Starting phenix.real_space_refine (version: dev) on Sat Dec 17 08:23:26 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qbx_4493/12_2022/6qbx_4493_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qbx_4493/12_2022/6qbx_4493.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qbx_4493/12_2022/6qbx_4493_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qbx_4493/12_2022/6qbx_4493_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qbx_4493/12_2022/6qbx_4493_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qbx_4493/12_2022/6qbx_4493.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qbx_4493/12_2022/6qbx_4493.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qbx_4493/12_2022/6qbx_4493_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qbx_4493/12_2022/6qbx_4493_updated.pdb" } resolution = 4.2 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= 0.025 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 "a2 ARG 240": "NH1" <-> "NH2" Residue "b1 TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c1 ARG 237": "NH1" <-> "NH2" Residue "d1 ARG 48": "NH1" <-> "NH2" Residue "d1 TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q1 ARG 2": "NH1" <-> "NH2" Residue "h1 ARG 34": "NH1" <-> "NH2" Residue "a3 TYR 98": "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 "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 "S1 TYR 362": "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 "S8 PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V3 PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S6 TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S4 ARG 64": "NH1" <-> "NH2" Residue "A9 ARG 97": "NH1" <-> "NH2" Residue "A9 ARG 186": "NH1" <-> "NH2" Residue "A9 TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A9 ARG 292": "NH1" <-> "NH2" Residue "A9 ARG 320": "NH1" <-> "NH2" Residue "A2 ARG 33": "NH1" <-> "NH2" Residue "A2 TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A6 ARG 22": "NH1" <-> "NH2" Residue "AL ARG 106": "NH1" <-> "NH2" Residue "AA TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AM ARG 26": "NH1" <-> "NH2" Residue "AM ARG 81": "NH1" <-> "NH2" Residue "D3 ARG 48": "NH1" <-> "NH2" Residue "D1 ARG 195": "NH1" <-> "NH2" Residue "D1 PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D1 TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D6 ARG 173": "NH1" <-> "NH2" Residue "4L TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4L PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D5 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "D2 PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AK ARG 19": "NH1" <-> "NH2" Residue "B5 ARG 26": "NH1" <-> "NH2" Residue "AJ ARG 95": "NH1" <-> "NH2" Residue "AJ TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AJ ARG 305": "NH1" <-> "NH2" Residue "A3 ARG 46": "NH1" <-> "NH2" Residue "B3 PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C2 ARG 5": "NH1" <-> "NH2" Residue "C2 ARG 120": "NH1" <-> "NH2" Residue "B4 ARG 41": "NH1" <-> "NH2" Residue "B6 PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "A1 ARG 25": "NH1" <-> "NH2" Time to flip residues: 0.23s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 97049 Number of models: 1 Model: "" Number of chains: 83 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: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1909 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 22, '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: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 114 Classifications: {'peptide': 23} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 22} Link IDs: {'TRANS': 22} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 23} Unresolved non-hydrogen planarities: 23 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: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 130 Classifications: {'peptide': 26} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'TRANS': 25} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'UNK:plan-1': 26} Unresolved non-hydrogen planarities: 26 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: "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: {'PTRANS': 32, 'TRANS': 655} Chain: "S2" Number of atoms: 3455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3455 Classifications: {'peptide': 430} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 401} 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: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1248 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 145} Chain: "S8" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1415 Classifications: {'peptide': 176} Modifications used: {'COO': 1} 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: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1025 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "A9" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2344 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 14, 'TRANS': 277} Chain breaks: 2 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: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 766 Classifications: {'peptide': 96} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 83} Chain breaks: 1 Chain: "AL" Number of atoms: 1044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1044 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 11, 'TRANS': 111} 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: "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: "D3" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 923 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "D1" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2529 Classifications: {'peptide': 318} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 295} Chain: "D6" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1345 Classifications: {'peptide': 175} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 170} 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': 5, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 299} 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': 1, 'PTRANS': 10, 'TRANS': 107} 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: "B6" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 804 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 12, 'TRANS': 82} Chain breaks: 1 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: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 555 Classifications: {'peptide': 64} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 55} 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: "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: "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: "S2" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 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 Chain: "D5" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "AK" 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 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12558 SG CYSf1 139 135.578 106.795 62.337 1.00135.90 S ATOM 12694 SG CYSf1 158 138.220 104.161 62.804 1.00118.43 S ATOM 28172 SG CYSf2 139 199.477 120.858 53.495 1.00131.36 S ATOM 28308 SG CYSf2 158 197.530 122.814 50.660 1.00120.93 S ATOM 33966 SG CYSV1 365 46.868 166.231 208.525 1.00 34.60 S ATOM 34290 SG CYSV1 405 48.634 168.680 214.313 1.00 33.15 S ATOM 33946 SG CYSV1 362 52.658 166.723 209.632 1.00 49.90 S ATOM 33927 SG CYSV1 359 49.445 172.418 209.015 1.00 51.31 S ATOM 35367 SG CYSV2 103 29.071 175.702 215.966 1.00101.33 S ATOM 35401 SG CYSV2 108 26.619 173.602 218.475 1.00 60.45 S ATOM 35681 SG CYSV2 144 33.342 174.753 219.093 1.00 79.10 S ATOM 35704 SG CYSV2 148 31.234 173.496 221.901 1.00 85.83 S ATOM 37036 SG CYSS1 114 58.195 159.175 189.996 1.00 18.34 S ATOM 36975 SG CYSS1 105 53.023 156.741 186.940 1.00 26.80 S ATOM 36996 SG CYSS1 108 55.697 162.360 184.977 1.00 13.31 S ATOM 37368 SG CYSS1 156 58.425 168.740 196.951 1.00 18.98 S ATOM 37345 SG CYSS1 153 52.549 170.222 194.330 1.00 14.84 S ATOM 37392 SG CYSS1 159 57.450 174.526 194.206 1.00 29.40 S ATOM 37722 SG CYSS1 203 57.868 169.141 190.610 1.00 18.99 S ATOM 36481 SG CYSS1 41 60.342 167.352 203.773 1.00 23.37 S ATOM 36567 SG CYSS1 52 59.581 163.597 202.952 1.00 22.12 S ATOM 36592 SG CYSS1 55 62.874 162.313 207.413 1.00 29.83 S ATOM 36693 SG CYSS1 69 63.427 166.288 207.755 1.00 45.10 S ATOM 47419 SG CYSS7 119 66.805 133.050 163.532 1.00 17.09 S ATOM 47649 SG CYSS7 149 61.303 132.939 166.231 1.00 16.30 S ATOM 46921 SG CYSS7 55 62.183 129.492 160.514 1.00 29.16 S ATOM 46915 SG CYSS7 54 64.488 127.331 166.012 1.00 29.27 S ATOM 48842 SG CYSS8 116 57.406 141.076 165.731 1.00 22.33 S ATOM 48889 SG CYSS8 122 54.429 144.189 170.609 1.00 9.44 S ATOM 48616 SG CYSS8 87 60.827 144.949 169.749 1.00 21.70 S ATOM 48918 SG CYSS8 126 49.776 149.792 173.578 1.00 12.70 S ATOM 48589 SG CYSS8 83 55.979 150.481 171.591 1.00 11.54 S ATOM 48547 SG CYSS8 77 51.668 155.242 170.491 1.00 13.34 S ATOM 48566 SG CYSS8 80 53.673 153.781 176.622 1.00 17.01 S ATOM 50140 SG CYSS6 59 38.124 159.560 179.555 1.00 17.48 S ATOM 50318 SG CYSS6 84 41.759 161.513 178.631 1.00 13.86 S ATOM 50340 SG CYSS6 87 39.087 159.419 177.247 1.00 16.17 S Time building chain proxies: 41.27, per 1000 atoms: 0.43 Number of scatterers: 97049 At