Starting phenix.real_space_refine (version: dev) on Mon Dec 19 03:08:02 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc4_4496/12_2022/6qc4_4496_updated_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc4_4496/12_2022/6qc4_4496.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc4_4496/12_2022/6qc4_4496_updated_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc4_4496/12_2022/6qc4_4496_updated_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc4_4496/12_2022/6qc4_4496_updated_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc4_4496/12_2022/6qc4_4496.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc4_4496/12_2022/6qc4_4496.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc4_4496/12_2022/6qc4_4496_updated_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc4_4496/12_2022/6qc4_4496_updated_updated.pdb" } resolution = 4.6 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= 0.018 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 "a1 TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a1 PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a2 ARG 240": "NH1" <-> "NH2" Residue "a2 PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b1 PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c1 ARG 237": "NH1" <-> "NH2" Residue "d1 ARG 48": "NH1" <-> "NH2" Residue "q1 ARG 2": "NH1" <-> "NH2" Residue "h1 ARG 34": "NH1" <-> "NH2" Residue "a3 PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a4 ARG 240": "NH1" <-> "NH2" Residue "b2 TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b2 ARG 313": "NH1" <-> "NH2" Residue "c2 ARG 139": "NH1" <-> "NH2" Residue "d2 TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h2 PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D1 TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D1 ARG 195": "NH1" <-> "NH2" Residue "D1 TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D6 PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D6 ARG 173": "NH1" <-> "NH2" Residue "D5 TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D5 TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D5 PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D5 TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D4 TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AK ARG 19": "NH1" <-> "NH2" Residue "B5 ARG 26": "NH1" <-> "NH2" Residue "AJ ARG 95": "NH1" <-> "NH2" Residue "AJ PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AJ TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AJ ARG 305": "NH1" <-> "NH2" Residue "A3 ARG 46": "NH1" <-> "NH2" Residue "A3 TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C2 ARG 5": "NH1" <-> "NH2" Residue "C2 ARG 120": "NH1" <-> "NH2" Residue "B4 ARG 41": "NH1" <-> "NH2" Residue "AM ARG 26": "NH1" <-> "NH2" Residue "AM ARG 27": "NH1" <-> "NH2" Residue "AM ARG 81": "NH1" <-> "NH2" Residue "B9 ARG 92": "NH1" <-> "NH2" Residue "B9 ARG 128": "NH1" <-> "NH2" Residue "B9 ARG 176": "NH1" <-> "NH2" Residue "B8 ARG 70": "NH1" <-> "NH2" Residue "BK TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A1 ARG 25": "NH1" <-> "NH2" Residue "V1 ARG 32": "NH1" <-> "NH2" Residue "V1 ARG 237": "NH1" <-> "NH2" Residue "V1 ARG 423": "NH1" <-> "NH2" Residue "V2 ARG 187": "NH1" <-> "NH2" Residue "V2 PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V2 PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S2 TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S2 TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S3 PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S7 ARG 174": "NH1" <-> "NH2" Residue "S7 ARG 178": "NH1" <-> "NH2" Residue "V3 PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S4 ARG 64": "NH1" <-> "NH2" Residue "A9 ARG 97": "NH1" <-> "NH2" Residue "A9 ARG 292": "NH1" <-> "NH2" Residue "A2 ARG 33": "NH1" <-> "NH2" Residue "A6 ARG 22": "NH1" <-> "NH2" Residue "AL ARG 106": "NH1" <-> "NH2" Residue "AA TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.21s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 96705 Number of models: 1 Model: "" Number of chains: 81 Chain: "a1" Number of atoms: 3409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3409 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 18, 'TRANS': 420} Chain breaks: 1 Chain: "a2" Number of atoms: 3126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3126 Classifications: {'peptide': 414} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 399} Chain breaks: 1 Chain: "b1" Number of atoms: 3019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3019 Classifications: {'peptide': 378} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 353} Chain: "c1" Number of atoms: 1902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1902 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 21, 'TRANS': 216} Chain: "f1" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1520 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "d1" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 886 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "q1" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 618 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 5, 'TRANS': 67} Chain: "h1" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "x1" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 164 Classifications: {'peptide': 33} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 32} Link IDs: {'TRANS': 32} Chain breaks: 1 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 33} Unresolved non-hydrogen planarities: 33 Chain: "i1" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 459 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "a3" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3447 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 18, 'TRANS': 425} Chain: "a4" Number of atoms: 3122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3122 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 398} Chain breaks: 1 Chain: "b2" Number of atoms: 3019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3019 Classifications: {'peptide': 378} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 353} Chain: "c2" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1903 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 22, 'TRANS': 215} Chain: "f2" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1514 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "d2" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 888 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "q2" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 631 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 6, 'TRANS': 68} Chain: "h2" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "x2" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 150 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'TRANS': 29} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'UNK:plan-1': 30} Unresolved non-hydrogen planarities: 30 Chain: "i2" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 473 Classifications: {'peptide': 57} Link IDs: {'TRANS': 56} Chain: "D3" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 719 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 4, 'TRANS': 84} Chain breaks: 1 Chain: "D1" Number of atoms: 2372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2372 Classifications: {'peptide': 298} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 18, 'TRANS': 275} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "D6" Number of atoms: 1308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1308 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 3, 'TRANS': 164} Chain breaks: 1 Chain: "4L" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 748 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 96} Chain: "D5" Number of atoms: 4805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4805 Classifications: {'peptide': 606} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 26, 'TRANS': 578} Chain: "D4" Number of atoms: 3646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3646 Classifications: {'peptide': 459} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 437} Chain: "D2" Number of atoms: 2724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2724 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 326} Chain: "AK" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1025 Classifications: {'peptide': 140} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 4, 'TRANS': 132} Chain: "B5" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1156 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 128} Chain: "AB" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 702 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain: "A8" Number of atoms: 1404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1404 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 12, 'TRANS': 156} Chain: "BJ" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1441 Classifications: {'peptide': 171} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 159} Chain: "AJ" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2583 Classifications: {'peptide': 319} Link IDs: {'CIS': 6, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 298} Chain: "S5" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 822 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "A3" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 582 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 62} Chain: "B3" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 578 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "C2" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 997 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 10, 'TRANS': 106} Chain: "B4" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1059 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 117} Chain: "AM" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1143 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 131} Chain: "B6" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 809 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 83} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B7" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1026 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain: "B9" Number of atoms: 1515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1515 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 16, 'TRANS': 159} Chain: "B2" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 560 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 56} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B8" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1324 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 135} Chain: "BK" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 853 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 93} Chain: "C1" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 391 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 3, 'TRANS': 42} Chain: "B1" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 449 Classifications: {'peptide': 52} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 49} Chain: "A1" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 577 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "V1" Number of atoms: 3312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3312 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 21, 'TRANS': 408} Chain: "V2" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1647 Classifications: {'peptide': 212} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 