O TYR L 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 63 No H-bonds generated for 'chain 'M' and resid 61 through 63' Processing helix chain 'M' and resid 77 through 89 Processing helix chain 'M' and resid 89 through 96 Processing helix chain 'M' and resid 97 through 111 Processing helix chain 'M' and resid 113 through 135 Processing helix chain 'N' and resid 3 through 12 Processing helix chain 'N' and resid 16 through 33 removed outlier: 3.816A pdb=" N TRP N 28 " --> pdb=" O ARG N 24 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS N 33 " --> pdb=" O GLU N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 52 Processing helix chain 'N' and resid 97 through 110 removed outlier: 3.615A pdb=" N VAL N 106 " --> pdb=" O ALA N 102 " (cutoff:3.500A) Processing helix chain 'N' and resid 139 through 144 Processing helix chain 'N' and resid 148 through 157 Proline residue: N 154 - end of helix removed outlier: 3.591A pdb=" N LYS N 157 " --> pdb=" O PRO N 154 " (cutoff:3.500A) Processing helix chain 'N' and resid 165 through 173 Processing helix chain 'N' and resid 183 through 196 Processing helix chain 'O' and resid 16 through 29 removed outlier: 3.503A pdb=" N LEU O 28 " --> pdb=" O ALA O 24 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 39 No H-bonds generated for 'chain 'O' and resid 37 through 39' Processing helix chain 'O' and resid 46 through 59 removed outlier: 3.665A pdb=" N ASN O 50 " --> pdb=" O GLU O 46 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 88 removed outlier: 3.623A pdb=" N MET O 87 " --> pdb=" O ALA O 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 101 Processing helix chain 'O' and resid 111 through 115 Processing helix chain 'O' and resid 120 through 123 Processing helix chain 'O' and resid 124 through 129 Processing helix chain 'O' and resid 138 through 146 Processing helix chain 'O' and resid 149 through 186 Processing helix chain 'O' and resid 188 through 198 Processing helix chain 'P' and resid 25 through 37 removed outlier: 3.580A pdb=" N ILE P 36 " --> pdb=" O THR P 32 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN P 37 " --> pdb=" O ALA P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 53 Processing helix chain 'P' and resid 84 through 106 removed outlier: 3.534A pdb=" N VAL P 88 " --> pdb=" O PRO P 84 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE P 90 " --> pdb=" O LYS P 86 " (cutoff:3.500A) Processing helix chain 'Q' and resid 23 through 40 Processing helix chain 'Q' and resid 42 through 53 removed outlier: 4.445A pdb=" N LYS Q 46 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 72 Processing helix chain 'Q' and resid 107 through 117 Processing helix chain 'Q' and resid 124 through 131 Processing helix chain 'S' and resid 33 through 49 removed outlier: 3.895A pdb=" N LYS S 47 " --> pdb=" O TYR S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 98 through 115 removed outlier: 3.524A pdb=" N ALA S 102 " --> pdb=" O SER S 98 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG S 115 " --> pdb=" O ALA S 111 " (cutoff:3.500A) Processing helix chain 'S' and resid 137 through 142 Processing helix chain 'S' and resid 143 through 145 No H-bonds generated for 'chain 'S' and resid 143 through 145' Processing helix chain 'V' and resid 119 through 126 Processing helix chain 'V' and resid 126 through 132 Processing helix chain 'W' and resid 379 through 385 removed outlier: 3.537A pdb=" N LYS W 383 " --> pdb=" O PRO W 379 " (cutoff:3.500A) Processing helix chain 'W' and resid 398 through 404 Processing helix chain 'W' and resid 425 through 430 removed outlier: 3.847A pdb=" N ASN W 429 " --> pdb=" O ASP W 425 " (cutoff:3.500A) Processing helix chain 'W' and resid 448 through 466 removed outlier: 4.416A pdb=" N LYS W 452 " --> pdb=" O GLU W 448 " (cutoff:3.500A) Processing helix chain 'Y' and resid 11 through 21 removed outlier: 3.521A pdb=" N THR Y 21 " --> pdb=" O LYS Y 17 " (cutoff:3.500A) Processing helix chain 'Y' and resid 23 through 31 removed outlier: 3.915A pdb=" N VAL Y 29 " --> pdb=" O SER Y 25 " (cutoff:3.500A) Processing helix chain 'Y' and resid 36 through 44 Processing helix chain 'Y' and resid 75 through 78 Processing helix chain 'Y' and resid 100 through 102 No H-bonds generated for 'chain 'Y' and resid 100 through 102' Processing helix chain 'Y' and resid 112 through 122 Processing helix chain '7' and resid 3 through 12 Processing helix chain '7' and resid 33 through 40 Processing helix chain '7' and resid 45 through 54 Processing helix chain '7' and resid 157 through 168 Processing helix chain '7' and resid 178 through 192 Processing helix chain '7' and resid 196 through 201 removed outlier: 3.512A pdb=" N PHE 7 201 " --> pdb=" O LYS 7 197 " (cutoff:3.500A) Processing helix chain '7' and resid 213 through 226 Processing helix chain '8' and resid 297 through 314 removed outlier: 3.566A pdb=" N LYS 8 314 " --> pdb=" O LYS 8 310 " (cutoff:3.500A) Processing helix chain '8' and resid 315 through 337 Processing helix chain '8' and resid 343 through 393 removed outlier: 3.552A pdb=" N LEU 8 347 " --> pdb=" O ASP 8 343 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG 8 348 " --> pdb=" O GLU 8 344 " (cutoff:3.500A) Processing helix chain 'b' and resid 42 through 56 removed outlier: 4.141A pdb=" N LEU b 48 " --> pdb=" O ARG b 44 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ILE b 49 " --> pdb=" O HIS b 45 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN b 50 " --> pdb=" O ARG b 46 " (cutoff:3.500A) Processing helix chain 'b' and resid 71 through 82 removed outlier: 4.201A pdb=" N ASN b 75 " --> pdb=" O LEU b 71 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU b 76 " --> pdb=" O GLN b 72 " (cutoff:3.500A) Processing helix chain 'b' and resid 146 through 161 Processing helix chain 'b' and resid 244 through 276 removed outlier: 3.512A pdb=" N VAL b 248 " --> pdb=" O SER b 244 " (cutoff:3.500A) Processing helix chain 'b' and resid 285 through 290 Processing helix chain 'e' and resid 54 through 58 Processing helix chain 'e' and resid 78 through 83 Processing helix chain 'e' and resid 84 through 86 No H-bonds generated for 'chain 'e' and resid 84 through 86' Processing helix chain 'e' and resid 101 through 116 removed outlier: 3.727A pdb=" N VAL e 106 " --> pdb=" O ALA e 102 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL e 107 " --> pdb=" O LYS e 103 " (cutoff:3.500A) Processing helix chain 'f' and resid 37 through 44 removed outlier: 3.969A pdb=" N PHE f 43 " --> pdb=" O GLN f 39 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR f 44 " --> pdb=" O ASP f 40 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 11 removed outlier: 3.880A pdb=" N LEU h 9 " --> pdb=" O LYS h 5 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR h 11 " --> pdb=" O TYR h 7 " (cutoff:3.500A) Processing helix chain 'h' and resid 13 through 36 removed outlier: 3.556A pdb=" N VAL h 33 " --> pdb=" O ALA h 29 " (cutoff:3.500A) Processing helix chain 'h' and resid 41 through 70 removed outlier: 4.494A pdb=" N LYS h 45 " --> pdb=" O LEU h 41 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR h 46 " --> pdb=" O PRO h 42 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS h 49 " --> pdb=" O LYS h 45 " (cutoff:3.500A) Processing helix chain 'h' and resid 77 through 81 Processing helix chain 'h' and resid 94 through 99 Processing helix chain 'h' and resid 101 through 111 Processing helix chain 'i' and resid 27 through 31 Processing helix chain 'i' and resid 34 through 49 removed outlier: 3.582A pdb=" N GLU i 46 " --> pdb=" O SER i 42 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE i 47 " --> pdb=" O LEU i 43 " (cutoff:3.500A) Processing helix chain 'i' and resid 51 through 77 removed outlier: 3.647A pdb=" N ASP i 59 " --> pdb=" O ARG i 55 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N GLU i 66 " --> pdb=" O ARG i 62 " (cutoff:3.500A) removed outlier: 9.352A pdb=" N LYS i 67 " --> pdb=" O ASN i 63 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG i 68 " --> pdb=" O SER i 64 " (cutoff:3.500A) Processing helix chain 'i' and resid 80 through 98 Processing helix chain 'j' and resid 50 through 56 Processing helix chain 'j' and resid 66 through 68 No H-bonds generated for 'chain 'j' and resid 66 through 68' Processing helix chain 'j' and resid 69 through 77 removed outlier: 3.665A pdb=" N ARG j 73 " --> pdb=" O HIS j 69 " (cutoff:3.500A) Processing helix chain 'x' and resid 175 through 189 Processing helix chain 'm' and resid 197 through 208 Processing helix chain 'm' and resid 234 through 258 Processing helix chain 'm' and resid 261 through 269 Processing helix chain 'n' and resid 17 through 25 Processing helix chain 'n' and resid 28 through 40 Processing helix chain 'n' and resid 64 through 72 Processing helix chain 'n' and resid 74 through 96 Processing helix chain 'n' and resid 98 through 108 removed outlier: 3.592A pdb=" N ALA n 102 " --> pdb=" O GLU n 98 " (cutoff:3.500A) Processing helix chain 'n' and resid 114 through 120 Processing helix chain 'n' and resid 124 through 145 removed outlier: 4.769A pdb=" N ASP n 133 " --> pdb=" O ILE n 129 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ASP n 134 " --> pdb=" O ARG n 130 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA n 135 " --> pdb=" O ASP n 131 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASN n 137 " --> pdb=" O ASP n 133 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET n 138 " --> pdb=" O ASP n 134 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU n 139 " --> pdb=" O ALA n 135 " (cutoff:3.500A) Processing helix chain 'n' and resid 152 through 174 removed outlier: 3.506A pdb=" N LYS n 172 " --> pdb=" O ALA n 168 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU n 173 " --> pdb=" O TYR n 169 " (cutoff:3.500A) Processing