special positions: 0 Unit cell: (246.4, 226.8, 263.2, 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 628 16.00 P 9 15.00 O 17497 8.00 N 16481 7.00 C 62395 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=2.03 Simple disulfide: pdb=" SG CYSh1 40 " - pdb=" SG CYSh1 54 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYSAK 17 " - pdb=" SG CYSAK 74 " distance=2.04 Simple disulfide: pdb=" SG CYSAK 94 " - pdb=" SG CYSAK 114 " distance=2.04 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=2.04 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: 32.05 Conformation dependent library (CDL) restraints added in 10.9 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=" FE2 FESV2 300 " - pdb=" SG CYSV2 148 " pdb=" FE1 FESV2 300 " - pdb=" SG CYSV2 103 " pdb=" FE2 FESV2 300 " - pdb=" SG CYSV2 144 " pdb=" FE1 FESV2 300 " - pdb=" SG CYSV2 108 " pdb=" FESf1 501 " pdb=" FE2 FESf1 501 " - pdb=" ND1 HISf1 161 " pdb=" FE1 FESf1 501 " - pdb=" SG CYSf1 158 " pdb=" FE2 FESf1 501 " - pdb=" ND1 HISf1 141 " pdb=" FE1 FESf1 501 " - pdb=" SG CYSf1 139 " pdb=" FESf2 501 " pdb=" FE2 FESf2 501 " - pdb=" ND1 HISf2 161 " pdb=" FE1 FESf2 501 " - pdb=" SG CYSf2 139 " pdb=" FE2 FESf2 501 " - pdb=" ND1 HISf2 141 " pdb=" FE1 FESf2 501 " - pdb=" SG CYSf2 158 " pdb=" SF4S1 801 " pdb=" FE3 SF4S1 801 " - pdb=" NE2 HISS1 101 " pdb=" FE4 SF4S1 801 " - pdb=" SG CYSS1 108 " pdb=" FE1 SF4S1 801 " - pdb=" SG CYSS1 114 " pdb=" FE2 SF4S1 801 " - pdb=" SG CYSS1 105 " pdb=" SF4S1 802 " pdb=" FE2 SF4S1 802 " - pdb=" SG CYSS1 153 " pdb=" FE4 SF4S1 802 " - pdb=" SG CYSS1 203 " pdb=" FE3 SF4S1 802 " - pdb=" SG CYSS1 159 " pdb=" FE1 SF4S1 802 " - pdb=" SG CYSS1 156 " pdb=" SF4S7 300 " pdb=" FE1 SF4S7 300 " - pdb=" SG CYSS7 119 " pdb=" FE2 SF4S7 300 " - pdb=" SG CYSS7 149 " pdb=" FE4 SF4S7 300 " - pdb=" SG CYSS7 54 " pdb=" FE3 SF4S7 300 " - pdb=" SG CYSS7 55 " pdb=" SF4S8 201 " 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=" FE1 SF4S8 201 " - pdb=" SG CYSS8 119 " pdb=" FE2 SF4S8 201 " - pdb=" NE2 HISS8 65 " pdb=" SF4S8 202 " pdb=" FE2 SF4S8 202 " - pdb=" SG CYSS8 83 " pdb=" FE4 SF4S8 202 " - pdb=" SG CYSS8 80 " pdb=" FE1 SF4S8 202 " - pdb=" SG CYSS8 126 " pdb=" FE3 SF4S8 202 " - pdb=" SG CYSS8 77 " pdb=" SF4V1 500 " pdb=" FE1 SF4V1 500 " - pdb=" SG CYSV1 365 " pdb=" FE3 SF4V1 500 " - pdb=" SG CYSV1 362 " pdb=" FE2 SF4V1 500 " - pdb=" SG CYSV1 405 " pdb=" FE4 SF4V1 500 " - pdb=" SG CYSV1 359 " 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 23806 Ramachandran restraints generated. 11903 Oldfield, 0 Emsley, 11903 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 22708 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 467 helices and 38 sheets defined 48.5% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.79 Creating SS restraints... Processing helix chain 'a1' and resid 4 through 9 Processing helix chain 'a1' and resid 55 through 62 Processing helix chain 'a1' and resid 72 through 82 Processing helix chain 'a1' and resid 103 through 118 Proline residue: a1 107 - end of helix removed outlier: 3.509A pdb=" N LEUa1 112 " --> pdb=" O ALAa1 109 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEUa1 113 " --> pdb=" O VALa1 110 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLNa1 118 " --> pdb=" O ASPa1 115 " (cutoff:3.500A) 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 Processing helix chain 'a1' and resid 179 through 188 Processing helix chain 'a1' and resid 206 through 215 Processing helix chain 'a1' and resid 265 through 276 Processing helix chain 'a1' and resid 293 through 300 Processing helix chain 'a1' and resid 332 through 347 Processing helix chain 'a1' and resid 352 through 368 Processing helix chain 'a1' and resid 372 through 383 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 66 through 70 Processing helix chain 'a2' and resid 82 through 92 Processing helix chain 'a2' and resid 117 through 128 Processing helix chain 'a2' and resid 134 through 152 Processing helix chain 'a2' and resid 155 through 164 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 222 Processing helix chain 'a2' and resid 267 through 279 Processing helix chain 'a2' and resid 295 through 302 Processing helix chain 'a2' and resid 333 through 348 Processing helix chain 'a2' and resid 354 through 370 Processing helix chain 'a2' and resid 375 through 388 Processing helix chain 'a2' and resid 395 through 403 Processing helix chain 'a2' and resid 408 through 419 Processing helix chain 'a2' and resid 430 through 432 No H-bonds generated for 'chain 'a2' and resid 430 through 432' Processing helix chain 'b1' and resid 11 through 17 Processing helix chain 'b1' and resid 