189} Chain: "S1" Number of atoms: 5275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5275 Classifications: {'peptide': 688} Link IDs: {'CIS': 3, 'PTRANS': 32, 'TRANS': 652} Chain: "S2" Number of atoms: 3435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3435 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 28, 'TRANS': 397} Chain breaks: 1 Chain: "S3" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1726 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "S7" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1247 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 145} Chain: "S8" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1414 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 10, 'TRANS': 165} Chain: "V3" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 345 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 3, 'TRANS': 37} Chain: "S6" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 737 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "S4" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1024 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "A9" Number of atoms: 2270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2270 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 14, 'TRANS': 273} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "A2" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 665 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "A5" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 901 Classifications: {'peptide': 111} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 101} Chain: "A6" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 969 Classifications: {'peptide': 114} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 106} Chain: "A7" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 757 Classifications: {'peptide': 95} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 82} Chain breaks: 1 Chain: "AL" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1209 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 11, 'TRANS': 133} Chain: "AA" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 645 Classifications: {'peptide': 80} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 76} Chain: "b1" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'HEM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "c1" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "f1" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "b2" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'HEM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "c2" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "f2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "D2" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Chain: "AB" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Chain: "V1" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "S1" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "S7" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "S8" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A9" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "AA" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12551 SG CYSf1 139 141.520 103.554 62.505 1.00270.83 S ATOM 12687 SG CYSf1 158 143.456 100.990 64.582 1.00262.63 S ATOM 28215 SG CYSf2 139 205.407 116.051 52.768 1.00223.66 S ATOM 28351 SG CYSf2 158 203.301 118.387 50.399 1.00222.21 S ATOM 71347 SG CYSV1 365 47.597 162.906 213.911 1.00 81.19 S ATOM 71671 SG CYSV1 405 48.809 165.142 220.032 1.00108.04 S ATOM 71327 SG CYSV1 362 53.295 163.064 215.690 1.00101.38 S ATOM 71308 SG CYSV1 359 50.228 168.872 215.050 1.00 92.81 S ATOM 72748 SG CYSV2 103 29.232 172.817 220.497 1.00146.77 S ATOM 72782 SG CYSV2 108 26.541 170.337 222.396 1.00120.66 S ATOM 73062 SG CYSV2 144 33.184 171.410 223.681 1.00142.78 S ATOM 73085 SG CYSV2 148 30.892 169.745 226.143 1.00171.97 S ATOM 74417 SG CYSS1 114 59.992 156.694 196.068 1.00 58.45 S ATOM 74356 SG CYSS1 105 55.466 154.434 192.395 1.00 57.78 S ATOM 74377 SG CYSS1 108 58.037 160.236 190.863 1.00 54.84 S ATOM 74749 SG CYSS1 156 59.938 165.779 203.229 1.00 63.53 S ATOM 74726 SG CYSS1 153 54.237 167.832 200.245 1.00 77.65 S ATOM 74773 SG CYSS1 159 59.279 171.784 201.095 1.00 78.80 S ATOM 75103 SG CYSS1 203 59.936 166.770 197.058 1.00 80.73 S ATOM 73862 SG CYSS1 41 61.487 163.375 209.927 1.00 67.47 S ATOM 73948 SG CYSS1 52 61.150 159.339 209.507 1.00 77.16 S ATOM 73973 SG CYSS1 55 63.240 158.569 214.210 1.00 93.93 S ATOM 74074 SG CYSS1 69 63.920 162.351 214.844 1.00 95.68 S ATOM 84780 SG CYSS7 119 70.738 131.400 168.557 1.00 64.39 S ATOM 85010 SG CYSS7 149 64.964 132.169 170.738 1.00 67.07 S ATOM 84282 SG CYSS7 55 65.974 128.600 165.152 1.00 97.79 S ATOM 84276 SG CYSS7 54 67.244 126.157 170.844 1.00 91.85 S ATOM 86228 SG CYSS8 119 61.910 137.821 176.771 1.00 57.90 S ATOM 86202 SG CYSS8 116 61.189 139.730 170.723 1.00 54.36 S ATOM 86249 SG CYSS8 122 57.922 142.837 175.269 1.00 58.18 S ATOM 85976 SG CYSS8 87 64.488 143.381 175.073 1.00 42.79 S ATOM 86278 SG CYSS8 126 52.974 148.817 178.578 1.00 49.14 S ATOM 85949 SG CYSS8 83 59.355 149.104 176.995 1.00 51.64 S ATOM 85907 SG CYSS8 77 55.461 154.187 175.848 1.00 62.46 S ATOM 85926 SG CYSS8 80 56.787 152.336 182.070 1.00 60.10 S ATOM 87499 SG CYSS6 59 40.901 158.436 183.827 1.00 58.75 S ATOM 87677 SG CYSS6 84 44.578 160.110 183.851 1.00 58.14 S ATOM 87699 SG CYSS6 87 42.103 158.343 181.463 1.00 60.26 S Time building chain proxies: 38.51, per 1000 atoms: 0.40 Number of scatterers: 96705 At special positions: 0 Unit cell: (249.2, 224, 270.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 38 26.01 S 627 16.00 P 7 15.00 O 17424 8.00 N 16441 7.00 C 62167 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYSf1 144 " - pdb=" SG CYSf1 160 " distance=2.03 Simple disulfide: pdb=" SG CYSh1 24 " - pdb=" SG CYSh1 68 " distance=2.04 Simple disulfide: pdb=" SG CYSh1 40 " - pdb=" SG CYSh1 54 " distance=2.03 Simple disulfide: pdb=" SG CYSf2 144 " - pdb=" SG CYSf2 160 " distance=2.03 Simple disulfide: pdb=" SG CYSh2 24 " - pdb=" SG CYSh2 68 " distance=2.03 Simple disulfide: pdb=" SG CYSh2 40 " - pdb=" SG CYSh2 54 " distance=2.03 Simple disulfide: pdb=" SG CYSAK 17 " - pdb=" SG CYSAK 74 " distance=2.02 Simple disulfide: pdb=" SG CYSAK 94 " - pdb=" SG CYSAK 114 " distance=2.03 Simple disulfide: pdb=" SG CYSA8 35 " - pdb=" SG CYSA8 65 " distance=2.04 Simple disulfide: pdb=" SG CYSA8 45 " - pdb=" SG CYSA8 55 " distance=2.04 Simple disulfide: pdb=" SG CYSA8 77 " - pdb=" SG CYSA8 109 " distance=2.03 Simple disulfide: pdb=" SG CYSA8 87 " - pdb=" SG CYSA8 99 " distance=2.03 Simple disulfide: pdb=" SG CYSBJ 76 " - pdb=" SG CYSBJ 83 " distance=2.04 Simple disulfide: pdb=" SG CYSBJ 112 " - pdb=" SG CYSBJ 124 " distance=2.04 Simple disulfide: pdb=" SG CYSS5 32 " - pdb=" SG CYSS5 65 " distance=2.04 Simple disulfide: pdb=" SG CYSS5 42 " - pdb=" SG CYSS5 55 " distance=2.04 Simple disulfide: pdb=" SG CYSB7 58 " - pdb=" SG CYSB7 89 " distance=2.03 Simple disulfide: pdb=" SG CYSB7 68 " - pdb=" SG CYSB7 79 " distance=2.03 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 29.47 Conformation dependent library (CDL) restraints added in 11.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FESS1 803 " pdb=" FE1 FESS1 803 " - pdb=" SG CYSS1 52 " pdb=" FE1 FESS1 803 " - pdb=" SG CYSS1 41 " pdb=" FE2 FESS1 803 " - pdb=" SG CYSS1 55 " pdb=" FE2 FESS1 803 " - pdb=" SG CYSS1 69 " pdb=" FESV2 300 " pdb=" FE1 FESV2 300 " - pdb=" SG CYSV2 103 " pdb=" FE2 FESV2 300 " - pdb=" SG CYSV2 148 " pdb=" FE2 FESV2 300 " - pdb=" SG CYSV2 144 " pdb=" FE1 FESV2 300 " - pdb=" SG CYSV2 108 " pdb=" FESf1 501 " pdb=" FE1 FESf1 501 " - pdb=" SG CYSf1 158 " pdb=" FE1 FESf1 501 " - pdb=" SG CYSf1 139 " pdb=" FE2 FESf1 501 " - pdb=" ND1 HISf1 141 " pdb=" FE2 FESf1 501 " - pdb=" ND1 HISf1 161 " pdb=" FESf2 501 " pdb=" FE2 FESf2 501 " - pdb=" ND1 HISf2 141 " pdb=" FE2 FESf2 501 " - pdb=" ND1 HISf2 161 " pdb=" FE1 FESf2 501 " - pdb=" SG CYSf2 158 " pdb=" FE1 FESf2 501 " - pdb=" SG CYSf2 139 " pdb=" SF4S1 801 " pdb=" FE3 SF4S1 801 " - pdb=" NE2 HISS1 101 " pdb=" FE4 SF4S1 801 " - pdb=" SG CYSS1 108 " pdb=" FE2 SF4S1 801 " - pdb=" SG CYSS1 105 " pdb=" FE1 SF4S1 801 " - pdb=" SG CYSS1 114 " pdb=" SF4S1 802 " pdb=" FE1 SF4S1 802 " - pdb=" SG CYSS1 156 " pdb=" FE3 SF4S1 802 " - pdb=" SG CYSS1 159 " pdb=" FE2 SF4S1 802 " - pdb=" SG CYSS1 153 " pdb=" FE4 SF4S1 802 " - pdb=" SG CYSS1 203 " pdb=" SF4S7 300 " pdb=" FE1 SF4S7 300 " - pdb=" SG CYSS7 119 " pdb=" FE4 SF4S7 300 " - pdb=" SG CYSS7 54 " pdb=" FE3 SF4S7 300 " - pdb=" SG CYSS7 55 " pdb=" FE2 SF4S7 300 " - pdb=" SG CYSS7 149 " pdb=" SF4S8 201 " pdb=" FE1 SF4S8 201 " - pdb=" SG CYSS8 119 " pdb=" FE2 SF4S8 201 " - pdb=" SG CYSS8 116 " pdb=" FE3 SF4S8 201 " - pdb=" SG CYSS8 122 " pdb=" FE4 SF4S8 201 " - pdb=" SG CYSS8 87 " pdb=" SF4S8 202 " pdb=" FE4 SF4S8 202 " - pdb=" SG CYSS8 80 " pdb=" FE3 SF4S8 202 " - pdb=" SG CYSS8 77 " pdb=" FE1 SF4S8 202 " - pdb=" SG CYSS8 126 " pdb=" FE2 SF4S8 202 " - pdb=" SG CYSS8 83 " pdb=" SF4V1 500 " pdb=" FE1 SF4V1 500 " - pdb=" SG CYSV1 365 " pdb=" FE2 SF4V1 500 " - pdb=" SG CYSV1 405 " pdb=" FE4 SF4V1 500 " - pdb=" SG CYSV1 359 " pdb=" FE3 SF4V1 500 " - pdb=" SG CYSV1 362 " Number of angles added : 87 Zn2+ tetrahedral coordination pdb=" ZNS6 300 " pdb="ZN ZNS6 300 " - pdb=" NE2 HISS6 68 " pdb="ZN ZNS6 300 " - pdb=" SG CYSS6 59 " pdb="ZN ZNS6 300 " - pdb=" SG CYSS6 87 " pdb="ZN ZNS6 300 " - pdb=" SG CYSS6 84 " Number of angles added : 3 23712 Ramachandran restraints generated. 11856 Oldfield, 0 Emsley, 11856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 22666 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 471 helices and 40 sheets defined 49.1% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.63 Creating SS restraints... Processing helix chain 'a1' and resid 4 through 9 Processing helix chain 'a1' and resid 55 through 64 removed outlier: 5.250A pdb=" N PHEa1 64 " --> pdb=" O GLUa1 60 " (cutoff:3.500A) Processing helix chain 'a1' and resid 74 through 82 Processing helix chain 'a1' and resid 106 through 118 Processing helix chain 'a1' and resid 124 through 141 Processing helix chain 'a1' and resid 145 through 157 Processing helix chain 'a1' and resid 162 through 164 No H-bonds generated for 'chain 'a1' and resid 162 through 164' Processing helix chain 'a1' and resid 171 through 176 removed outlier: 3.667A pdb=" N LYSa1 176 " --> pdb=" O GLUa1 172 " (cutoff:3.500A) Processing helix chain 'a1' and resid 179 through 188 Processing helix chain 'a1' and resid 205 through 215 Processing helix chain 'a1' and resid 266 through 276 Processing helix chain 'a1' and resid 293 through 301 Processing helix chain 'a1' and resid 332 through 347 Processing helix chain 'a1' and resid 352 through 368 Processing helix chain 'a1' and resid 373 through 385 Processing helix chain 'a1' and resid 392 through 400 Processing helix chain 'a1' and resid 404 through 414 Processing helix chain 'a1' and resid 434 through 441 Processing helix chain 'a2' and resid 55 through 57 No H-bonds generated for 'chain 'a2' and resid 55 through 57' Processing helix chain 'a2' and resid 60 through 62 No H-bonds generated for 'chain 'a2' and resid 60 through 62' Processing helix chain 'a2' and resid 65 through 70 Processing helix chain 'a2' and resid 72 through 74 No H-bonds generated for 'chain 'a2' and resid 72 through 74' Processing helix chain 'a2' and resid 82 through 92 Processing helix chain 'a2' and resid 116 through 128 Processing helix chain 'a2' and resid 134 through 152 Processing helix chain 'a2' and resid 155 through 167 Processing