helix chain 'n' and resid 214 through 240 removed outlier: 4.378A pdb=" N MET n 218 " --> pdb=" O ASP n 214 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N THR n 220 " --> pdb=" O ARG n 216 " (cutoff:3.500A) Processing helix chain 'n' and resid 249 through 256 Processing helix chain 'n' and resid 258 through 262 Processing helix chain 'n' and resid 372 through 384 removed outlier: 4.029A pdb=" N LEU n 376 " --> pdb=" O PRO n 372 " (cutoff:3.500A) Processing helix chain 'n' and resid 389 through 394 Processing helix chain 'n' and resid 429 through 439 removed outlier: 3.650A pdb=" N ASN n 437 " --> pdb=" O PHE n 433 " (cutoff:3.500A) Processing helix chain 'o' and resid 103 through 112 Processing helix chain 'o' and resid 141 through 151 Processing helix chain 'o' and resid 192 through 215 removed outlier: 4.581A pdb=" N GLY o 215 " --> pdb=" O LEU o 211 " (cutoff:3.500A) Processing helix chain 'p' and resid 50 through 60 Processing helix chain 'p' and resid 66 through 79 Proline residue: p 74 - end of helix Processing helix chain 'p' and resid 91 through 108 removed outlier: 3.583A pdb=" N PHE p 96 " --> pdb=" O LYS p 92 " (cutoff:3.500A) Proline residue: p 99 - end of helix Processing helix chain 'p' and resid 123 through 141 removed outlier: 4.597A pdb=" N GLU p 136 " --> pdb=" O GLY p 132 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU p 137 " --> pdb=" O VAL p 133 " (cutoff:3.500A) Processing helix chain 'p' and resid 153 through 164 Processing helix chain 'p' and resid 171 through 182 removed outlier: 3.664A pdb=" N LEU p 175 " --> pdb=" O THR p 171 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU p 176 " --> pdb=" O PRO p 172 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP p 177 " --> pdb=" O GLY p 173 " (cutoff:3.500A) Processing helix chain 'p' and resid 197 through 205 Processing helix chain 'p' and resid 206 through 217 Processing helix chain 'p' and resid 232 through 243 Processing helix chain 'p' and resid 275 through 287 Processing helix chain 'p' and resid 298 through 312 Processing helix chain 'p' and resid 324 through 339 Processing helix chain 'p' and resid 347 through 352 Processing helix chain 'p' and resid 369 through 384 Processing helix chain 'p' and resid 398 through 409 removed outlier: 4.056A pdb=" N LEU p 402 " --> pdb=" O GLU p 398 " (cutoff:3.500A) Processing helix chain 'p' and resid 425 through 436 Processing helix chain 'p' and resid 436 through 456 Processing helix chain 'p' and resid 464 through 468 Processing helix chain 'p' and resid 469 through 478 Processing helix chain 's' and resid 269 through 285 Processing helix chain 's' and resid 290 through 308 removed outlier: 4.009A pdb=" N UNK s 303 " --> pdb=" O UNK s 299 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N UNK s 306 " --> pdb=" O UNK s 302 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N UNK s 308 " --> pdb=" O UNK s 304 " (cutoff:3.500A) Processing helix chain 's' and resid 344 through 350 Processing helix chain 's' and resid 350 through 357 Processing helix chain 's' and resid 358 through 366 removed outlier: 4.403A pdb=" N UNK s 364 " --> pdb=" O UNK s 360 " (cutoff:3.500A) Processing helix chain 's' and resid 380 through 395 removed outlier: 4.653A pdb=" N ILE s 384 " --> pdb=" O TYR s 380 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG s 385 " --> pdb=" O GLY s 381 " (cutoff:3.500A) Processing helix chain 't' and resid 59 through 87 removed outlier: 3.534A pdb=" N THR t 65 " --> pdb=" O ILE t 61 " (cutoff:3.500A) Processing helix chain 't' and resid 156 through 166 Processing helix chain 't' and resid 183 through 191 removed outlier: 3.973A pdb=" N LEU t 187 " --> pdb=" O VAL t 183 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS t 188 " --> pdb=" O TYR t 184 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL t 189 " --> pdb=" O PRO t 185 " (cutoff:3.500A) Processing helix chain 't' and resid 200 through 211 Processing helix chain 't' and resid 231 through 239 Processing helix chain 't' and resid 247 through 257 Processing helix chain 't' and resid 261 through 268 Processing helix chain 't' and resid 281 through 299 removed outlier: 3.601A pdb=" N ARG t 285 " --> pdb=" O GLY t 281 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU t 286 " --> pdb=" O SER t 282 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG t 287 " --> pdb=" O LEU t 283 " (cutoff:3.500A) Processing helix chain 't' and resid 313 through 322 removed outlier: 3.786A pdb=" N ALA t 319 " --> pdb=" O ASP t 315 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS t 320 " --> pdb=" O SER t 316 " (cutoff:3.500A) Processing helix chain 'u' and resid 33 through 42 Processing helix chain 'u' and resid 52 through 60 Processing helix chain 'u' and resid 66 through 72 removed outlier: 3.583A pdb=" N THR u 70 " --> pdb=" O SER u 67 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE u 71 " --> pdb=" O THR u 68 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA u 72 " --> pdb=" O LEU u 69 " (cutoff:3.500A) Processing helix chain 'u' and resid 82 through 109 removed outlier: 3.720A pdb=" N VAL u 86 " --> pdb=" O ASN u 82 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA u 87 " --> pdb=" O ARG u 83 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR u 88 " --> pdb=" O GLU u 84 " (cutoff:3.500A) Processing helix chain 'u' and resid 113 through 124 removed outlier: 3.687A pdb=" N GLU u 117 " --> pdb=" O ARG u 113 " (cutoff:3.500A) Processing helix chain 'v' and resid 31 through 37 Processing helix chain 'v' and resid 37 through 51 removed outlier: 3.621A pdb=" N ASN v 41 " --> pdb=" O ASN v 37 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN v 42 " --> pdb=" O HIS v 38 " (cutoff:3.500A) Processing helix chain 'v' and resid 70 through 75 removed outlier: 4.145A pdb=" N CYS v 74 " --> pdb=" O PHE v 70 " (cutoff:3.500A) Processing helix chain 'v' and resid 76 through 78 No H-bonds generated for 'chain 'v' and resid 76 through 78' Processing helix chain 'v' and resid 116 through 124 Processing helix chain 'v' and resid 132 through 136 removed outlier: 3.776A pdb=" N VAL v 135 " --> pdb=" O ASN v 132 " (cutoff:3.500A) Processing helix chain 'v' and resid 156 through 173 removed outlier: 3.935A pdb=" N PHE v 173 " --> pdb=" O PHE v 169 " (cutoff:3.500A) Processing helix chain 'w' and resid 175 through 215 removed outlier: 3.611A pdb=" N LYS w 182 " --> pdb=" O LYS w 178 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY w 193 " --> pdb=" O ILE w 189 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA w 194 " --> pdb=" O ALA w 190 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN w 215 " --> pdb=" O GLU w 211 " (cutoff:3.500A) Processing helix chain 'w' and resid 225 through 243 Processing helix chain 'y' and resid 32 through 42 Processing helix chain 'y' and resid 77 through 88 Processing helix chain 'y' and resid 122 through 133 removed outlier: 3.868A pdb=" N SER y 130 " --> pdb=" O GLU y 126 " (cutoff:3.500A) Processing helix chain 'y' and resid 166 through 178 removed outlier: 4.046A pdb=" N LEU y 176 " --> pdb=" O GLU y 172 " (cutoff:3.500A) Processing helix chain 'y' and resid 192 through 196 Processing helix chain 'y' and resid 211 through 222 Processing helix chain 'z' and resid 2 through 11 Processing helix chain 'z' and resid 14 through 29 removed outlier: 3.570A pdb=" N ARG z 18 " --> pdb=" O ASN z 14 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS z 27 " --> pdb=" O GLU z 23 " (cutoff:3.500A) Processing helix chain 'z' and resid 31 through 37 removed outlier: 3.699A pdb=" N LYS z 35 " --> pdb=" O ALA z 31 " (cutoff:3.500A) Processing helix chain 'z' and resid 38 through 55 removed outlier: 3.725A pdb=" N PHE z 42 " --> pdb=" O LYS z 38 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE z 55 " --> pdb=" O TYR z 51 " (cutoff:3.500A) Processing helix chain 'z' and resid 58 through 76 removed outlier: 3.607A pdb=" N HIS z 73 " --> pdb=" O LEU z 69 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N TYR z 76 " --> pdb=" O LEU z 72 " (cutoff:3.500A) Processing helix chain 'z' and resid 78 through 85 removed outlier: 3.846A pdb=" N ASN z 82 " --> pdb=" O ASP z 78 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER z 83 " --> pdb=" O PRO z 79 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA z 85 " --> pdb=" O ASP z 81 " (cutoff:3.500A) Processing helix chain 'z' and resid 89 through 110 Processing helix chain 'z' and resid 111 through 113 No H-bonds generated for 'chain 'z' and resid 111 through 113' Processing helix chain 'z' and resid 117 through 139 removed outlier: 4.072A pdb=" N TYR z 121 " --> pdb=" O ARG z 117 " (cutoff:3.500A) Processing helix chain 'z' and resid 142 through 152 Processing helix chain 'z' and resid 157 through 161 removed outlier: 4.113A pdb=" N GLY z 161 " --> pdb=" O PRO z 158 " (cutoff:3.500A) Processing helix chain 'z' and resid 167 through 186 removed outlier: 5.045A pdb=" N LEU z 178 " --> pdb=" O VAL z 174 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ASP z 179 " --> pdb=" O ASP z 175 " (cutoff:3.500A) Processing helix chain 'z' and resid 198 through 211 Processing helix chain 'z' and resid 213 through 227 removed outlier: 3.794A pdb=" N VAL z 217 " --> pdb=" O PRO z 213 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA z 219 " --> pdb=" O ALA z 215 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE z 220 " --> pdb=" O ASP z 216 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE z 221 " --> pdb=" O VAL z 217 " (cutoff:3.500A) Processing helix chain 'z' and resid 231 through 242 Processing helix chain 'z' and resid 245 through 251 removed outlier: 4.198A pdb=" N VAL z 249 " --> pdb=" O ASP z 245 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 38 removed outlier: 4.299A pdb=" N PHE A 406 " --> pdb=" O SER A 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 53 removed outlier: 3.593A pdb=" N GLU A 57 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL A 67 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER A 113 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU A 69 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 145 removed outlier: 3.714A pdb=" N THR A 142 " --> pdb=" O ALA A 158 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS A 144 " --> pdb=" O VAL A 156 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LEU A 164 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER A 180 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE A 166 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 189 through 192 removed outlier: 3.864A pdb=" N PHE A 189 " --> pdb=" O GLY A 208 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY A 208 " --> pdb=" O PHE A 189 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N TYR A 203 " --> pdb=" O GLU A 218 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU A 218 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE A 205 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU A 216 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N TYR A 207 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE A 214 " --> pdb=" O TYR A 207 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ILE A 214 " --> pdb=" O GLU A 231 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLU A 231 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU A 216 " --> pdb=" O ILE A 229 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 248 through 253 removed outlier: 6.569A pdb=" N ILE A 273 " --> pdb=" O MET A 249 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU A 251 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA A 271 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N PHE A 253 " --> pdb=" O GLN A 269 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N GLN A 269 " --> pdb=" O PHE A 253 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N HIS A 278 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA A 292 " --> pdb=" O LYS A 281 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 303 through 308 removed outlier: 6.367A pdb=" N THR A 336 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N MET A 306 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE A 334 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY A 353 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 366 through 370 removed outlier: 6.459A pdb=" N VAL A 384 " --> pdb=" O LYS A 397 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS A 397 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE A 386 " --> pdb=" O LEU A 395 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 355 through 359 removed outlier: 4.754A pdb=" N SER B 355 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP B 59 " --> pdb=" O SER B 355 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL B 57 " --> pdb=" O LYS B 357 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ILE B 359 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N THR B 55 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ILE B 335 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N VAL B 220 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ALA B 217 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ILE B 278 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ALA B 219 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N THR B 276 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N LYS B 281 " --> pdb=" O LYS B 325 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N MET B 323 " --> pdb=" O TYR B 283 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL B 285 " --> pdb=" O PHE B 321 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE B 321 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG B 70 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY B 52 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ASP B 80 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LYS B 50 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 98 through 106 removed outlier: 5.098A pdb=" N LEU B 99 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N THR B 95 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N SER B 101 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL B 93 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR B 103 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY B 91 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N VAL B 86 " --> pdb=" O HIS B 163 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N HIS B 163 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 98 through 106 removed outlier: 5.098A pdb=" N LEU B 99 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N THR B 95 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N SER B 101 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL B 93 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR B 103 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY B 91 " --> pdb=" O THR B 103 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 5 through 9 removed outlier: 5.939A pdb=" N ASN C 18 " --> pdb=" O VAL C 8 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 150 through 152 removed outlier: 4.266A pdb=" N LEU C 150 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LEU C 206 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N THR C 251 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL C 208 " --> pdb=" O THR C 251 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL C 207 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 186 through 187 Processing sheet with id=AB5, first strand: chain 'D' and resid 18 through 20 Processing sheet with id=AB6, first strand: chain 'D' and resid 50 through 55 Processing sheet with id=AB7, first strand: chain 'D' and resid 133 through 135 removed outlier: 3.667A pdb=" N HIS D 133 " --> pdb=" O GLU e 129 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 77 through 80 removed outlier: 3.593A pdb=" N LYS E 56 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N SER E 66 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N TYR E 54 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR E 38 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N VAL E 39 " --> pdb=" O THR E 87 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 205 through 206 removed outlier: 4.570A pdb=" N SER F 113 " --> pdb=" O ARG F 88 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 153 through 154 Processing sheet with id=AC2, first strand: chain 'G' and resid 177 through 180 removed outlier: 6.060A pdb=" N VAL G 151 " --> pdb=" O ALA G 178 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL G 180 " --> pdb=" O VAL G 151 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ILE G 153 " --> pdb=" O VAL G 180 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 121 through 125 removed outlier: 4.162A pdb=" N THR I 99 " --> pdb=" O VAL I 124 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE I 147 " --> pdb=" O PHE I 162 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE I 162 " --> pdb=" O ILE I 147 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE I 149 " --> pdb=" O LEU I 160 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU I 160 " --> pdb=" O ILE I 149 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASN I 151 " --> pdb=" O THR I 158 " (cutoff:3.500A) removed outlier: 12.272A pdb=" N LYS I 156 " --> pdb=" O SER I 177 " (cutoff:3.500A) removed outlier: 10.222A pdb=" N SER I 177 " --> pdb=" O LYS I 156 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N THR I 158 " --> pdb=" O LEU I 175 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR I 170 " --> pdb=" O LEU I 270 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU I 270 " --> pdb=" O THR I 170 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TYR I 172 " --> pdb=" O LYS I 268 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR I 264 " --> pdb=" O SER I 176 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N PHE I 178 " --> pdb=" O GLN I 262 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLN I 262 " --> pdb=" O PHE I 178 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 121 through 125 removed outlier: 4.162A pdb=" N THR I 99 " --> pdb=" O VAL I 124 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE I 147 " --> pdb=" O PHE I 162 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE I 162 " --> pdb=" O ILE I 147 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE I 149 " --> pdb=" O LEU I 160 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU I 160 " --> pdb=" O ILE I 149 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASN I 151 " --> pdb=" O THR I 158 " (cutoff:3.500A) removed outlier: 12.272A pdb=" N LYS I 156 " --> pdb=" O SER I 177 " (cutoff:3.500A) removed outlier: 10.222A pdb=" N SER I 177 " --> pdb=" O LYS I 156 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N THR I 158 " --> pdb=" O LEU I 175 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR I 170 " --> pdb=" O LEU I 270 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU I 270 " --> pdb=" O THR I 170 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TYR I 172 " --> pdb=" O LYS I 268 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR I 264 " --> pdb=" O SER I 176 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N PHE I 178 " --> pdb=" O GLN I 262 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLN I 262 " --> pdb=" O PHE I 178 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N LYS I 268 " --> pdb=" O GLU I 281 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLU I 281 " --> pdb=" O LYS I 268 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU I 270 " --> pdb=" O GLU I 279 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 247 through 248 Processing sheet with id=AC6, first strand: chain 'K' and resid 243 through 250 removed outlier: 6.222A pdb=" N GLN K 79 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ARG K 277 " --> pdb=" O TYR K 293 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N TYR K 293 " --> pdb=" O ARG K 277 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE K 279 " --> pdb=" O LEU K 291 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 100 through 101 Processing sheet with id=AC8, first strand: chain 'K' and resid 153 through 156 removed outlier: 6.297A pdb=" N VAL K 123 " --> pdb=" O GLU K 153 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ILE K 155 " --> pdb=" O VAL K 123 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU K 125 " --> pdb=" O ILE K 155 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 23 through 24 removed outlier: 6.620A pdb=" N LYS L 23 " --> pdb=" O LEU N 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'L' and resid 57 through 59 Processing sheet with id=AD2, first strand: chain 'L' and resid 124 through 126 removed outlier: 4.438A pdb=" N LYS h 115 " --> pdb=" O PHE L 126 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 53 through 59 removed outlier: 4.207A pdb=" N GLY M 48 " --> pdb=" O PRO M 54 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ASP M 47 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ILE M 35 " --> pdb=" O ASP M 47 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ARG M 19 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N VAL M 20 " --> pdb=" O THR M 66 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 36 through 39 removed outlier: 4.566A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N TYR N 127 " --> pdb=" O ASN N 122 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ASN N 122 " --> pdb=" O TYR N 127 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N TYR N 129 " --> pdb=" O TRP N 120 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N TRP N 120 " --> pdb=" O TYR N 129 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLU N 131 " --> pdb=" O SER N 118 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N SER N 118 " --> pdb=" O GLU N 131 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE N 133 " --> pdb=" O LEU N 116 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 6 through 10 Processing sheet with id=AD6, first strand: chain 'O' and resid 14 through 15 removed outlier: 5.715A pdb=" N HIS O 14 " --> pdb=" O ASN O 42 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N SER O 44 " --> pdb=" O HIS O 14 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'P' and resid 14 through 22 removed outlier: 5.041A pdb=" N SER P 144 " --> pdb=" O TYR P 21 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N HIS P 145 " --> pdb=" O VAL P 119 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL P 119 " --> pdb=" O HIS P 145 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLU P 147 " --> pdb=" O ILE P 117 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ILE P 117 " --> pdb=" O GLU P 147 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL P 149 " --> pdb=" O SER P 115 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'P' and resid 58 through 59 Processing sheet with id=AD9, first strand: chain 'Q' and resid 62 through 63 removed outlier: 6.294A pdb=" N VAL Q 81 " --> pdb=" O ALA Q 102 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N LEU Q 104 " --> pdb=" O VAL Q 81 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N VAL Q 83 " --> pdb=" O LEU Q 104 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N PHE Q 106 " --> pdb=" O VAL Q 83 " (cutoff:3.500A) removed outlier: 11.232A pdb=" N GLY Q 85 " --> pdb=" O PHE Q 106 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL Q 101 " --> pdb=" O ILE Q 122 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Q' and resid 62 through 63 Processing sheet with id=AE2, first strand: chain 'S' and resid 25 through 31 removed outlier: 7.324A pdb=" N GLU S 6 " --> pdb=" O GLN S 63 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLN S 63 " --> pdb=" O GLU S 6 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLN S 8 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE S 61 " --> pdb=" O GLN S 8 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE S 10 " --> pdb=" O VAL S 59 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'S' and resid 86 through 96 removed outlier: 3.641A pdb=" N TYR S 81 " --> pdb=" O HIS S 88 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASN S 74 " --> pdb=" O ILE S 129 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ARG S 80 " --> pdb=" O ILE S 123 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ILE S 123 " --> pdb=" O ARG S 80 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'V' and resid 21 through 25 removed outlier: 3.779A pdb=" N ALA V 21 " --> pdb=" O ILE V 36 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N MET V 59 " --> pdb=" O ILE V 37 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL V 39 " --> pdb=" O MET V 57 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N MET V 57 " --> pdb=" O VAL V 39 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ALA V 99 " --> pdb=" O VAL V 79 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N GLY V 100 " --> pdb=" O ILE V 22 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ASN V 24 " --> pdb=" O GLY V 100 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE V 102 " --> pdb=" O ASN V 24 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'V' and resid 85 through 86 removed outlier: 3.540A pdb=" N LEU V 93 " --> pdb=" O TRP V 85 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N PHE V 92 " --> pdb=" O MET u 20 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N VAL u 22 " --> pdb=" O PHE V 92 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TYR V 94 " --> pdb=" O VAL u 22 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'V' and resid 114 through 118 removed outlier: 5.554A pdb=" N SER V 133 " --> pdb=" O ILE V 114 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N GLY V 116 " --> pdb=" O SER V 133 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL V 135 " --> pdb=" O GLY V 116 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'W' and resid 435 through 436 Processing sheet with id=AE8, first strand: chain 'Y' and resid 32 through 34 Processing sheet with id=AE9, first strand: chain 'Y' and resid 94 through 99 removed outlier: 6.839A pdb=" N VAL Y 85 " --> pdb=" O ILE Y 97 " (cutoff:3.500A) removed outlier: 9.932A pdb=" N LEU Y 99 " --> pdb=" O ASP Y 83 " (cutoff:3.500A) removed outlier: 10.558A pdb=" N ASP Y 83 " --> pdb=" O LEU Y 99 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA Y 79 " --> pdb=" O VAL Y 73 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N VAL Y 73 " --> pdb=" O ALA Y 79 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLN Y 81 " --> pdb=" O SER Y 71 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N LYS Y 69 " --> pdb=" O ASP Y 83 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N VAL Y 85 " --> pdb=" O GLU Y 67 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N GLU Y 67 " --> pdb=" O VAL Y 85 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LEU Y 57 " --> pdb=" O ILE Y 106 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ILE Y 106 " --> pdb=" O LEU Y 57 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'b' and resid 33 through 37 removed outlier: 6.036A pdb=" N LEU b 34 " --> pdb=" O LEU b 87 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N PHE b 89 " --> pdb=" O LEU b 34 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE b 36 " --> pdb=" O PHE b 89 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ALA b 91 " --> pdb=" O ILE b 36 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N LEU b 97 " --> pdb=" O ILE b 114 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU b 101 " --> pdb=" O ILE b 110 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE b 110 " --> pdb=" O LEU b 101 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N THR b 109 " --> pdb=" O ILE b 226 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE b 226 " --> pdb=" O THR b 109 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LYS b 111 " --> pdb=" O ILE b 224 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU b 117 " --> pdb=" O ARG b 218 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ARG b 218 " --> pdb=" O LEU b 117 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'b' and resid 213 through 214 removed outlier: 3.838A pdb=" N VAL b 213 " --> pdb=" O GLU b 192 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 218 through 227 current: chain 'b' and resid 136 through 139 Processing sheet with id=AF3, first strand: chain 'e' and resid 72 through 76 removed outlier: 6.143A pdb=" N LYS e 72 " --> pdb=" O ALA e 93 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLU e 95 " --> pdb=" O LYS e 72 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N PHE e 74 " --> pdb=" O GLU e 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'f' and resid 8 through 18 removed outlier: 9.821A pdb=" N VAL f 9 " --> pdb=" O ILE f 32 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ILE f 32 " --> pdb=" O VAL f 9 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N GLY f 11 " --> pdb=" O ILE f 30 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ILE f 30 " --> pdb=" O GLY f 11 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N HIS f 13 " --> pdb=" O SER f 28 " (cutoff:3.500A) removed outlier: 9.772A pdb=" N SER f 28 " --> pdb=" O HIS f 13 " (cutoff:3.500A) removed outlier: 10.538A pdb=" N SER f 15 " --> pdb=" O ASN f 26 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N