29 through 53 removed outlier: 4.284A pdb=" N PHEb1 33 " --> pdb=" O TRPb1 30 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLYb1 34 " --> pdb=" O TRPb1 31 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THRb1 47 " --> pdb=" O GLNb1 44 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLYb1 48 " --> pdb=" O ILEb1 45 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEUb1 51 " --> pdb=" O GLYb1 48 " (cutoff:3.500A) Processing helix chain 'b1' and resid 61 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 111 through 133 Processing helix chain 'b1' and resid 137 through 152 Processing helix chain 'b1' and resid 157 through 163 Processing helix chain 'b1' and resid 172 through 203 Proline residue: b1 186 - end of helix Processing helix chain 'b1' and resid 214 through 216 No H-bonds generated for 'chain 'b1' and resid 214 through 216' Processing helix chain 'b1' and resid 224 through 244 Processing helix chain 'b1' and resid 253 through 255 No H-bonds generated for 'chain 'b1' and resid 253 through 255' Processing helix chain 'b1' and resid 272 through 279 removed outlier: 3.925A pdb=" N LEUb1 275 " --> pdb=" O TRPb1 272 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N PHEb1 276 " --> pdb=" O TYRb1 273 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALAb1 277 " --> pdb=" O PHEb1 274 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALAb1 279 " --> pdb=" O PHEb1 276 " (cutoff:3.500A) Processing helix chain 'b1' and resid 287 through 306 Proline residue: b1 305 - end of helix Processing helix chain 'b1' and resid 319 through 339 Processing helix chain 'b1' and resid 345 through 363 Processing helix chain 'b1' and resid 365 through 377 removed outlier: 3.723A 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 52 removed outlier: 3.828A pdb=" N VALc1 52 " --> pdb=" O ARGc1 49 " (cutoff:3.500A) Processing helix chain 'c1' and resid 58 through 67 Processing helix chain 'c1' and resid 98 through 104 removed outlier: 3.824A pdb=" N ALAc1 104 " --> pdb=" O ALAc1 100 " (cutoff:3.500A) 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 231 Proline residue: c1 216 - end of helix removed outlier: 3.561A pdb=" N TYRc1 219 " --> pdb=" O LEUc1 215 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VALc1 228 " --> pdb=" O HISc1 224 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LEUc1 229 " --> pdb=" O LYSc1 225 " (cutoff:3.500A) Processing helix chain 'f1' and resid 2 through 4 No H-bonds generated for 'chain 'f1' and resid 2 through 4' 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 29 through 61 Processing helix chain 'f1' and resid 103 through 110 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 33 through 35 No H-bonds generated for 'chain 'd1' and resid 33 through 35' Processing helix chain 'd1' and resid 41 through 48 Processing helix chain 'd1' and resid 52 through 71 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 33 through 70 removed outlier: 3.838A pdb=" N CYSq1 44 " --> pdb=" O ARGq1 40 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N LEUq1 46 " --> pdb=" O ARGq1 42 " (cutoff:3.500A) removed outlier: 4.804A 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 71 Processing helix chain 'i1' and resid 6 through 13 Processing helix chain 'i1' and resid 17 through 45 Processing helix chain 'i1' and resid 52 through 58 Processing helix chain 'a3' and resid 4 through 8 Processing helix chain 'a3' and resid 56 through 62 Processing helix chain 'a3' and resid 74 through 81 Processing helix chain 'a3' and resid 106 through 117 Processing helix chain 'a3' and resid 124 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 174 No H-bonds generated for 'chain 'a3' and resid 171 through 174' Processing helix chain 'a3' and resid 179 through 188 Processing helix chain 'a3' and resid 205 through 215 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 385 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 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 116 through 128 Processing helix chain 'a4' and resid 134 through 151 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 201 through 203 No H-bonds generated for 'chain 'a4' and resid 201 through 203' 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 333 through 348 Processing helix chain 'a4' and resid 354 through 371 Processing helix chain 'a4' and resid 375 through 388 Processing helix chain 'a4' and resid 395 through 402 Processing helix chain 'a4' and resid 407 through 418 Processing helix chain 'b2' and resid 9 through 18 removed outlier: 3.887A pdb=" N ILEb2 13 " --> pdb=" O PROb2 9 " (cutoff:3.500A) Processing helix chain 'b2' and