helix chain 'a2' and resid 171 through 173 No H-bonds generated for 'chain 'a2' and resid 171 through 173' Processing helix chain 'a2' and resid 188 through 198 Processing helix chain 'a2' and resid 201 through 203 No H-bonds generated for 'chain 'a2' and resid 201 through 203' Processing helix chain 'a2' and resid 213 through 223 Processing helix chain 'a2' and resid 267 through 279 Processing helix chain 'a2' and resid 294 through 302 Processing helix chain 'a2' and resid 334 through 348 Processing helix chain 'a2' and resid 354 through 370 Processing helix chain 'a2' and resid 375 through 389 Processing helix chain 'a2' and resid 395 through 403 Processing helix chain 'a2' and resid 407 through 419 Processing helix chain 'b1' and resid 4 through 6 No H-bonds generated for 'chain 'b1' and resid 4 through 6' Processing helix chain 'b1' and resid 9 through 18 Processing helix chain 'b1' and resid 29 through 31 No H-bonds generated for 'chain 'b1' and resid 29 through 31' Processing helix chain 'b1' and resid 33 through 54 Processing helix chain 'b1' and resid 62 through 71 Processing helix chain 'b1' and resid 76 through 103 Processing helix chain 'b1' and resid 106 through 108 No H-bonds generated for 'chain 'b1' and resid 106 through 108' Processing helix chain 'b1' and resid 110 through 133 Processing helix chain 'b1' and resid 137 through 152 Processing helix chain 'b1' and resid 157 through 165 Processing helix chain 'b1' and resid 172 through 203 Proline residue: b1 186 - end of helix Processing helix chain 'b1' and resid 223 through 244 Processing helix chain 'b1' and resid 254 through 256 No H-bonds generated for 'chain 'b1' and resid 254 through 256' Processing helix chain 'b1' and resid 272 through 282 removed outlier: 4.391A pdb=" N PHEb1 276 " --> pdb=" O TRPb1 272 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ALAb1 277 " --> pdb=" O TYRb1 273 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILEb1 280 " --> pdb=" O PHEb1 276 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEUb1 281 " --> pdb=" O ALAb1 277 " (cutoff:3.500A) Processing helix chain 'b1' and resid 287 through 307 Proline residue: b1 305 - end of helix Processing helix chain 'b1' and resid 319 through 339 Processing helix chain 'b1' and resid 345 through 377 removed outlier: 4.282A pdb=" N METb1 366 " --> pdb=" O ILEb1 362 " (cutoff:3.500A) Proline residue: b1 367 - end of helix removed outlier: 3.759A pdb=" N LEUb1 377 " --> pdb=" O GLUb1 373 " (cutoff:3.500A) Processing helix chain 'c1' and resid 23 through 35 Processing helix chain 'c1' and resid 37 through 39 No H-bonds generated for 'chain 'c1' and resid 37 through 39' Processing helix chain 'c1' and resid 48 through 50 No H-bonds generated for 'chain 'c1' and resid 48 through 50' Processing helix chain 'c1' and resid 58 through 67 Processing helix chain 'c1' and resid 98 through 103 Processing helix chain 'c1' and resid 117 through 119 No H-bonds generated for 'chain 'c1' and resid 117 through 119' Processing helix chain 'c1' and resid 124 through 132 Processing helix chain 'c1' and resid 178 through 193 Processing helix chain 'c1' and resid 197 through 225 Proline residue: c1 216 - end of helix removed outlier: 3.645A pdb=" N TYRc1 219 " --> pdb=" O LEUc1 215 " (cutoff:3.500A) Processing helix chain 'f1' and resid 16 through 18 No H-bonds generated for 'chain 'f1' and resid 16 through 18' Processing helix chain 'f1' and resid 25 through 27 No H-bonds generated for 'chain 'f1' and resid 25 through 27' Processing helix chain 'f1' and resid 29 through 61 Processing helix chain 'f1' and resid 103 through 111 Processing helix chain 'f1' and resid 123 through 125 No H-bonds generated for 'chain 'f1' and resid 123 through 125' Processing helix chain 'd1' and resid 12 through 24 Processing helix chain 'd1' and resid 41 through 48 Processing helix chain 'd1' and resid 52 through 70 Processing helix chain 'd1' and resid 77 through 79 No H-bonds generated for 'chain 'd1' and resid 77 through 79' Processing helix chain 'd1' and resid 90 through 109 Processing helix chain 'q1' and resid 30 through 69 removed outlier: 4.001A pdb=" N ILEq1 34 " --> pdb=" O PHEq1 30 " (cutoff:3.500A) Proline residue: q1 35 - end of helix removed outlier: 3.834A pdb=" N CYSq1 44 " --> pdb=" O ARGq1 40 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LEUq1 46 " --> pdb=" O ARGq1 42 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ARGq1 47 " --> pdb=" O ALAq1 43 " (cutoff:3.500A) Proline residue: q1 50 - end of helix Processing helix chain 'h1' and resid 16 through 24 Processing helix chain 'h1' and resid 28 through 46 Processing helix chain 'h1' and resid 56 through 72 Processing helix chain 'i1' and resid 7 through 13 Processing helix chain 'i1' and resid 17 through 45 Processing helix chain 'i1' and resid 52 through 57 Processing helix chain 'a3' and resid 4 through 9 Processing helix chain 'a3' and resid 55 through 62 Processing helix chain 'a3' and resid 74 through 82 Processing helix chain 'a3' and resid 106 through 118 Processing helix chain 'a3' and resid 125 through 141 Processing helix chain 'a3' and resid 145 through 157 Processing helix chain 'a3' and resid 162 through 164 No H-bonds generated for 'chain 'a3' and resid 162 through 164' Processing helix chain 'a3' and resid 171 through 176 removed outlier: 3.759A pdb=" N LYSa3 176 " --> pdb=" O GLUa3 172 " (cutoff:3.500A) Processing helix chain 'a3' and resid 179 through 188 Processing helix chain 'a3' and resid 192 through 194 No H-bonds generated for 'chain 'a3' and resid 192 through 194' Processing helix chain 'a3' and resid 205 through 214 Processing helix chain 'a3' and resid 266 through 276 Processing helix chain 'a3' and resid 287 through 289 No H-bonds generated for 'chain 'a3' and resid 287 through 289' Processing helix chain 'a3' and resid 293 through 300 Processing helix chain 'a3' and resid 331 through 347 Processing helix chain 'a3' and resid 351 through 368 Processing helix chain 'a3' and resid 372 through 383 Processing helix chain 'a3' and resid 392 through 400 Processing helix chain 'a3' and resid 404 through 414 Processing helix chain 'a3' and resid 434 through 441 Processing helix chain 'a4' and resid 55 through 57 No H-bonds generated for 'chain 'a4' and resid 55 through 57' Processing helix chain 'a4' and resid 60 through 62 No H-bonds generated for 'chain 'a4' and resid 60 through 62' Processing helix chain 'a4' and resid 65 through 70 Processing helix chain 'a4' and resid 72 through 74 No H-bonds generated for 'chain 'a4' and resid 72 through 74' Processing helix chain 'a4' and resid 82 through 92 Processing helix chain 'a4' and resid 113 through 128 removed outlier: 4.196A pdb=" N VALa4 116 " --> pdb=" O ARGa4 113 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ASPa4 117 " --> pdb=" O ASPa4 114 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILEa4 118 " --> pdb=" O ASPa4 115 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEUa4 119 " --> pdb=" O VALa4 116 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THRa4 128 " --> pdb=" O ASNa4 125 " (cutoff:3.500A) Processing helix chain 'a4' and resid 134 through 153 Processing helix chain 'a4' and resid 155 through 167 Processing helix chain 'a4' and resid 171 through 173 No H-bonds generated for 'chain 'a4' and resid 171 through 173' Processing helix chain 'a4' and resid 188 through 198 Processing helix chain 'a4' and resid 213 through 222 Processing helix chain 'a4' and resid 267 through 279 Processing helix chain 'a4' and resid 294 through 302 Processing helix chain 'a4' and resid 334 through 348 Processing helix chain 'a4' and resid 354 through 372 removed outlier: 3.962A pdb=" N VALa4 372 " --> pdb=" O TYRa4 368 " (cutoff:3.500A) Processing helix chain 'a4' and resid 375 through 388 Processing helix chain 'a4' and resid 395 through 403 Processing helix chain 'a4' and resid 407 through 419 Processing helix chain 'b2' and resid 4 through 7 No H-bonds generated for 'chain 'b2' and resid 4 through 7' Processing helix chain 'b2' and resid 9 through 17 removed outlier: 3.649A pdb=" N ILEb2 13 " --> pdb=" O PROb2 9 " (cutoff:3.500A) Processing helix chain 'b2' and resid 29 through 52 removed outlier: 3.826A pdb=" N PHEb2 33 " --> pdb=" O TRPb2 30 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLYb2 34 " --> pdb=" O TRPb2 31 " (cutoff:3.500A) Processing helix chain 'b2' and resid 62 through 71 Processing helix chain 'b2' and resid 76 through 103 Processing helix chain 'b2' and resid 110 through 132 Processing helix chain 'b2' and resid 137 through 152 Processing helix chain 'b2' and resid 157 through 164 Processing helix chain 'b2' and resid 172 through 203 Proline residue: b2 186 - end of helix Processing helix chain 'b2' and resid 223 through 244 Processing helix chain 'b2' and resid 253 through 256 Processing helix chain 'b2' and resid 272 through 281 removed outlier: 3.510A pdb=" N LEUb2 275 " --> pdb=" O TRPb2 272 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N PHEb2 276 " --> pdb=" O TYRb2 273 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TYRb2 278 " --> pdb=" O LEUb2 275 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALAb2 279 " --> pdb=" O PHEb2 276 " (cutoff:3.500A) Processing helix chain 'b2' and resid 287 through 302 Processing helix chain 'b2' and resid 305 through 307 No H-bonds generated for 'chain 'b2' and resid 305 through 307' Processing helix chain 'b2' and resid 319 through 339 Processing helix chain 'b2' and resid 345 through 363 Processing helix chain 'b2' and resid 365 through 377 removed outlier: 4.301A pdb=" N LEUb2 377 " --> pdb=" O GLUb2 373 " (cutoff:3.500A) Processing helix chain 'c2' and resid 23 through 35 Processing helix chain 'c2' and resid 48 through 50 No H-bonds generated for 'chain 'c2' and resid 48 through 50' Processing helix chain 'c2' and resid 58 through 66 Processing helix chain 'c2' and resid 98 through 104 Processing helix chain 'c2' and resid 124 through 132 Processing helix chain 'c2' and resid 179 through 193 Processing helix chain 'c2' and resid 197 through 213 Processing helix chain 'c2' and resid 215 through 225 Processing helix chain 'f2' and resid 16 through 18 No H-bonds generated for 'chain 'f2' and resid 16 through 18' Processing helix chain 'f2' and resid 27 through 63 removed outlier: 4.322A pdb=" N ALAf2 31 " --> pdb=" O GLUf2 27 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARGf2 32 " --> pdb=" O SERf2 28 " (cutoff:3.500A) Processing helix chain 'f2' and resid 66 through 69 Processing helix chain 'f2' and resid 103 through 110 Processing helix chain 'd2' and resid 11 through 24 Processing helix chain 'd2' and resid 26 through 29 Processing helix chain 'd2' and resid 33 through 35 No H-bonds generated for 'chain 'd2' and resid 33 through 35' Processing helix chain 'd2' and resid 41 through 48 Processing helix chain 'd2' and resid 52 through 70 Processing helix chain 'd2' and resid 77 through 79 No H-bonds generated for 'chain 'd2' and resid 77 through 79' Processing helix chain 'd2' and resid 90 through 108 Processing helix chain 'q2' and resid 33 through 42 Processing helix chain 'q2' and resid 45 through 70 Proline residue: q2 50 - end of helix removed outlier: 3.616A pdb=" N VALq2 53 " --> pdb=" O ALAq2 49 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VALq2 54 " --> pdb=" O PROq2 50 " (cutoff:3.500A) Processing helix chain 'h2' and resid 16 through 24 Processing helix chain 'h2' and resid 29 through 45 Processing helix chain 'h2' and resid 56 through 72 removed outlier: 3.752A pdb=" N LYSh2 