ASN f 26 " --> pdb=" O SER f 15 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N ASN f 26 " --> pdb=" O PHE f 85 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N PHE f 85 " --> pdb=" O ASN f 26 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL f 80 " --> pdb=" O HIS f 75 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG f 73 " --> pdb=" O ARG f 82 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N THR f 84 " --> pdb=" O VAL f 71 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N VAL f 71 " --> pdb=" O THR f 84 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG f 48 " --> pdb=" O PHE f 101 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N VAL f 52 " --> pdb=" O SER f 97 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N SER f 97 " --> pdb=" O VAL f 52 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA f 96 " --> pdb=" O HIS f 13 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'j' and resid 16 through 17 Processing sheet with id=AF6, first strand: chain 'n' and resid 187 through 191 Processing sheet with id=AF7, first strand: chain 'n' and resid 365 through 367 Processing sheet with id=AF8, first strand: chain 'o' and resid 117 through 124 removed outlier: 4.758A pdb=" N LEU o 117 " --> pdb=" O GLU o 138 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLU o 138 " --> pdb=" O LEU o 117 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU o 119 " --> pdb=" O PHE o 136 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N PHE o 136 " --> pdb=" O GLU o 119 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ARG o 121 " --> pdb=" O TYR o 134 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N TYR o 134 " --> pdb=" O ARG o 121 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA o 123 " --> pdb=" O ARG o 132 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE o 139 " --> pdb=" O GLY o 91 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N GLY o 91 " --> pdb=" O PHE o 139 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ILE o 92 " --> pdb=" O LEU o 167 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN o 163 " --> pdb=" O SER o 96 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'p' and resid 146 through 148 removed outlier: 3.602A pdb=" N ILE p 169 " --> pdb=" O GLY p 146 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE p 117 " --> pdb=" O LEU p 168 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ALA p 170 " --> pdb=" O ILE p 117 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N VAL p 119 " --> pdb=" O ALA p 170 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU p 193 " --> pdb=" O MET p 225 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N PHE p 227 " --> pdb=" O LEU p 193 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE p 195 " --> pdb=" O PHE p 227 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE p 250 " --> pdb=" O LEU p 83 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'p' and resid 316 through 319 removed outlier: 3.662A pdb=" N THR p 346 " --> pdb=" O LEU p 319 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N GLN p 266 " --> pdb=" O ASN p 413 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'q' and resid 97 through 102 removed outlier: 6.585A pdb=" N UNK q 423 " --> pdb=" O UNK q 99 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N UNK q 101 " --> pdb=" O UNK q 421 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N UNK q 421 " --> pdb=" O UNK q 101 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'q' and resid 109 through 113 removed outlier: 3.634A pdb=" N UNK q 113 " --> pdb=" O UNK q 120 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N UNK q 120 " --> pdb=" O UNK q 113 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N UNK q 128 " --> pdb=" O UNK q 141 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N UNK q 141 " --> pdb=" O UNK q 128 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N UNK q 130 " --> pdb=" O UNK q 139 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'q' and resid 149 through 154 removed outlier: 6.779A pdb=" N UNK q 179 " --> pdb=" O UNK q 150 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N UNK q 152 " --> pdb=" O UNK q 177 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N UNK q 177 " --> pdb=" O UNK q 152 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N UNK q 154 " --> pdb=" O UNK q 175 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N UNK q 175 " --> pdb=" O UNK q 154 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N UNK q 189 " --> pdb=" O UNK q 195 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N UNK q 195 " --> pdb=" O UNK q 189 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'q' and resid 206 through 211 removed outlier: 6.744A pdb=" N UNK q 221 " --> pdb=" O UNK q 207 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N UNK q 209 " --> pdb=" O UNK q 219 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N UNK q 219 " --> pdb=" O UNK q 209 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'q' and resid 251 through 257 removed outlier: 6.885A pdb=" N UNK q 265 " --> pdb=" O UNK q 252 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N UNK q 254 " --> pdb=" O UNK q 263 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N UNK q 263 " --> pdb=" O UNK q 254 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N UNK q 256 " --> pdb=" O UNK q 261 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N UNK q 261 " --> pdb=" O UNK q 256 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N UNK q 266 " --> pdb=" O UNK q 270 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N UNK q 270 " --> pdb=" O UNK q 266 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N UNK q 275 " --> pdb=" O UNK q 281 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N UNK q 281 " --> pdb=" O UNK q 275 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'q' and resid 294 through 297 removed outlier: 3.883A pdb=" N UNK q 294 " --> pdb=" O UNK q 311 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N UNK q 311 " --> pdb=" O UNK q 294 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N UNK q 296 " --> pdb=" O UNK q 309 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N UNK q 317 " --> pdb=" O UNK q 349 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N UNK q 349 " --> pdb=" O UNK q 317 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N UNK q 319 " --> pdb=" O UNK q 347 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'q' and resid 361 through 362 removed outlier: 6.206A pdb=" N UNK q 380 " --> pdb=" O UNK q 393 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N UNK q 393 " --> pdb=" O UNK q 380 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N UNK q 382 " --> pdb=" O UNK q 391 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N UNK q 389 " --> pdb=" O UNK q 384 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 't' and resid 130 through 134 Processing sheet with id=AH1, first strand: chain 't' and resid 174 through 179 Processing sheet with id=AH2, first strand: chain 't' and resid 213 through 215 Processing sheet with id=AH3, first strand: chain 'u' and resid 4 through 5 Processing sheet with id=AH4, first strand: chain 'v' and resid 28 through 29 removed outlier: 6.278A pdb=" N VAL v 94 " --> pdb=" O VAL v 111 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS v 341 " --> pdb=" O THR v 108 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N GLN v 110 " --> pdb=" O LEU v 339 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N LEU v 339 " --> pdb=" O GLN v 110 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N LEU v 112 " --> pdb=" O LEU v 337 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LEU v 337 " --> pdb=" O LEU v 112 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'v' and resid 142 through 144 removed outlier: 3.815A pdb=" N LYS v 194 " --> pdb=" O ASN v 144 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP v 195 " --> pdb=" O GLU v 200 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU v 200 " --> pdb=" O ASP v 195 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA v 325 " --> pdb=" O ARG v 211 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'y' and resid 3 through 4 removed outlier: 6.195A pdb=" N THR y 3 " --> pdb=" O THR y 206 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'y' and resid 17 through 19 removed outlier: 6.618A pdb=" N CYS y 24 " --> pdb=" O VAL y 49 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'y' and resid 64 through 65 Processing sheet with id=AH9, first strand: chain 'y' and resid 109 through 110 Processing sheet with id=AI1, first strand: chain 'y' and resid 152 through 154 removed outlier: 3.607A pdb=" N VAL y 182 " --> pdb=" O GLY y 159 " (cutoff:3.500A) 2520 hydrogen bonds defined for protein. 7254 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1236 hydrogen bonds 1970 hydrogen bond angles 0 basepair planarities 501 basepair parallelities 845 stacking parallelities Total time for adding SS restraints: 54.12 Time building geometry restraints manager: 39.