72 " --> pdb=" O CYSh2 68 " (cutoff:3.500A) Processing helix chain 'h2' and resid 74 through 76 No H-bonds generated for 'chain 'h2' and resid 74 through 76' Processing helix chain 'x2' and resid 4 through 6 No H-bonds generated for 'chain 'x2' and resid 4 through 6' Processing helix chain 'i2' and resid 4 through 13 Processing helix chain 'i2' and resid 18 through 46 Processing helix chain 'i2' and resid 54 through 57 No H-bonds generated for 'chain 'i2' and resid 54 through 57' Processing helix chain 'D3' and resid 2 through 22 Processing helix chain 'D3' and resid 56 through 75 removed outlier: 3.694A pdb=" N ILED3 60 " --> pdb=" O PHED3 56 " (cutoff:3.500A) Proline residue: D3 74 - end of helix Processing helix chain 'D3' and resid 84 through 107 Processing helix chain 'D1' and resid 2 through 10 Processing helix chain 'D1' and resid 12 through 31 Processing helix chain 'D1' and resid 46 through 57 Processing helix chain 'D1' and resid 68 through 84 Proline residue: D1 75 - end of helix Processing helix chain 'D1' and resid 102 through 122 Processing helix chain 'D1' and resid 127 through 155 removed outlier: 4.889A pdb=" N TYRD1 142 " --> pdb=" O GLND1 138 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLUD1 143 " --> pdb=" O THRD1 139 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N VALD1 144 " --> pdb=" O ILED1 140 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N THRD1 145 " --> pdb=" O SERD1 141 " (cutoff:3.500A) Processing helix chain 'D1' and resid 163 through 170 removed outlier: 3.866A pdb=" N GLUD1 170 " --> pdb=" O ILED1 166 " (cutoff:3.500A) Processing helix chain 'D1' and resid 174 through 177 No H-bonds generated for 'chain 'D1' and resid 174 through 177' Processing helix chain 'D1' and resid 179 through 193 Processing helix chain 'D1' and resid 220 through 242 Processing helix chain 'D1' and resid 252 through 274 Processing helix chain 'D1' and resid 282 through 311 Proline residue: D1 295 - end of helix Proline residue: D1 308 - end of helix Processing helix chain 'D6' and resid 5 through 21 Processing helix chain 'D6' and resid 26 through 47 Processing helix chain 'D6' and resid 52 through 55 No H-bonds generated for 'chain 'D6' and resid 52 through 55' Processing helix chain 'D6' and resid 57 through 60 No H-bonds generated for 'chain 'D6' and resid 57 through 60' Processing helix chain 'D6' and resid 64 through 73 Processing helix chain 'D6' and resid 87 through 108 Processing helix chain 'D6' and resid 139 through 143 Processing helix chain 'D6' and resid 151 through 171 removed outlier: 3.644A pdb=" N ILED6 155 " --> pdb=" O THRD6 151 " (cutoff:3.500A) Processing helix chain '4L' and resid 3 through 20 Processing helix chain '4L' and resid 26 through 51 Processing helix chain '4L' and resid 59 through 84 Processing helix chain 'D5' and resid 2 through 23 removed outlier: 4.403A pdb=" N LEUD5 15 " --> pdb=" O THRD5 11 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THRD5 16 " --> pdb=" O LEUD5 12 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N METD5 17 " --> pdb=" O ILED5 13 " (cutoff:3.500A) Proline residue: D5 18 - end of helix Processing helix chain 'D5' and resid 32 through 57 removed outlier: 4.446A pdb=" N ILED5 49 " --> pdb=" O ILED5 45 " (cutoff:3.500A) Proline residue: D5 50 - end of helix Processing helix chain 'D5' and resid 84 through 107 removed outlier: 4.506A pdb=" N VALD5 90 " --> pdb=" O SERD5 86 " (cutoff:3.500A) Proline residue: D5 91 - end of helix Processing helix chain 'D5' and resid 114 through 133 Processing helix chain 'D5' and resid 137 through 157 Processing helix chain 'D5' and resid 162 through 192 Processing helix chain 'D5' and resid 198 through 203 Processing helix chain 'D5' and resid 210 through 223 Processing helix chain 'D5' and resid 232 through 237 Processing helix chain 'D5' and resid 241 through 248 Processing helix chain 'D5' and resid 255 through 262 removed outlier: 3.577A pdb=" N LEUD5 259 " --> pdb=" O ALAD5 255 " (cutoff:3.500A) Processing helix chain 'D5' and resid 264 through 267 No H-bonds generated for 'chain 'D5' and resid 264 through 267' Processing helix chain 'D5' and resid 271 through 292 Processing helix chain 'D5' and resid 298 through 318 Processing helix chain 'D5' and resid 322 through 350 Processing helix chain 'D5' and resid 367 through 379 Processing helix chain 'D5' and resid 387 through 400 removed outlier: 4.759A pdb=" N SERD5 391 " --> pdb=" O THRD5 387 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYSD5 392 " --> pdb=" O GLYD5 388 " (cutoff:3.500A) Processing helix chain 'D5' and resid 408 through 431 Processing helix chain 'D5' and resid 448 through 462 Processing helix chain 'D5' and resid 464 through 470 Processing helix chain 'D5' and resid 489 through 508 Processing helix chain 'D5' and resid 519 through 524 Processing helix chain 'D5' and resid 526 through 546 Proline residue: D5 530 - end of helix removed outlier: 3.641A pdb=" N METD5 533 " --> pdb=" O PROD5 530 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HISD5 534 " --> pdb=" O THRD5 531 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N THRD5 537 " --> pdb=" O HISD5 534 " (cutoff:3.500A) Proline residue: D5 538 - end of helix removed outlier: 3.972A pdb=" N ASND5 541 " --> pdb=" O PROD5 538 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEUD5 542 " --> pdb=" O TYRD5 539 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N METD5 544 " --> pdb=" O ASND5 541 " (cutoff:3.500A) Processing helix chain 'D5' and resid 555 through 577 Proline residue: D5 563 - end of helix removed outlier: 3.884A pdb=" N ILED5 566 " --> pdb=" O LEUD5 562 " (cutoff:3.500A) Processing helix chain 'D5' and resid 584 through 599 Processing helix chain 'D4' and resid 2 through 16 Proline residue: D4 7 - end of helix Proline residue: D4 13 - end of helix removed outlier: 4.353A pdb=" N TRPD4 16 " --> pdb=" O METD4 12 " (cutoff:3.500A) Processing helix chain 'D4' and resid 23 through 41 removed outlier: 4.002A pdb=" N LEUD4 41 " --> pdb=" O THRD4 37 " (cutoff:3.500A) Processing helix chain 'D4' and resid 60 through 79 Proline residue: D4 64 - end of helix Proline residue: D4 74 - end of helix Processing helix chain 'D4' and resid 89 through 110 Processing helix chain 'D4' and resid 115 through 135 Proline residue: D4 128 - end of helix removed outlier: 3.546A pdb=" N ILED4 131 " --> pdb=" O VALD4 127 " (cutoff:3.500A) Processing helix chain 'D4' and resid 142 through 156 Processing helix chain 'D4' and resid 158 through 171 removed outlier: 4.155A pdb=" N VALD4 162 " --> pdb=" O LEUD4 158 " (cutoff:3.500A) Processing helix chain 'D4' and resid 176 through 179 No H-bonds generated for 'chain 'D4' and resid 176 through 179' Processing helix chain 'D4' and resid 191 through 206 Processing helix chain 'D4' and resid 214 through 221 removed outlier: 4.149A pdb=" N LYSD4 218 " --> pdb=" O LEUD4 214 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALAD4 219 " --> pdb=" O TRPD4 215 " (cutoff:3.500A) Processing helix chain 'D4' and resid 225 through 248 removed outlier: 5.089A pdb=" N LEUD4 248 " --> pdb=" O METD4 244 " (cutoff:3.500A) Processing helix chain 'D4' and resid 251 through 257 removed outlier: 4.290A pdb=" N ASPD4 255 " --> pdb=" O ASND4 251 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N PHED4 256 " --> pdb=" O PROD4 252 " (cutoff:3.500A) Processing helix chain 'D4' and resid 259 through 277 removed outlier: 3.848A pdb=" N LEUD4 277 " --> pdb=" O SERD4 273 " (cutoff:3.500A) Processing helix chain 'D4' and resid 282 through 302 removed outlier: 3.556A pdb=" N ILED4 286 " --> pdb=" O LYSD4 283 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYRD4 288 " --> pdb=" O LEUD4 285 " (cutoff:3.500A) Processing helix chain 'D4' and resid 306 through 336 Processing helix chain 'D4' and resid 353 through 366 removed outlier: 3.778A pdb=" N ASND4 366 " --> pdb=" O SERD4 363 " (cutoff:3.500A) Processing helix chain 'D4' and resid 373 through 388 Processing helix chain 'D4' and resid 393 through 414 removed outlier: 4.520A pdb=" N THRD4 414 " --> pdb=" O METD4 410 " (cutoff:3.500A) Processing helix chain 'D4' and resid 431 through 449 Proline residue: D4 443 - end of helix Processing helix chain 'D4' and resid 451 through 453 No H-bonds generated for 'chain 'D4' and resid 451 through 453' Processing helix chain 'D2' and resid 3 through 22 Processing helix chain 'D2' and resid 26 through 43 Proline residue: D2 42 - end of helix Processing helix chain 'D2' and resid 50 through 79 Processing helix chain 'D2' and resid 92 through 106 Processing helix chain 'D2' and resid 115 through 120 Processing helix chain 'D2' and resid 124 through 148 Proline residue: D2 138 - end of helix removed outlier: 4.143A pdb=" N VALD2 141 " --> pdb=" O ALAD2 137 " (cutoff:3.500A) Proline residue: D2 147 - end of helix Processing helix chain 'D2' and resid 151 through 167 Processing helix chain 'D2' and resid 175 through 192 Processing helix chain 'D2' and resid 198 through 220 Processing helix chain 'D2' and resid 227 through 236 Processing helix chain 'D2' and resid 239 through 252 Processing helix chain 'D2' and resid 258 through 271 Proline residue: D2 262 - end of helix removed outlier: 4.096A pdb=" N METD2 265 " --> pdb=" O PROD2 262 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLUD2 269 " --> pdb=" O ILED2 266 " (cutoff:3.500A) Processing helix chain 'D2' and resid 277 through 300 removed outlier: 4.355A pdb=" N LEUD2 290 " --> pdb=" O ALAD2 286 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N TYRD2 291 " --> pdb=" O LEUD2 287 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N PHED2 292 " --> pdb=" O LEUD2 288 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N TYRD2 293 " --> pdb=" O ASND2 289 " (cutoff:3.500A) Processing helix chain 'D2' and resid 311 through 316 removed outlier: 4.004A pdb=" N GLND2 316 " --> pdb=" O LYSD2 312 " (cutoff:3.500A) Processing helix chain 'D2' and resid 327 through 334 Processing helix chain 'D2' and resid 341 through 345 removed outlier: 3.687A pdb=" N SERD2 344 " --> pdb=" O PROD2 341 " (cutoff:3.500A) Processing helix chain 'AK' and resid 2 through 10 Processing helix chain 'AK' and resid 19 through 41 Processing helix chain 'AK' and resid 48 through 80 Processing helix chain 'AK' and resid 87 through 104 Processing helix chain 'AK' and resid 107 through 130 Processing helix chain 'B5' and resid 16 through 31 Processing helix chain 'B5' and resid 34 through 46 Processing helix chain 'B5' and resid 70 through 78 Processing helix chain 'B5' and resid 83 through 117 Processing helix chain 'AB' and resid 8 through 20 Processing helix chain 'AB' and resid 44 through 58 Processing helix chain 'AB' and resid 64 through 67 No H-bonds generated for 'chain 'AB' and resid 64 through 67' Processing helix chain 'AB' and resid 73 through 84 Processing helix chain 'A8' and resid 21 through 26 Processing helix chain 'A8' and resid 28 through 33 Processing helix chain 'A8' and resid 39 through 48 Processing helix chain 'A8' and resid 56 through 75 Processing helix chain 'A8' and resid 80 through 88 Processing helix chain 'A8' and resid 100 through 113 Processing helix chain 'BJ' and resid 28 through 56 removed outlier: 5.236A pdb=" N ARGBJ 42 " --> pdb=" O LEUBJ 38 " (cutoff:3.500A) Proline residue: BJ 43 - end of helix Processing helix chain 'BJ' and resid 81 through 116 Processing helix chain 'BJ' and resid 125 through 141 Processing helix chain 'BJ' and resid 152 through 172 Processing helix chain 'AJ' and resid 5 through 10 Processing helix chain 'AJ' and resid 36 through 44 Processing helix chain 'AJ' and resid 58 through 61 No H-bonds generated for 'chain 'AJ' and resid 58 through 61' Processing helix chain 'AJ' and resid 71 through 74 No H-bonds generated for 'chain 'AJ' and resid 71 through 74' Processing helix chain 'AJ' and resid 79 through 84 Processing helix chain 'AJ' and resid 93 through 116 Processing helix chain 'AJ' and resid 128 through 140 Processing helix chain 'AJ' and resid 146 through 162 removed outlier: 4.737A pdb=" N CYSAJ 161 " --> pdb=" O LYSAJ 157 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N GLUAJ 162 " --> pdb=" O VALAJ 158 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 176 through 186 Processing helix chain 'AJ' and resid 189 through 192 No H-bonds generated for 'chain 'AJ' and resid 189 through 192' Processing helix chain 'AJ' and resid 196 through 208 Processing helix chain 'AJ' and resid 210 through 214 Processing helix chain 'AJ' and resid 232 through 239 Processing helix chain 'AJ' and resid 247 through 249 No H-bonds generated for 'chain 'AJ' and resid 247 through 249' Processing helix chain 'AJ' and resid 254 through 263 Processing helix chain 'AJ' and resid 286 through 298 Processing helix chain 'S5' and resid 5 through 8 No H-bonds generated for 'chain 'S5' and resid 5 through 8' Processing helix chain 'S5' and resid 33 through 42 Processing helix chain 'S5' and resid 50 through 54 Processing helix chain 'S5' and resid 56 through 67 Processing helix chain 'S5' and resid 69 through 88 Processing helix chain 'A3' and resid 16 through 33 Proline residue: A3 32 - end of helix Processing helix chain 'A3' and resid 38 through 46 Processing helix chain 'B3' and resid 26 through 38 Processing helix chain 'B3' and resid 62 through 69 removed outlier: 3.783A pdb=" N LEUB3 66 " --> pdb=" O PHEB3 62 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLYB3 69 " --> pdb=" O ALAB3 65 " (cutoff:3.500A) Processing helix chain 'B3' and resid 73 through 82 Processing helix chain 'C2' and resid 16 through 19 Processing helix chain 'C2' and resid 29 through 48 Processing helix chain 'C2' and resid 58 through 96 Processing helix chain 'B4' and resid 26 through 48 Processing helix chain 'B4' and resid 62 through 72 Processing helix chain 'B4' and resid 83 through 93 Processing helix chain 'B4' and resid 95 through 117 Processing helix chain 'AM' and resid 32 through 96 Proline residue: AM 72 - end of helix Processing helix chain 'AM' and resid 130 through 135 Processing helix chain 'AM' and resid 138 through 141 No H-bonds generated for 'chain 'AM' and resid 138 through 141' Processing helix chain 'B6' and resid 5 through 25 Processing helix chain 'B6' and resid 68 through 84 Proline residue: B6 77 - end of helix Processing helix chain 'B6' and resid 87 through 91 Processing helix chain 'B7' and resid 2 through 9 Processing helix chain 'B7' and resid 42 through 47 Processing helix chain 'B7' and resid 59 through 71 Processing helix chain 'B7' and resid 81 through 117 Processing helix chain 'B9' and resid 12 through 29 Processing helix chain 'B9' and resid 34 through 50 removed outlier: 4.412A pdb=" N HISB9 50 " --> pdb=" O ARGB9 46 " (cutoff:3.500A) Processing helix chain 'B9' and resid 57 through 72 Processing helix chain 'B9' and resid 94 through 96 No H-bonds generated for 'chain 'B9' and resid 94 through 96' Processing helix chain 'B9' and resid 108 through 113 Processing helix chain 'B9' and resid 115 through 130 Processing helix chain 'B9' and resid 134 through 142 Processing helix chain 'B9' and resid 166 through 170 Processing helix chain 'B2' and resid 19 through 41 Processing helix chain 'B8' and resid 5 through 7 No H-bonds generated for 'chain 'B8' and resid 5 through 7' Processing helix chain 'B8' and resid 18 through 26 Processing helix chain 'B8' and resid 60 through 62 No H-bonds generated for 'chain 'B8' and resid 60 through 62' Processing helix chain 'B8' and resid 81 through 83 No H-bonds generated for 'chain 'B8' and resid 81 through 83' Processing helix chain 'B8' and resid 99 through 121 Processing helix chain 'BK' and resid 51 through 64 removed outlier: 3.662A pdb=" N VALBK 55 " --> pdb=" O PROBK 51 " (cutoff:3.500A) Processing helix chain 'BK' and resid 70 through 78 Processing helix chain 'BK' and resid 86 through 102 Processing helix chain 'C1' and resid 14 through 45 Processing helix chain 'B1' and resid 15 through 33 Processing helix chain 'A1' and resid 2 through 4 No H-bonds generated for 'chain 'A1' and resid 2 through 4' Processing helix chain 'A1' and resid 6 through 29 Proline residue: A1 19 - end of helix Processing helix chain 'A1' and resid 42 through 54 Processing helix chain 'V1' and resid 33 through 39 Processing helix chain 'V1' and resid 46 through 49 No H-bonds generated for 'chain 'V1' and resid 46 through 49' Processing helix chain 'V1' and resid 53 through 63 Processing helix chain 'V1' and resid 75 through 81 Processing helix chain 'V1' and resid 108 through 113 Processing helix chain 'V1' and resid 116 through 129 removed outlier: 3.583A pdb=" N METV1 129 " --> pdb=" O GLYV1 125 " (cutoff:3.500A) Processing helix chain 'V1' and resid 143 through 158 Processing helix chain 'V1' and resid 166 through 168 No H-bonds generated for 'chain 'V1' and resid 166 through 168' Processing helix chain 'V1' and resid 185 through 187 No H-bonds generated for 'chain 'V1' and resid 185 through 187' Processing helix chain 'V1' and resid 190 through 196 Processing helix chain 'V1' and resid 225 through 236 Proline residue: V1 232 - end of helix Processing helix chain 'V1' and resid 242 through 244 No H-bonds generated for 'chain 'V1' and resid 242 through 244' Processing helix chain 'V1' and resid 276 through 283 removed outlier: 3.655A pdb=" N HISV1 283 " --> pdb=" O LEUV1 279 " (cutoff:3.500A) Processing helix chain 'V1' and resid 291 through 293 No H-bonds generated for 'chain 'V1' and resid 291 through 293' Processing helix chain 'V1' and resid 309 through 312 No H-bonds generated for 'chain 'V1' and resid 309 through 312' Processing helix chain 'V1' and resid 319 through 324 Processing helix chain 'V1' and resid 343 through 356 Processing helix chain 'V1' and resid 363 through 381 Processing helix chain 'V1' and resid 386 through 399 Processing helix chain 'V1' and resid 407 through 421 Proline residue: V1 414 - end of helix Processing helix chain 'V1' and resid 423 through 437 Processing helix chain 'V2' and resid 25 through 37 Processing helix chain 'V2' and resid 43 through 57 removed outlier: 3.685A pdb=" N ALAV2 46 " --> pdb=" O LYSV2 43 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VALV2 47 " --> pdb=" O ALAV2 44 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEUV2 48 " --> pdb=" O ALAV2 45 " (cutoff:3.500A) Proline residue: V2 49 - end of helix Processing helix chain 'V2' and resid 63 through 72 Processing helix chain 'V2' and resid 77 through 86 Processing helix chain 'V2' and resid 107 through 110 No H-bonds generated for 'chain 'V2' and resid 107 through 110' Processing helix chain 'V2' and resid 114 through 124 Processing helix chain 'V2' and resid 166 through 177 Processing helix chain 'S1' and resid 13 through 15 No H-bonds generated for 'chain 'S1' and resid 13 through 15' Processing helix chain 'S1' and resid 26 through 33 Processing helix chain 'S1' and resid 84 through 97 Processing helix chain 'S1' and resid 116 through 123 Processing helix chain 'S1' and resid 150 through 152 No H-bonds generated for 'chain 'S1' and resid 150 through 152' Processing helix chain 'S1' and resid 159 through 165 Processing helix chain 'S1' and resid 198 through 202 removed outlier: 3.763A pdb=" N ASPS1 201 " --> pdb=" O ASNS1 198 " (cutoff:3.500A) Processing helix chain 'S1' and resid 265 through 268 No H-bonds generated for 'chain 'S1' and resid 265 through 268' Processing helix chain 'S1' and resid 271 through 275 Processing helix chain 'S1' and resid 296 through 309 Processing helix chain 'S1' and resid 326 through 338 Processing helix chain 'S1' and resid 359 through 362 Processing helix chain 'S1' and resid 369 through 372 Processing helix chain 'S1' and resid 389 through 401 Processing helix chain 'S1' and resid 426 through 434 Processing helix chain 'S1' and resid 440 through 444 Processing helix chain 'S1' and resid 456 through 458 No H-bonds generated for 'chain 'S1' and resid 456 through 458' Processing helix chain 'S1' and resid 463 through 479 Processing helix chain 'S1' and resid 497 through 505 Processing helix chain 'S1' and resid 512 through 516 Processing helix chain 'S1' and resid 534 through 536 No H-bonds generated for 'chain 'S1' and resid 534 through 536' Processing helix chain 'S1' and resid 596 through 606 Processing helix chain 'S1' and resid 616 through 626 Processing helix chain 'S1' and resid 628 through 630 No H-bonds generated for 'chain 'S1' and resid 628 through 630' Processing helix chain 'S1' and resid 642 through 648 Processing helix chain 'S1' and resid 668 through 673 Processing helix chain 'S1' and resid 676 through 679 No H-bonds generated for 'chain 'S1' and resid 676 through 679' Processing helix chain 'S1' and resid 683 through 692 Processing helix chain 'S2' and resid 8 through 13 Processing helix chain 'S2' and resid 87 through 92 Processing helix chain 'S2' and resid 96 through 105 Proline residue: S2 101 - end of helix Processing helix chain 'S2' and resid 113 through 126 Processing helix chain 'S2' and resid 132 through 161 Processing helix chain 'S2' and resid 164 through 184 removed outlier: 3.917A pdb=" N PHES2 168 " --> pdb=" O METS2 164 " (cutoff:3.500A) Processing helix chain 'S2' and resid 208 through 228 Processing helix chain 'S2' and resid 233 through 238 Processing helix chain 'S2' and resid 247 through 252 Processing helix chain 'S2' and resid 258 through 262 Processing helix chain 'S2' and resid 269 through 272 No H-bonds generated for 'chain 'S2' and resid 269 through 272' Processing helix chain 'S2' and resid 277 through 279 No H-bonds generated for 'chain 'S2' and resid 277 through 279' Processing helix chain 'S2' and resid 293 through 316 Processing helix chain 'S2' and resid 335 through 338 No H-bonds generated for 'chain 'S2' and resid 335 through 338' Processing helix chain 'S2' and resid 342 through 353 Processing helix chain 'S2' and resid 394 through 408 removed outlier: 4.180A pdb=" N GLYS2 401 " --> pdb=" O ALAS2 397 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LEUS2 402 " --> pdb=" O HISS2 398 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ASPS2 403 " --> pdb=" O LEUS2 399 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LYSS2 404 " --> pdb=" O ALAS2 400 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLYS2 408 " --> pdb=" O LYSS2 404 " (cutoff:3.500A) Processing helix chain 'S2' and resid 411 through 420 Processing helix chain 'S3' and resid 16 through 32 Processing helix chain 'S3' and resid 57 through 64 Processing helix chain 'S3' and resid 120 through 122 No H-bonds generated for 'chain 'S3' and resid 120 through 122' Processing helix chain 'S3' and resid 125 through 137 removed outlier: 4.319A pdb=" N ASNS3 128 " --> pdb=" O LYSS3 125 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N TRPS3 129 " --> pdb=" O ALAS3 126 " (cutoff:3.500A) Processing helix chain 'S3' and resid 207 through 209 No H-bonds generated for 'chain 'S3' and resid 207 through 209' Processing helix chain 'S7' and resid 25 through 43 Processing helix chain 'S7' and resid 55 through 62 Processing helix chain 'S7' and resid 70 through 72 No H-bonds