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 18171 1.33 - 1.46: 37292 1.46 - 1.60: 39730 1.60 - 1.73: 1356 1.73 - 1.87: 227 Bond restraints: 96776 Sorted by residual: bond pdb=" CA UNK q 314 " pdb=" C UNK q 314 " ideal model delta sigma weight residual 1.525 1.598 -0.073 2.10e-02 2.27e+03 1.22e+01 bond pdb=" CA ARG B 37 " pdb=" C ARG B 37 " ideal model delta sigma weight residual 1.523 1.474 0.049 1.48e-02 4.57e+03 1.09e+01 bond pdb=" C LEU Y 99 " pdb=" N HIS Y 100 " ideal model delta sigma weight residual 1.332 1.290 0.043 1.40e-02 5.10e+03 9.31e+00 bond pdb=" C LYS G 128 " pdb=" N PRO G 129 " ideal model delta sigma weight residual 1.334 1.301 0.033 1.11e-02 8.12e+03 8.89e+00 bond pdb=" CG LEU b 99 " pdb=" CD2 LEU b 99 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.79e+00 ... (remaining 96771 not shown) Histogram of bond angle deviations from ideal: 96.81 - 105.08: 8242 105.08 - 113.35: 58261 113.35 - 121.63: 49527 121.63 - 129.90: 21194 129.90 - 138.17: 1157 Bond angle restraints: 138381 Sorted by residual: angle pdb=" C ARG S 13 " pdb=" N LEU S 14 " pdb=" CA LEU S 14 " ideal model delta sigma weight residual 121.80 138.17 -16.37 2.44e+00 1.68e-01 4.50e+01 angle pdb=" C ASN F 157 " pdb=" N LYS F 158 " pdb=" CA LYS F 158 " ideal model delta sigma weight residual 121.54 132.70 -11.16 1.91e+00 2.74e-01 3.42e+01 angle pdb=" C LYS A 265 " pdb=" N LEU A 266 " pdb=" CA LEU A 266 " ideal model delta sigma weight residual 121.54 132.39 -10.85 1.91e+00 2.74e-01 3.22e+01 angle pdb=" C LEU 7 44 " pdb=" N THR 7 45 " pdb=" CA THR 7 45 " ideal model delta sigma weight residual 121.54 132.30 -10.76 1.91e+00 2.74e-01 3.17e+01 angle pdb=" C GLU A 414 " pdb=" N ILE A 415 " pdb=" CA ILE A 415 " ideal model delta sigma weight residual 120.77 128.10 -7.33 1.31e+00 5.83e-01 3.13e+01 ... (remaining 138376 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 53729 35.88 - 71.77: 1381 71.77 - 107.65: 147 107.65 - 143.53: 22 143.53 - 179.42: 40 Dihedral angle restraints: 55319 sinusoidal: 33917 harmonic: 21402 Sorted by residual: dihedral pdb=" CA ALA A 185 " pdb=" C ALA A 185 " pdb=" N PRO A 186 " pdb=" CA PRO A 186 " ideal model delta harmonic sigma weight residual -180.00 -115.10 -64.90 0 5.00e+00 4.00e-02 1.68e+02 dihedral pdb=" C5' U 13351 " pdb=" C4' U 13351 " pdb=" C3' U 13351 " pdb=" O3' U 13351 " ideal model delta sinusoidal sigma weight residual 147.00 71.64 75.36 1 8.00e+00 1.56e-02 1.12e+02 dihedral pdb=" CA SER S 83 " pdb=" C SER S 83 " pdb=" N ARG S 84 " pdb=" CA ARG S 84 " ideal model delta harmonic sigma weight residual -180.00 -128.07 -51.93 0 5.00e+00 4.00e-02 1.08e+02 ... (remaining 55316 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 15968 0.103 - 0.205: 829 0.205 - 0.308: 71 0.308 - 0.411: 8 0.411 - 0.514: 1 Chirality restraints: 16877 Sorted by residual: chirality pdb=" C3' U 13351 " pdb=" C4' U 13351 " pdb=" O3' U 13351 " pdb=" C2' U 13351 " both_signs ideal model delta sigma weight residual False -2.74 -2.23 -0.51 2.00e-01 2.50e+01 6.60e+00 chirality pdb=" CB ILE p 194 " pdb=" CA ILE p 194 " pdb=" CG1 ILE p 194 " pdb=" CG2 ILE p 194 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CB VAL G 190 " pdb=" CA VAL G 190 " pdb=" CG1 VAL G 190 " pdb=" CG2 VAL G 190 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.41e+00 ... (remaining 16874 not shown) Planarity restraints: 11636 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 1 406 " -0.085 2.00e-02 2.50e+03 3.80e-02 4.33e+01 pdb=" N9 G 1 406 " 0.095 2.00e-02 2.50e+03 pdb=" C8 G 1 406 " 0.005 2.00e-02 2.50e+03 pdb=" N7 G 1 406 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G 1 406 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G 1 406 " -0.013 2.00e-02 2.50e+03 pdb=" O6 G 1 406 " -0.018 2.00e-02 2.50e+03 pdb=" N1 G 1 406 " -0.010 2.00e-02 2.50e+03 pdb=" C2 G 1 406 " -0.006 2.00e-02 2.50e+03 pdb=" N2 G 1 406 " 0.018 2.00e-02 2.50e+03 pdb=" N3 G 1 406 " 0.009 2.00e-02 2.50e+03 pdb=" C4 G 1 406 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 185 " 0.071 5.00e-02 4.00e+02 1.07e-01 1.82e+01 pdb=" N PRO A 186 " -0.185 5.00e-02 4.00e+02 pdb=" CA PRO A 186 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO A 186 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G 2 39 " -0.057 2.00e-02 2.50e+03 2.35e-02 1.66e+01 pdb=" N9 G 2 39 " 0.053 2.00e-02 2.50e+03 pdb=" C8 G 2 39 " 0.006 2.00e-02 2.50e+03 pdb=" N7 G 2 39 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G 2 39 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G 2 39 " -0.008 2.00e-02 2.50e+03 pdb=" O6 G 2 39 " -0.015 2.00e-02 2.50e+03 pdb=" N1 G 2 39 " -0.006 2.00e-02 2.50e+03 pdb=" C2 G 2 39 " 0.007 2.00e-02 2.50e+03 pdb=" N2 G 2 39 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G 2 39 " 0.013 2.00e-02 2.50e+03 pdb=" C4 G 2 39 " 0.007 2.00e-02 2.50e+03 ... (remaining 11633 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 1137 2.57 - 3.15: 70333 3.15 - 3.73: 175825 3.73 - 4.32: 230676 4.32 - 4.90: 329202 Nonbonded interactions: 807173 Sorted by model distance: nonbonded pdb=" OE2 GLU A 57 " pdb=" NZ LYS A 169 " model vdw 1.985 2.520 nonbonded pdb=" NH1 ARG v 334 " pdb=" OE2 GLU w 183 " model vdw 1.985 2.520 nonbonded pdb=" OE2 GLU G 144 " pdb=" OH TYR N 6 " model vdw 2.007 2.440 nonbonded pdb=" OP2 A 1 438 " pdb=" NZ LYS I 104 " model vdw 2.023 2.520 nonbonded pdb=" O2' A 1 533 " pdb=" OP2 G 1 535 " model vdw 2.027 2.440 ... (remaining 807168 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 1602 5.49 5 S 137 5.16 5 C 51832 2.51 5 N 16655 2.21 5 O 21513 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.160 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: 0.090 Extract box with map and model: 27.680 Check model and map are aligned: 1.010 Convert atoms to be neutral: 0.590 Process input model: 230.040 Find NCS groups from input model: 2.270 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 269.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.077 96776 Z= 0.407 Angle : 1.027 16.373 138381 Z= 0.551 Chirality : 0.052 0.514 16877 Planarity : 0.007 0.107 11636 Dihedral : 14.972 179.418 41393 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.17 % Favored : 94.75 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.06 % Twisted Proline : 0.74 % Twisted General : 0.18 % 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: -2.72 (0.08), residues: 6729 helix: -1.82 (0.08), residues: 2612 sheet: -1.13 (0.16), residues: 928 loop : -1.91 (0.09), residues: 3189 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13458 Ramachandran restraints generated. 6729 Oldfield, 0 Emsley, 6729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13458 Ramachandran restraints generated. 6729 Oldfield, 0 Emsley, 6729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1843 residues out of total 5975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 1826 time to evaluate : 6.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 3 residues processed: 1838 average time/residue: 0.9141 time to fit residues: 2788.2798 Evaluate side-chains 940 residues out of total 5975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 937 time to evaluate : 6.038 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.6660 time to fit residues: 11.4945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 857 random chunks: chunk 723 optimal weight: 50.0000 chunk 649 optimal weight: 1.9990 chunk 360 optimal weight: 2.9990 chunk 221 optimal weight: 10.0000 chunk 438 optimal weight: 0.9990 chunk 347 optimal weight: 0.9990 chunk 671 optimal weight: 1.9990 chunk 259 optimal weight: 0.9990 chunk 408 optimal weight: 3.9990 chunk 499 optimal weight: 30.0000 chunk 778 optimal weight: 6.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 GLN A 332 ASN C 45 ASN C 48 GLN C 110 ASN C 114 ASN C 116 ASN C 221 ASN ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 GLN ** D 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 GLN F 61 ASN F 172 ASN ** F 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 GLN G 95 ASN G 137 ASN G 138 HIS ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 ASN ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 ASN I 164 HIS I 203 GLN I 228 GLN ** I 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 200 ASN ** K 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 ASN ** L 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 GLN N 37 HIS N 175 ASN N 194 GLN N 195 ASN O 50 ASN P 28 ASN P 45 GLN P 92 GLN P 97 ASN P 145 HIS ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 78 ASN S 46 GLN S 74 ASN S 89 ASN V 24 ASN W 384 ASN Y 120 GLN 7 29 ASN 7 31 GLN ** 7 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 49 ASN ** 7 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 210 GLN 8 319 GLN b 75 ASN b 118 HIS b 158 HIS b 254 GLN e 31 ASN e 52 GLN f 42 GLN h 108 GLN i 91 ASN ** i 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 48 ASN n 73 HIS n 160 GLN ** n 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 100 HIS ** o 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 69 GLN ** p 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 141 HIS p 153 ASN p 156 GLN ** p 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 325 GLN p 330 ASN p 413 ASN p 441 GLN t 92 HIS ** t 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 45 ASN u 82 ASN u 115 ASN v 81 HIS v 137 ASN v 171 ASN ** v 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 221 ASN ** y 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 178 GLN ** z 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 39 GLN z 43 ASN z 132 GLN Total number of N/Q/H flips: 79 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 96776 Z= 0.202 Angle : 0.679 12.555 138381 Z= 0.347 Chirality : 0.039 0.278 16877 Planarity : 0.005 0.084 11636 Dihedral : 16.135 179.878 27160 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.18 % Favored : 95.76 % Rotamer Outliers : 3.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.06 % Twisted Proline : 0.74 % Twisted General : 0.11 % 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: 6729 helix: -0.21 (0.09), residues: 2726 sheet: -0.82 (0.16), residues: 924 loop : -1.44 (0.10), residues: 3079 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13458 Ramachandran restraints generated. 6729 Oldfield, 0 Emsley, 6729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13458 Ramachandran restraints generated. 6729 Oldfield, 0 Emsley, 6729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1271 residues out of total 5975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 1071 time to evaluate : 6.