generated for 'chain 'S7' and resid 70 through 72' Processing helix chain 'S7' and resid 97 through 105 Processing helix chain 'S7' and resid 124 through 126 No H-bonds generated for 'chain 'S7' and resid 124 through 126' Processing helix chain 'S7' and resid 136 through 138 No H-bonds generated for 'chain 'S7' and resid 136 through 138' Processing helix chain 'S7' and resid 153 through 168 Processing helix chain 'S7' and resid 172 through 178 Processing helix chain 'S8' and resid 14 through 26 Processing helix chain 'S8' and resid 29 through 41 Processing helix chain 'S8' and resid 82 through 86 Processing helix chain 'S8' and resid 121 through 125 Processing helix chain 'S8' and resid 145 through 147 No H-bonds generated for 'chain 'S8' and resid 145 through 147' Processing helix chain 'S8' and resid 151 through 158 Processing helix chain 'S8' and resid 163 through 172 Processing helix chain 'V3' and resid 50 through 57 Processing helix chain 'S6' and resid 24 through 27 No H-bonds generated for 'chain 'S6' and resid 24 through 27' Processing helix chain 'S6' and resid 40 through 46 removed outlier: 3.833A pdb=" N ILES6 44 " --> pdb=" O ALAS6 40 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALAS6 45 " --> pdb=" O ILES6 41 " (cutoff:3.500A) Processing helix chain 'S4' and resid 27 through 31 Processing helix chain 'S4' and resid 49 through 51 No H-bonds generated for 'chain 'S4' and resid 49 through 51' Processing helix chain 'S4' and resid 89 through 99 Processing helix chain 'S4' and resid 118 through 121 No H-bonds generated for 'chain 'S4' and resid 118 through 121' Processing helix chain 'A9' and resid 30 through 41 Processing helix chain 'A9' and resid 53 through 58 Processing helix chain 'A9' and resid 60 through 62 No H-bonds generated for 'chain 'A9' and resid 60 through 62' Processing helix chain 'A9' and resid 78 through 84 Processing helix chain 'A9' and resid 112 through 124 Processing helix chain 'A9' and resid 144 through 158 Processing helix chain 'A9' and resid 178 through 183 Processing helix chain 'A9' and resid 207 through 219 Processing helix chain 'A9' and resid 238 through 247 Processing helix chain 'A9' and resid 281 through 287 Processing helix chain 'A9' and resid 311 through 317 Processing helix chain 'A2' and resid 27 through 38 Processing helix chain 'A2' and resid 41 through 46 Processing helix chain 'A2' and resid 83 through 93 Processing helix chain 'A5' and resid 19 through 36 Processing helix chain 'A5' and resid 42 through 60 removed outlier: 4.297A pdb=" N ALAA5 60 " --> pdb=" O SERA5 56 " (cutoff:3.500A) Processing helix chain 'A5' and resid 65 through 70 Processing helix chain 'A5' and resid 77 through 94 Processing helix chain 'A6' and resid 24 through 48 Proline residue: A6 43 - end of helix Processing helix chain 'A6' and resid 55 through 69 removed outlier: 3.991A pdb=" N ASNA6 69 " --> pdb=" O META6 65 " (cutoff:3.500A) Processing helix chain 'A6' and resid 75 through 93 Processing helix chain 'A6' and resid 99 through 105 Processing helix chain 'A6' and resid 117 through 122 Processing helix chain 'A7' and resid 5 through 14 Processing helix chain 'A7' and resid 59 through 61 No H-bonds generated for 'chain 'A7' and resid 59 through 61' Processing helix chain 'AL' and resid 5 through 15 removed outlier: 4.115A pdb=" N VALAL 14 " --> pdb=" O GLYAL 10 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SERAL 15 " --> pdb=" O LEUAL 11 " (cutoff:3.500A) Processing helix chain 'AL' and resid 21 through 29 Processing helix chain 'AL' and resid 84 through 90 Processing helix chain 'AA' and resid 8 through 21 Processing helix chain 'AA' and resid 44 through 58 Processing helix chain 'AA' and resid 64 through 68 Processing helix chain 'AA' and resid 73 through 83 Processing sheet with id= A, first strand: chain 'a1' and resid 15 through 19 Processing sheet with id= B, first strand: chain 'a1' and resid 240 through 244 removed outlier: 6.046A pdb=" N VALa1 422 " --> pdb=" O ILEa1 241 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N HISa1 243 " --> pdb=" O VALa1 422 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLYa1 424 " --> pdb=" O HISa1 243 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'a2' and resid 25 through 29 Processing sheet with id= D, first strand: chain 'a2' and resid 242 through 247 Processing sheet with id= E, first strand: chain 'b1' and resid 22 through 24 Processing sheet with id= F, first strand: chain 'f1' and resid 74 through 77 Processing sheet with id= G, first strand: chain 'f1' and resid 85 through 88 Processing sheet with id= H, first strand: chain 'a3' and resid 15 through 19 Processing sheet with id= I, first strand: chain 'a3' and resid 240 through 244 removed outlier: 6.098A pdb=" N VALa3 422 " --> pdb=" O ILEa3 241 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N HISa3 243 " --> pdb=" O VALa3 422 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLYa3 424 " --> pdb=" O HISa3 243 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'a4' and resid 25 through 29 removed outlier: 6.730A pdb=" N METa4 204 " --> pdb=" O VALa4 34 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N ALAa4 36 " --> pdb=" O METa4 204 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEUa4 206 " --> pdb=" O ALAa4 36 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N LEUa4 38 " --> pdb=" O LEUa4 206 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLYa4 208 " --> pdb=" O LEUa4 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'a4' and resid 242 through 247 Processing sheet with id= L, first strand: chain 'f2' and resid 74 through 77 Processing sheet with id= M, first strand: chain 'f2' and resid 86 through 88 Processing sheet with id= N, first strand: chain 'D5' and resid 61 through 65 Processing sheet with id= O, first strand: chain 'D4' and resid 50 through 52 Processing sheet with id= P, first strand: chain 'AJ' and resid 122 through 125 removed outlier: 6.837A pdb=" N VALAJ 168 " --> pdb=" O THRAJ 26 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ASPAJ 28 " --> pdb=" O VALAJ 168 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILEAJ 170 " --> pdb=" O ASPAJ 28 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N GLUAJ 219 " --> pdb=" O VALAJ 169 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N TYRAJ 171 " --> pdb=" O GLUAJ 219 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEUAJ 221 " --> pdb=" O TYRAJ 171 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'V1' and resid 221 through 224 removed outlier: 6.490A pdb=" N ALAV1 133 " --> pdb=" O LEUV1 93 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N VALV1 95 " --> pdb=" O ALAV1 133 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N TYRV1 135 " --> pdb=" O VALV1 95 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ALAV1 97 " --> pdb=" O TYRV1 135 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N TYRV1 137 " --> pdb=" O ALAV1 97 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASPV1 174 " --> pdb=" O ALAV1 134 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ILEV1 136 " --> pdb=" O ASPV1 174 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N PHEV1 176 " --> pdb=" O ILEV1 136 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ILEV1 138 " --> pdb=" O PHEV1 176 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VALV1 178 " --> pdb=" O ILEV1 138 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'V1' and resid 253 through 258 Processing sheet with id= S, first strand: chain 'V1' and resid 294 through 298 removed outlier: 6.785A pdb=" N METV1 337 " --> pdb=" O LEUV1 295 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N VALV1 297 " --> pdb=" O ILEV1 335 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILEV1 335 " --> pdb=" O VALV1 297 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'V2' and resid 138 through 142 Processing sheet with id= U, first strand: chain 'S1' and resid 16 through 20 removed outlier: 6.987A pdb=" N TRPS1 77 " --> pdb=" O PHES1 12 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'S1' and resid 146 through 148 Processing sheet with id= W, first strand: chain 'S1' and resid 173 through 177 Processing sheet with id= X, first strand: chain 'S1' and resid 223 through 228 Processing sheet with id= Y, first strand: chain 'S1' and resid 283 through 286 Processing sheet with id= Z, first strand: chain 'S1' and resid 342 through 345 removed outlier: 6.651A pdb=" N METS1 521 " --> pdb=" O ALAS1 316 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ILES1 318 " --> pdb=" O METS1 521 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N PHES1 523 " --> pdb=" O ILES1 318 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VALS1 559 " --> pdb=" O TYRS1 545 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N GLYS1 547 " --> pdb=" O VALS1 559 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEUS1 561 " --> pdb=" O GLYS1 547 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'S1' and resid 405 through 409 Processing sheet with id= AB, first strand: chain 'S1' and resid 572 through 574 Processing sheet with id= AC, first strand: chain 'S2' and resid 47 through 51 Processing sheet with id= AD, first strand: chain 'S2' and resid 361 through 368 Processing sheet with id= AE, first strand: chain 'S3' and resid 74 through 76 removed outlier: 6.675A pdb=" N LEUS3 48 " --> pdb=" O ARGS3 106 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LYSS3 108 " --> pdb=" O LEUS3 48 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ILES3 50 " --> pdb=" O LYSS3 108 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N TYRS3 110 " --> pdb=" O ILES3 50 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ILES3 52 " --> pdb=" O TYRS3 110 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'S3' and resid 174 through 177 Processing sheet with id= AG, first strand: chain 'S7' and resid 85 through 88 removed outlier: 6.120A pdb=" N TYRS7 112 " --> pdb=" O METS7 86 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VALS7 88 " --> pdb=" O TYRS7 112 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VALS7 114 " --> pdb=" O VALS7 88 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILES7 144 " --> pdb=" O SERS7 115 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'S8' and resid 92 through 96 Processing sheet with id= AI, first strand: chain 'S6' and resid 56 through 59 Processing sheet with id= AJ, first strand: chain 'S4' and resid 103 through 105 removed outlier: 6.795A pdb=" N ALAS4 35 " --> pdb=" O ASPS4 104 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'S4' and resid 64 through 66 Processing sheet with id= AL, first strand: chain 'A9' and resid 164 through 168 removed outlier: 4.053A pdb=" N VALA9 91 " --> pdb=" O GLUA9 127 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHEA9 129 " --> pdb=" O VALA9 91 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ASNA9 93 " --> pdb=" O PHEA9 129 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N HISA9 131 " --> pdb=" O ASNA9 93 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLNA9 44 " --> pdb=" O ALAA9 21 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N VALA9 23 " --> pdb=" O GLNA9 44 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILEA9 46 " --> pdb=" O VALA9 23 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'A2' and resid 53 through 56 Processing sheet with id= AN, first strand: chain 'AL' and resid 40 through 42 4328 hydrogen bonds defined for protein. 12447 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 33.14 Time building geometry restraints manager: 32.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 40594 1.40 - 1.63: 57446 1.63 - 1.86: 1006 1.86 - 2.08: 24 2.08 - 2.31: 88 Bond restraints: 99158 Sorted by residual: bond pdb=" C2D HECc2 501 " pdb=" C3D HECc2 501 " ideal model delta sigma weight residual 1.544 1.319 0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C2D HECc1 501 " pdb=" C3D HECc1 501 " ideal model delta sigma weight residual 1.544 1.325 0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" CAC HECc2 501 " pdb=" CBC HECc2 501 " ideal model delta sigma weight residual 1.544 1.363 0.181 2.00e-02 2.50e+03 8.22e+01 bond pdb=" CAC HECc1 501 " pdb=" CBC HECc1 501 " ideal model delta sigma weight residual 1.544 1.363 0.181 2.00e-02 2.50e+03 8.19e+01 bond pdb=" CAB HECc2 501 " pdb=" CBB HECc2 501 " ideal model delta sigma weight residual 1.544 1.402 0.142 2.00e-02 2.50e+03 5.06e+01 ... (remaining 99153 not shown) Histogram of bond angle deviations from ideal: 69.87 - 91.80: 106 91.80 - 113.74: 58367 113.74 - 135.67: 76119 135.67 - 157.60: 9 157.60 - 179.53: 12 Bond angle restraints: 134613 Sorted by residual: angle pdb=" S1 FESf2 501 " pdb=" FE2 FESf2 501 " pdb=" S2 FESf2 501 " ideal model delta sigma weight residual 104.33 89.89 14.44 1.14e+00 7.69e-01 1.60e+02 angle pdb=" FE1 FESf2 501 " pdb=" S2 FESf2 501 " pdb=" FE2 FESf2 501 " ideal model delta sigma weight residual 75.66 89.86 -14.20 1.14e+00 7.69e-01 1.55e+02 angle pdb=" S1 FESf1 501 " pdb=" FE2 FESf1 501 " pdb=" S2 FESf1 501 " ideal model delta sigma weight residual 104.33 90.17 14.16 1.14e+00 7.69e-01 1.54e+02 angle pdb=" FE1 FESf2 501 " pdb=" S1 FESf2 501 " pdb=" FE2 FESf2 501 " ideal model delta sigma weight residual 75.66 90.38 -14.72 1.20e+00 6.94e-01 1.50e+02 angle pdb=" FE1 FESf1 501 " pdb=" S2 FESf1 501 " pdb=" FE2 FESf1 501 " ideal model delta sigma weight residual 75.66 89.59 -13.93 1.14e+00 7.69e-01 1.49e+02 ... (remaining 134608 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.08: 58203 29.08 - 58.17: 959 58.17 - 87.25: 110 87.25 - 116.33: 5 116.33 - 145.42: 3 Dihedral angle restraints: 59280 sinusoidal: 24137 harmonic: 35143 Sorted by residual: dihedral pdb=" CA PHEB7 30 " pdb=" C PHEB7 30 " pdb=" N PROB7 31 " pdb=" CA PROB7 31 " ideal model delta harmonic sigma weight residual -180.00 -117.06 -62.94 0 5.00e+00 4.00e-02 1.58e+02 dihedral pdb=" CA LEUD5 526 " pdb=" C LEUD5 526 " pdb=" N GLYD5 527 " pdb=" CA GLYD5 527 " ideal model delta harmonic sigma weight residual -180.00 -120.73 -59.27 0 5.00e+00 4.00e-02 1.41e+02 dihedral pdb=" CA LEUAJ 241 " pdb=" C LEUAJ 241 " pdb=" N LYSAJ 242 " pdb=" CA LYSAJ 242 " ideal model delta harmonic sigma weight residual 180.00 128.01 51.99 0 5.00e+00 4.00e-02 1.08e+02 ... (remaining 59277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.231: 14775 4.231 - 8.462: 0 8.462 - 12.693: 0 12.693 - 16.924: 0 16.924 - 21.155: 24 Chirality restraints: 14799 Sorted by residual: chirality pdb=" FE2 SF4S8 202 " pdb=" S1 SF4S8 202 " pdb=" S3 SF4S8 202 " pdb=" S4 SF4S8 202 " both_signs ideal model delta sigma weight residual False 10.55 -10.60 21.16 2.00e-01 2.50e+01 1.12e+04 chirality pdb=" FE4 SF4S1 802 " pdb=" S1 SF4S1 802 " pdb=" S2 SF4S1 802 " pdb=" S3 SF4S1 802 " both_signs ideal model delta sigma weight residual False 10.55 -10.57 21.13 2.00e-01 2.50e+01 1.12e+04 chirality pdb=" FE3 SF4V1 500 " pdb=" S1 SF4V1 500 " pdb=" S2 SF4V1 500 " pdb=" S4 SF4V1 500 " both_signs ideal model delta sigma weight residual False -10.55 10.56 -21.12 2.00e-01 2.50e+01 1.12e+04 ... (remaining 14796 not shown) Planarity restraints: 17092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMNV1 501 " 0.144 2.00e-02 2.50e+03 5.00e-02 1.19e+02 pdb=" C10 FMNV1 501 " 0.011 2.00e-02 2.50e+03 pdb=" C2 FMNV1 501 " -0.047 2.00e-02 2.50e+03 pdb=" C4 FMNV1 501 " 0.009 2.00e-02 2.50e+03 pdb=" C4A FMNV1 501 " 0.031 2.00e-02 2.50e+03 pdb=" C5A FMNV1 501 " 0.040 2.00e-02 2.50e+03 pdb=" C6 FMNV1 501 " 0.028 2.00e-02 2.50e+03 pdb=" C7 FMNV1 501 " -0.013 2.00e-02 2.50e+03 pdb=" C7M FMNV1 501 " -0.040 2.00e-02 2.50e+03 pdb=" C8 FMNV1 501 " -0.036 2.00e-02 2.50e+03 pdb=" C8M FMNV1 501 " -0.064 2.00e-02 2.50e+03 pdb=" C9 FMNV1 501 " -0.025 2.00e-02 2.50e+03 pdb=" C9A FMNV1 501 " 0.017 2.00e-02 2.50e+03 pdb=" N1 FMNV1 501 " -0.021 2.00e-02 2.50e+03 pdb=" N10 FMNV1 501 " 0.020 2.00e-02 2.50e+03 pdb=" N3 FMNV1 501 " -0.029 2.00e-02 2.50e+03 pdb=" N5 FMNV1 501 " 0.053 2.00e-02 2.50e+03 pdb=" O2 FMNV1 501 " -0.090 2.00e-02 2.50e+03 pdb=" O4 FMNV1 501 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VALS2 73 " -0.030 2.00e-02 2.50e+03 6.00e-02 3.60e+01 pdb=" C VALS2 73 " 0.104 2.00e-02 2.50e+03 pdb=" O VALS2 73 " -0.039 2.00e-02 2.50e+03 pdb=" N ARGS2 74 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHED5 84 " -0.029 2.00e-02 2.50e+03 5.85e-02 3.42e+01 pdb=" C PHED5 84 " 0.101 2.00e-02 2.50e+03 pdb=" O PHED5 84 " -0.038 2.00e-02 2.50e+03 pdb=" N PHED5 85 " -0.034 2.00e-02 2.50e+03 ... (remaining 17089 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 700 2.54 - 3.13: 73366 3.13 - 3.72: 156182 3.72 - 4.31: 207327 4.31 - 4.90: 334119 Nonbonded interactions: 771694 Sorted by model distance: nonbonded pdb=" SD METc1 159 " pdb="FE HECc1 501 " model vdw 1.949 3.360 nonbonded pdb=" NE2 HISb1 83 " pdb="FE HEMb1 401 " model vdw 1.982 3.080 nonbonded pdb=" NE2 HISb2 182 " pdb="FE HEMb2 401 " model vdw 2.007 3.080 nonbonded pdb=" O ALAS2 336 " pdb=" O LYSS2 339 " model vdw 2.108 3.040 nonbonded pdb=" CA ALAS3 80 " pdb=" O GLUS3 91 " model vdw 2.115 3.470 ... (remaining 771689 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'AA' and (resid 5 through 84 or (resid 101 and (name C10 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C19 or name C2 or name C20 or name C21 or name C3 or name C4 or name C5 \ or name C6 or name C7 or name C8 or name C9 or name N1 or name N2 or name O1 or \ name O2 or name O3 or name O4 or name O5 or name O6 or name O7 or name P1 or nam \ e S1 )))) selection = (chain 'AB' and (resid 5 through 84 or resid 101)) } ncs_group { reference = (chain 'a1' and resid 2 through 445) selection = (chain 'a3' and (resid 2 through 222 or resid 229 through 445)) } ncs_group { reference = (chain 'a2' and (resid 20 through 227 or resid 235 through 439)) selection = chain 'a4' } ncs_group { reference = chain 'b1' selection = chain 'b2' } ncs_group { reference = (chain 'c1' and (resid 2 through 238 or resid 501)) selection = (chain 'c2' and (resid 2 through 238 or resid 501)) } ncs_group { reference = (chain 'd1' and resid 11 through 109) selection = (chain 'd2' and resid 11 through 109) } ncs_group { reference = (chain 'f1' and (resid 2 through 196 or resid 501)) selection = chain 'f2' } ncs_group { reference = chain 'h1' selection = chain 'h2' } ncs_group { reference = chain 'i1' selection = (chain 'i2' and resid 5 through 59) } ncs_group { reference = (chain 'q1' and resid 2 through 73) selection = (chain 'q2' and resid 2 through 73) } ncs_group { reference = (chain 'x1' and resid 8 through 38) selection = (chain 'x2' and (resid 1 or (resid 2 and (name N or name CA or name C or name O \ )) or resid 3 through 48)) } 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: 7 Type Number sf(0) Gaussians Fe 38 7.16 5 Zn 1 6.06 5 P 7 5.49 5 S 627 5.16 5 C 62167 2.51 5 N 16441 2.21 5 O 17424 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: 4.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 32.420 Check model and map are aligned: 1.050 Convert atoms to be neutral: 0.640 Process input model: 210.120 Find NCS groups from input model: 4.390 Set up NCS constraints: 0.590 Set refine NCS operators: 0.000 Set scattering table: 0.040 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 255.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.225 99158 Z= 0.404 Angle : 1.111 21.217 134613 Z= 0.590 Chirality : 0.850 21.155 14799 Planarity : 0.008 0.101 17092 Dihedral : 11.146 145.417 36560 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.83 % Favored : 89.04 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.24 % Twisted Proline : 0.74 % Twisted General : 0.44 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.06), residues: 11856 helix: -1.82 (0.05), residues: 6180 sheet: -1.59 (0.18), residues: 733 loop : -3.50 (0.07), residues: 4943 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23712 Ramachandran restraints generated. 11856 Oldfield, 0 Emsley, 11856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23712 Ramachandran restraints generated. 11856 Oldfield, 0 Emsley, 11856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3584 residues out of total 10400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 3545 time to evaluate : 8.667 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 39 outliers final: 3 residues processed: 3568 average time/residue: 0.8951 time to fit residues: 5392.4884 Evaluate side-chains 1805 residues out of total 10400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1802 time to evaluate : 8.653 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.6862 time to fit residues: 15.4164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1174 random chunks: chunk 991 optimal weight: 9.9990 chunk 889 optimal weight: 20.0000 chunk 493 optimal weight: 3.9990 chunk 303 optimal weight: 0.2980 chunk 600 optimal weight: 4.9990 chunk 475 optimal weight: 5.9990 chunk 920 optimal weight: 0.6980 chunk 356 optimal weight: 0.0970 chunk 559 optimal weight: 10.0000 chunk 684 optimal weight: 0.9980 chunk 1066 optimal weight: 3.9990 overall best weight: 1.2180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a1 85 HIS a1 301 ASN a1 308 GLN a1 418 GLN a2 20 HIS a2 164 HIS a2 343 GLN a2 349 GLN b1 85 ASN b1 312 GLN b1 345 HIS c1 50 HIS c1 155 GLN c1 197 HIS f1 53 ASN f1 57 GLN f1 108 GLN f1 164 HIS q1 6 HIS q1 36 ASN h1 67 HIS a3 21 ASN a3 189 HIS a3 289 HIS a3 308 GLN a3 323 HIS ** a3 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a4 22 GLN a4 104 ASN a4 170 ASN a4 290 ASN a4 351 ASN b2 8 HIS b2 32 ASN ** b2 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b2 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 341 GLN b2 345 HIS c2 50 HIS c2 197 HIS ** d2 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i2 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D6 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4L 83 ASN D5 116 GLN ** D5 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 199 GLN D5 205 ASN D5 226 GLN D5 309 GLN D5 479 GLN D5 484 HIS D5 534 HIS D5 580 GLN ** D4 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4 43 ASN D4 81 GLN ** D4 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 180 GLN ** D4 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2 63 GLN D2 134 GLN D2 186 HIS D2 235 ASN ** B5 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B5 143 ASN BJ 55 HIS ** BJ 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 2 GLN AJ 76 ASN AJ 114 HIS AJ 204 ASN AJ 251 GLN S5 33 HIS A3 45 ASN A3 61 ASN A3 68 HIS A3 70 GLN C2 117 HIS ** B4 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B6 73 HIS B7 75 ASN B9 11 HIS B9 32 HIS B9 50 HIS ** B9 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B8 104 HIS A1 27 HIS ** V1 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V1 398 GLN V1 431 GLN ** V2 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V2 37 ASN V2 42 HIS V2 67 ASN S1 78 ASN S1 155 GLN S1 179 ASN ** S1 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1 259 ASN S1 336 ASN S1 392 ASN S1 430 GLN ** S1 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1 548 HIS S2 50 ASN S2 135 GLN ** S2 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S2 200 HIS S2 201 GLN S3 53 HIS S3 67 HIS S8 6 ASN S8 123 GLN S8 144 HIS S8 150 ASN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 44 ASN ** A9 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A9 288 HIS A2 47 ASN A5 36 HIS ** A5 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 57 GLN A6 107 HIS ** AA 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AA 74 GLN Total number of N/Q/H flips: 104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.270 99158 Z= 0.465 Angle : 1.445 51.286 134613 Z= 0.898 Chirality : 0.258 6.603 14799 Planarity : 0.006 0.085 17092 Dihedral : 7.829 123.483 13295 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.86 % Favored : 91.06 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.25 % Twisted Proline : 0.59 % Twisted General : 0.22 % 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: -2.35 (0.07), residues: 11856 helix: -0.46 (0.06), residues: 6188 sheet: -1.08 (0.19), residues: 698 loop : -3.11 (0.08), residues: 4970 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23712 Ramachandran restraints generated. 