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 outliers start: 200 outliers final: 94 residues processed: 1204 average time/residue: 0.8501 time to fit residues: 1732.6749 Evaluate side-chains 906 residues out of total 5975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 812 time to evaluate : 6.058 Switching outliers to nearest non-outliers outliers start: 94 outliers final: 0 residues processed: 94 average time/residue: 0.6919 time to fit residues: 127.3157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 857 random chunks: chunk 432 optimal weight: 7.9990 chunk 241 optimal weight: 0.6980 chunk 647 optimal weight: 0.9990 chunk 529 optimal weight: 0.7980 chunk 214 optimal weight: 9.9990 chunk 779 optimal weight: 4.9990 chunk 842 optimal weight: 3.9990 chunk 694 optimal weight: 0.9990 chunk 773 optimal weight: 6.9990 chunk 265 optimal weight: 1.9990 chunk 625 optimal weight: 20.0000 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 HIS D 110 GLN ** F 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 203 GLN ** K 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 45 GLN P 92 GLN Q 78 ASN S 3 HIS S 8 GLN W 429 ASN Y 120 GLN 7 10 ASN 7 31 GLN ** 7 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 254 GLN b 277 ASN e 20 HIS e 52 GLN f 42 GLN f 106 ASN h 34 GLN ** h 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 20 ASN j 48 ASN n 165 GLN ** n 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 141 HIS ** p 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 181 ASN ** p 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 426 GLN ** t 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 81 HIS ** y 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 13 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 96776 Z= 0.180 Angle : 0.629 14.963 138381 Z= 0.318 Chirality : 0.037 0.267 16877 Planarity : 0.004 0.066 11636 Dihedral : 15.805 179.735 27160 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.59 % Favored : 95.35 % Rotamer Outliers : 2.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.06 % Twisted Proline : 1.11 % Twisted General : 0.06 % 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: -0.79 (0.10), residues: 6729 helix: 0.36 (0.09), residues: 2720 sheet: -0.59 (0.16), residues: 959 loop : -1.26 (0.11), residues: 3050 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13458 Ramachandran restraints generated. 6729 Oldfield, 0 Emsley, 6729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13458 Ramachandran restraints generated. 6729 Oldfield, 0 Emsley, 6729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1027 residues out of total 5975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 907 time to evaluate : 6.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 outliers start: 120 outliers final: 46 residues processed: 986 average time/residue: 0.8216 time to fit residues: 1389.8420 Evaluate side-chains 806 residues out of total 5975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 760 time to evaluate : 6.048 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.6858 time to fit residues: 65.9321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 857 random chunks: chunk 770 optimal weight: 10.0000 chunk 586 optimal weight: 0.9980 chunk 404 optimal weight: 6.9990 chunk 86 optimal weight: 8.9990 chunk 372 optimal weight: 2.9990 chunk 523 optimal weight: 2.9990 chunk 782 optimal weight: 20.0000 chunk 828 optimal weight: 9.9990 chunk 408 optimal weight: 8.9990 chunk 741 optimal weight: 50.0000 chunk 223 optimal weight: 0.9980 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 GLN C 45 ASN ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 GLN E 120 ASN ** F 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 ASN ** K 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 143 GLN K 176 GLN L 37 ASN ** L 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 GLN ** O 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 45 GLN P 92 GLN ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 81 GLN W 413 ASN 7 25 GLN 7 48 GLN ** 7 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 20 HIS e 52 GLN e 104 ASN ** f 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 79 GLN ** n 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 230 HIS ** n 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 81 HIS w 175 ASN ** y 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.072 96776 Z= 0.281 Angle : 0.650 16.566 138381 Z= 0.332 Chirality : 0.039 0.233 16877 Planarity : 0.005 0.093 11636 Dihedral : 15.660 179.901 27160 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.90 % Favored : 95.05 % Rotamer Outliers : 2.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.06 % Twisted Proline : 0.74 % Twisted General : 0.05 % 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: -0.47 (0.10), residues: 6729 helix: 0.73 (0.10), residues: 2725 sheet: -0.54 (0.16), residues: 998 loop : -1.17 (0.11), residues: 3006 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13458 Ramachandran restraints generated. 6729 Oldfield, 0 Emsley, 6729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13458 Ramachandran restraints generated. 6729 Oldfield, 0 Emsley, 6729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 952 residues out of total 5975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 809 time to evaluate : 6.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 143 outliers final: 72 residues processed: 884 average time/residue: 0.8550 time to fit residues: 1288.8684 Evaluate side-chains 784 residues out of total 5975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 712 time to evaluate : 6.060 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 0 residues processed: 72 average time/residue: 0.7053 time to fit residues: 100.8927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 857 random chunks: chunk 689 optimal weight: 10.0000 chunk 470 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 616 optimal weight: 2.9990 chunk 341 optimal weight: 3.9990 chunk 706 optimal weight: 0.4980 chunk 572 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 422 optimal weight: 6.9990 chunk 743 optimal weight: 50.0000 chunk 209 optimal weight: 10.0000 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 45 ASN ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 ASN F 61 ASN ** F 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 GLN ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN L 25 HIS ** L 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 57 GLN ** O 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 34 GLN P 45 GLN P 92 GLN ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 63 GLN W 429 ASN W 454 GLN 7 39 ASN ** 7 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 20 HIS e 52 GLN ** f 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 69 GLN ** n 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 20 ASN z 132 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.075 96776 Z= 0.293 Angle : 0.650 16.711 138381 Z= 0.333 Chirality : 0.039 0.405 16877 Planarity : 0.005 0.066 11636 Dihedral : 15.599 179.749 27160 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 19.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.42 % Favored : 94.52 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.06 % Twisted Proline : 0.74 % Twisted General : 0.05 % 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: -0.38 (0.10), residues: 6729 helix: 0.84 (0.10), residues: 2731 sheet: -0.47 (0.16), residues: 975 loop : -1.15 (0.11), residues: 3023 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13458 Ramachandran restraints generated. 6729 Oldfield, 0 Emsley, 6729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13458 Ramachandran restraints generated. 6729 Oldfield, 0 Emsley, 6729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 886 residues out of total 5975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 779 time to evaluate : 6.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 107 outliers final: 49 residues processed: 847 average time/residue: 0.8265 time to fit residues: 1207.0400 Evaluate side-chains 744 residues out of total 5975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 695 time to evaluate : 6.074 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.6599 time to fit residues: 68.8521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 857 random chunks: chunk 278 optimal weight: 0.9990 chunk 745 optimal weight: 50.0000 chunk 163 optimal weight: 4.9990 chunk 486 optimal weight: 0.9990 chunk 204 optimal weight: 7.9990 chunk 829 optimal weight: 5.9990 chunk 688 optimal weight: 0.6980 chunk 383 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 274 optimal weight: 5.9990 chunk 435 optimal weight: 9.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 HIS ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN N 57 GLN ** O 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 45 GLN ** P 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 92 GLN ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 8 GLN S 62 ASN 7 10 ASN ** 7 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 31 GLN ** 7 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 239 ASN e 20 HIS e 31 ASN e 104 ASN f 42 GLN f 106 ASN h 34 GLN ** h 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 20 ASN j 57 HIS j 79 GLN ** n 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 132 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 96776 Z= 0.194 Angle : 0.613 14.583 138381 Z= 0.311 Chirality : 0.037 0.281 16877 Planarity : 0.004 0.060 11636 Dihedral : 15.484 179.943 27160 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.13 % Favored : 94.83 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.06 % Twisted Proline : 0.37 % Twisted General : 0.05 % 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: -0.26 (0.10), residues: 6729 helix: 0.92 (0.10), residues: 2749 sheet: -0.34 (0.16), residues: 986 loop : -1.11 (0.11), residues: 2994 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13458 Ramachandran restraints generated. 