11856 Oldfield, 0 Emsley, 11856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23712 Ramachandran restraints generated. 11856 Oldfield, 0 Emsley, 11856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2468 residues out of total 10400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 2450 time to evaluate : 8.765 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 18 outliers final: 5 residues processed: 2462 average time/residue: 0.8974 time to fit residues: 3812.3466 Evaluate side-chains 1668 residues out of total 10400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1663 time to evaluate : 8.754 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.6610 time to fit residues: 17.8376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1174 random chunks: chunk 592 optimal weight: 0.7980 chunk 330 optimal weight: 0.1980 chunk 887 optimal weight: 4.9990 chunk 725 optimal weight: 1.9990 chunk 294 optimal weight: 3.9990 chunk 1068 optimal weight: 10.0000 chunk 1153 optimal weight: 20.0000 chunk 951 optimal weight: 5.9990 chunk 1059 optimal weight: 0.9990 chunk 364 optimal weight: 10.0000 chunk 856 optimal weight: 10.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a1 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a2 104 ASN a2 284 HIS a2 349 GLN b1 148 ASN q1 6 HIS b2 8 HIS c2 197 HIS f2 53 ASN f2 57 GLN ** d2 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i2 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D6 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 59 GLN D5 194 ASN D5 226 GLN ** D5 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D5 452 ASN D5 546 GLN D4 81 GLN D4 82 HIS D4 144 ASN ** D4 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 279 GLN ** D4 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2 134 GLN D2 174 GLN D2 186 HIS D2 235 ASN BJ 106 GLN ** AJ 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 61 ASN A3 68 HIS C2 117 HIS B4 49 GLN ** B4 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 125 ASN AM 60 GLN ** B9 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B8 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V2 37 ASN V2 42 HIS S1 36 GLN S1 78 ASN ** S1 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1 336 ASN S1 392 ASN ** S1 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1 621 ASN ** S2 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 144 ASN ** S7 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S8 123 GLN ** S8 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S6 16 GLN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A9 87 HIS A5 52 ASN ** A5 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 57 GLN ** A6 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A6 125 HIS ** AL 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.246 99158 Z= 0.454 Angle : 1.428 50.806 134613 Z= 0.892 Chirality : 0.256 6.351 14799 Planarity : 0.005 0.073 17092 Dihedral : 7.390 119.202 13295 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.19 % Favored : 90.76 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.25 % Twisted Proline : 0.45 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.07), residues: 11856 helix: 0.04 (0.06), residues: 6193 sheet: -0.93 (0.20), residues: 706 loop : -2.93 (0.08), residues: 4957 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23712 Ramachandran restraints generated. 11856 Oldfield, 0 Emsley, 11856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23712 Ramachandran restraints generated. 11856 Oldfield, 0 Emsley, 11856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2248 residues out of total 10400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 2229 time to evaluate : 8.639 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 19 outliers final: 3 residues processed: 2243 average time/residue: 0.8575 time to fit residues: 3350.1448 Evaluate side-chains 1611 residues out of total 10400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1608 time to evaluate : 8.692 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.7204 time to fit residues: 15.3447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1174 random chunks: chunk 1055 optimal weight: 5.9990 chunk 802 optimal weight: 4.9990 chunk 554 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 509 optimal weight: 5.9990 chunk 717 optimal weight: 10.0000 chunk 1071 optimal weight: 10.0000 chunk 1134 optimal weight: 5.9990 chunk 560 optimal weight: 8.9990 chunk 1015 optimal weight: 9.9990 chunk 305 optimal weight: 0.4980 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a1 52 ASN ** a1 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a1 305 GLN a1 341 GLN a2 125 ASN ** a2 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a2 349 GLN b1 267 HIS ** c1 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f1 57 GLN ** q1 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h1 63 HIS a3 69 ASN b2 44 GLN b2 148 ASN b2 345 HIS c2 197 HIS f2 57 GLN ** d2 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q2 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i2 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 171 GLN D1 235 ASN ** D1 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 115 ASN ** D5 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 220 HIS ** D4 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 186 HIS D2 235 ASN ** B5 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 122 GLN ** AJ 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3 45 ASN ** A3 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2 117 HIS ** B4 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B7 91 HIS B9 11 HIS ** B9 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 21 GLN B8 3 HIS ** B8 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V1 373 ASN V1 421 HIS ** V2 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V2 37 ASN V2 157 ASN S1 78 ASN ** S1 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 336 ASN S1 392 ASN ** S1 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1 459 GLN S1 494 HIS S1 517 ASN ** S1 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 84 HIS S2 347 HIS ** S3 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 127 HIS ** S8 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S6 94 GLN ** S4 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 72 GLN ** A5 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A7 20 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.241 99158 Z= 0.498 Angle : 1.453 51.087 134613 Z= 0.905 Chirality : 0.257 6.523 14799 Planarity : 0.006 0.142 17092 Dihedral : 7.322 114.141 13295 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 21.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.21 % Favored : 89.74 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.25 % Twisted Proline : 0.45 % Twisted General : 0.20 % 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: -1.58 (0.08), residues: 11856 helix: 0.23 (0.06), residues: 6195 sheet: -0.99 (0.19), residues: 742 loop : -2.82 (0.08), residues: 4919 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23712 Ramachandran restraints generated. 11856 Oldfield, 0 Emsley, 11856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23712 Ramachandran restraints generated. 11856 Oldfield, 0 Emsley, 11856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2025 residues out of total 10400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 2016 time to evaluate : 9.933 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 outliers start: 9 outliers final: 1 residues processed: 2023 average time/residue: 0.8518 time to fit residues: 2995.8923 Evaluate side-chains 1481 residues out of total 10400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1480 time to evaluate : 8.697 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.6515 time to fit residues: 12.6733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- 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: 61.1284 > 50: distance: 45 - 50: 16.871 distance: 50 - 51: 11.186 distance: 51 - 52: 10.650 distance: 51 - 54: 12.055 distance: 52 - 53: 22.073 distance: 54 - 55: 15.958 distance: 55 - 56: 10.064 distance: 56 - 58: 13.138 distance: 57 - 59: 7.130 distance: 58 - 60: 5.902 distance: 59 - 60: 3.820 distance: 60 - 61: 7.936 distance: 62 - 63: 21.205 distance: 62 - 68: 22.164 distance: 63 - 64: 28.484 distance: 63 - 66: 29.093 distance: 64 - 65: 4.250 distance: 64 - 69: 17.178 distance: 66 - 67: 18.573 distance: 69 - 70: 8.552 distance: 70 - 71: 12.125 distance: 70 - 73: 22.846 distance: 71 - 72: 14.038 distance: 71 - 76: 23.221 distance: 73 - 74: 21.904 distance: 73 - 75: 54.786 distance: 76 - 77: 6.066 distance: 77 - 78: 15.247 distance: 77 - 80: 14.155 distance: 78 - 79: 14.662 distance: 78 - 85: 19.158 distance: 80 - 81: 16.599 distance: 81 - 82: 18.405 distance: 82 - 83: 17.698 distance: 83 - 84: 11.018 distance: 85 - 86: 25.149 distance: 86 - 87: 22.666 distance: 86 - 89: 24.085 distance: 87 - 88: 30.969 distance: 87 - 94: 11.704 distance: 89 - 90: 13.086 distance: 90 - 91: 33.196 distance: 91 - 92: 15.419 distance: 91 - 93: 30.338 distance: 94 - 95: 9.591 distance: 95 - 96: 14.409 distance: 95 - 98: 10.100 distance: 96 - 97: 14.756 distance: 96 - 101: 20.665 distance: 98 - 99: 24.108 distance: 98 - 100: 24.642 distance: 101 - 102: 15.957 distance: 102 - 103: 10.702 distance: 102 - 105: 19.194 distance: 103 - 104: 13.323 distance: 103 - 106: 17.304 distance: 106 - 107: 9.621 distance: 107 - 108: 13.856 distance: 107 - 110: 32.882 distance: 108 - 109: 17.124 distance: 108 - 116: 46.128 distance: 110 - 111: 16.103 distance: 111 - 112: 8.142 distance: 111 - 113: 27.703 distance: 112 - 114: 20.983 distance: 113 - 115: 9.654 distance: 114 - 115: 13.952 distance: 116 - 117: 29.961 distance: 117 - 118: 8.996 distance: 117 - 120: 21.699 distance: 118 - 119: 6.172 distance: 118 - 130: 13.550 distance: 120 - 121: 9.806 distance: 121 - 122: 19.542 distance: 121 - 123: 21.802 distance: 122 - 124: 16.343 distance: 123 - 125: 23.469 distance: 123 - 126: 23.745 distance: 124 - 125: 19.464 distance: 125 - 127: 8.577 distance: 126 - 128: 4.876 distance: 127 - 129: 26.737 distance: 128 - 129: 14.088 distance: 130 - 131: 10.014 distance: 131 - 132: 13.063 distance: 131 - 134: 17.858 distance: 132 - 133: 16.415 distance: 132 - 139: 15.535 distance: 134 - 135: 18.846 distance: 135 - 136: 6.641 distance: 136 - 137: 25.229 distance: 137 - 138: 36.069