6729 Oldfield, 0 Emsley, 6729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13458 Ramachandran restraints generated. 6729 Oldfield, 0 Emsley, 6729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 870 residues out of total 5975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 795 time to evaluate : 6.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 37 residues processed: 842 average time/residue: 0.8108 time to fit residues: 1183.8738 Evaluate side-chains 748 residues out of total 5975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 711 time to evaluate : 6.029 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.6816 time to fit residues: 54.4647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 857 random chunks: chunk 799 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 472 optimal weight: 2.9990 chunk 605 optimal weight: 8.9990 chunk 469 optimal weight: 6.9990 chunk 697 optimal weight: 1.9990 chunk 463 optimal weight: 0.9990 chunk 826 optimal weight: 50.0000 chunk 516 optimal weight: 0.7980 chunk 503 optimal weight: 10.0000 chunk 381 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 ASN F 244 ASN ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 34 GLN P 45 GLN ** P 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 92 GLN ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 10 ASN ** 7 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 20 HIS ** f 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 287 ASN ** t 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 96776 Z= 0.232 Angle : 0.625 15.494 138381 Z= 0.318 Chirality : 0.038 0.345 16877 Planarity : 0.004 0.069 11636 Dihedral : 15.405 179.509 27160 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.34 % Favored : 94.62 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.06 % Twisted Proline : 0.37 % Twisted General : 0.02 % 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: -0.21 (0.10), residues: 6729 helix: 0.95 (0.10), residues: 2745 sheet: -0.26 (0.16), residues: 951 loop : -1.10 (0.11), residues: 3033 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13458 Ramachandran restraints generated. 6729 Oldfield, 0 Emsley, 6729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13458 Ramachandran restraints generated. 6729 Oldfield, 0 Emsley, 6729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 5975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 750 time to evaluate : 6.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 34 residues processed: 788 average time/residue: 0.8254 time to fit residues: 1127.3488 Evaluate side-chains 730 residues out of total 5975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 696 time to evaluate : 6.125 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.6525 time to fit residues: 49.8730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 857 random chunks: chunk 511 optimal weight: 9.9990 chunk 329 optimal weight: 0.9990 chunk 493 optimal weight: 8.9990 chunk 248 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 chunk 160 optimal weight: 0.9980 chunk 525 optimal weight: 1.9990 chunk 562 optimal weight: 20.0000 chunk 408 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 649 optimal weight: 20.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 ASN ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 145 ASN ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 295 GLN N 123 GLN ** O 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 454 GLN 7 10 ASN ** 7 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 20 HIS ** f 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 79 GLN n 26 GLN ** n 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 11 ASN ** y 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 132 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 96776 Z= 0.260 Angle : 0.642 17.037 138381 Z= 0.326 Chirality : 0.038 0.279 16877 Planarity : 0.004 0.073 11636 Dihedral : 15.379 179.853 27160 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.41 % Favored : 94.53 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.06 % Twisted Proline : 0.74 % Twisted General : 0.02 % 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: -0.19 (0.10), residues: 6729 helix: 0.97 (0.10), residues: 2748 sheet: -0.31 (0.16), residues: 969 loop : -1.06 (0.11), residues: 3012 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13458 Ramachandran restraints generated. 6729 Oldfield, 0 Emsley, 6729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13458 Ramachandran restraints generated. 6729 Oldfield, 0 Emsley, 6729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 5975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 730 time to evaluate : 5.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 39 residues processed: 763 average time/residue: 0.8442 time to fit residues: 1114.0241 Evaluate side-chains 725 residues out of total 5975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 686 time to evaluate : 6.093 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.6668 time to fit residues: 56.6570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 857 random chunks: chunk 751 optimal weight: 8.9990 chunk 791 optimal weight: 8.9990 chunk 721 optimal weight: 50.0000 chunk 769 optimal weight: 6.9990 chunk 463 optimal weight: 2.9990 chunk 335 optimal weight: 0.3980 chunk 604 optimal weight: 10.0000 chunk 236 optimal weight: 0.8980 chunk 695 optimal weight: 0.5980 chunk 728 optimal weight: 40.0000 chunk 767 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 50 GLN Q 73 GLN ** Q 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 10 ASN ** 7 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 49 ASN ** 7 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 84 ASN ** b 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 20 HIS ** f 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 397 ASN ** t 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 175 ASN ** y 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 73 HIS z 132 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 96776 Z= 0.172 Angle : 0.619 15.410 138381 Z= 0.312 Chirality : 0.037 0.360 16877 Planarity : 0.004 0.067 11636 Dihedral : 15.249 179.732 27160 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.20 % Favored : 94.74 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.06 % Twisted Proline : 0.37 % Twisted General : 0.02 % 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: -0.11 (0.10), residues: 6729 helix: 1.02 (0.10), residues: 2759 sheet: -0.24 (0.16), residues: 950 loop : -1.01 (0.11), residues: 3020 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13458 Ramachandran restraints generated. 6729 Oldfield, 0 Emsley, 6729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13458 Ramachandran restraints generated. 6729 Oldfield, 0 Emsley, 6729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 790 residues out of total 5975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 761 time to evaluate : 6.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 10 residues processed: 774 average time/residue: 0.8315 time to fit residues: 1116.5715 Evaluate side-chains 719 residues out of total 5975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 709 time to evaluate : 6.072 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.6786 time to fit residues: 20.1982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.9948 > 50: distance: 32 - 48: 28.591 distance: 37 - 57: 12.717 distance: 45 - 48: 25.185 distance: 48 - 49: 28.322 distance: 49 - 50: 29.017 distance: 49 - 52: 23.466 distance: 50 - 51: 28.595 distance: 50 - 57: 22.749 distance: 52 - 53: 35.386 distance: 53 - 54: 32.381 distance: 54 - 55: 17.762 distance: 55 - 56: 15.660 distance: 57 - 58: 5.937 distance: 58 - 59: 16.125 distance: 58 - 61: 15.092 distance: 59 - 60: 15.607 distance: 59 - 66: 38.824 distance: 61 - 62: 20.288 distance: 62 - 63: 5.083 distance: 63 - 64: 17.696 distance: 64 - 65: 28.377 distance: 66 - 67: 41.560 distance: 67 - 68: 19.720 distance: 67 - 70: 21.489 distance: 68 - 69: 39.167 distance: 68 - 73: 30.524 distance: 73 - 74: 17.347 distance: 73 - 79: 15.864 distance: 74 - 75: 18.740 distance: 74 - 77: 11.737 distance: 75 - 76: 24.937 distance: 75 - 80: 16.829 distance: 77 - 78: 5.672 distance: 80 - 81: 5.942 distance: 81 - 82: 11.899 distance: 81 - 84: 11.439 distance: 82 - 83: 29.169 distance: 82 - 88: 17.380 distance: 83 - 108: 55.217 distance: 84 - 85: 15.227 distance: 85 - 86: 7.379 distance: 85 - 87: 17.386 distance: 88 - 89: 25.754 distance: 89 - 90: 4.175 distance: 89 - 92: 21.448 distance: 90 - 91: 9.819 distance: 93 - 94: 17.644 distance: 94 - 95: 18.178 distance: 94 - 97: 13.444 distance: 95 - 96: 18.182 distance: 95 - 101: 19.535 distance: 97 - 98: 3.085 distance: 98 - 100: 4.285 distance: 101 - 102: 24.698 distance: 102 - 103: 32.696 distance: 102 - 105: 45.340 distance: 103 - 104: 15.599 distance: 103 - 108: 30.161 distance: 105 - 106: 17.495 distance: 105 - 107: 13.715 distance: 108 - 109: 5.218 distance: 109 - 110: 26.894 distance: 109 - 112: 5.720 distance: 110 - 111: 11.566 distance: 110 - 116: 13.340 distance: 111 - 138: 21.185 distance: 112 - 114: 40.390 distance: 113 - 115: 39.351 distance: 116 - 117: 24.723 distance: 117 - 118: 27.423 distance: 117 - 120: 12.046 distance: 118 - 119: 27.671 distance: 118 - 121: 12.730 distance: 119 - 147: 20.071