resid 29 through 54 removed outlier: 3.708A pdb=" N PHEb2 33 " --> pdb=" O TRPb2 30 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLYb2 34 " --> pdb=" O TRPb2 31 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYSb2 40 " --> pdb=" O LEUb2 37 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THRb2 47 " --> pdb=" O GLNb2 44 " (cutoff:3.500A) Processing helix chain 'b2' and resid 61 through 71 Processing helix chain 'b2' and resid 76 through 103 Processing helix chain 'b2' and resid 106 through 108 No H-bonds generated for 'chain 'b2' and resid 106 through 108' Processing helix chain 'b2' and resid 111 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 224 through 244 Processing helix chain 'b2' and resid 247 through 249 No H-bonds generated for 'chain 'b2' and resid 247 through 249' Processing helix chain 'b2' and resid 253 through 256 Processing helix chain 'b2' and resid 272 through 274 No H-bonds generated for 'chain 'b2' and resid 272 through 274' Processing helix chain 'b2' and resid 276 through 279 No H-bonds generated for 'chain 'b2' and resid 276 through 279' Processing helix chain 'b2' and resid 287 through 307 Proline residue: b2 305 - end of helix 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 376 Processing helix chain 'c2' and resid 23 through 35 Processing helix chain 'c2' and resid 48 through 51 Processing helix chain 'c2' and resid 58 through 66 Processing helix chain 'c2' and resid 98 through 102 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 225 removed outlier: 3.505A pdb=" N LEUc2 215 " --> pdb=" O METc2 211 " (cutoff:3.500A) Proline residue: c2 216 - end of helix Processing helix chain 'f2' and resid 27 through 61 removed outlier: 4.724A pdb=" N ALAf2 31 " --> pdb=" O GLUf2 27 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARGf2 32 " --> pdb=" O SERf2 28 " (cutoff:3.500A) Processing helix chain 'f2' and resid 103 through 111 Processing helix chain 'f2' and resid 123 through 125 No H-bonds generated for 'chain 'f2' and resid 123 through 125' Processing helix chain 'd2' and resid 10 through 22 Processing helix chain 'd2' and resid 34 through 36 No H-bonds generated for 'chain 'd2' and resid 34 through 36' Processing helix chain 'd2' and resid 41 through 48 Processing helix chain 'd2' and resid 52 through 70 Processing helix chain 'd2' and resid 91 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: 4.010A pdb=" N VALq2 53 " --> pdb=" O ALAq2 49 " (cutoff:3.500A) Processing helix chain 'h2' and resid 17 through 25 removed outlier: 3.748A pdb=" N GLUh2 25 " --> pdb=" O ARGh2 21 " (cutoff:3.500A) Processing helix chain 'h2' and resid 29 through 45 Processing helix chain 'h2' and resid 56 through 70 Processing helix chain 'i2' and resid 4 through 13 Processing helix chain 'i2' and resid 18 through 47 removed outlier: 4.142A pdb=" N ASNi2 47 " --> pdb=" O TYRi2 43 " (cutoff:3.500A) Processing helix chain 'i2' and resid 54 through 57 No H-bonds generated for 'chain 'i2' and resid 54 through 57' Processing helix chain 'V1' and resid 33 through 39 Processing helix chain 'V1' and resid 45 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 107 through 113 Processing helix chain 'V1' and resid 115 through 128 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 191 through 196 Processing helix chain 'V1' and resid 225 through 236 Proline residue: V1 232 - end of helix removed outlier: 3.847A pdb=" N CYSV1 235 " --> pdb=" O SERV1 231 " (cutoff:3.500A) Processing helix chain 'V1' and resid 276 through 281 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 380 Processing helix chain 'V1' and resid 387 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 36 Processing helix chain 'V2' and resid 43 through 57 removed outlier: 3.748A pdb=" N ALAV2 46 " --> pdb=" O LYSV2 43 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VALV2 47 " --> pdb=" O ALAV2 44 " (cutoff:3.500A) removed outlier: 4.338A 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 85 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 113 through 124 Processing helix chain 'V2' and resid 166 through 178 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 159 through 165 Processing helix chain 'S1' and resid 196 through 199 removed outlier: 4.001A pdb=" N ILES1 199 " --> pdb=" O SERS1 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'S1' and resid 196 through 199' Processing helix chain 'S1' and resid 219 through 221 No H-bonds generated for 'chain 'S1' and resid 219 through 221' 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 296 through 309 Processing helix chain 'S1' and resid 325 through 338 Processing helix chain 'S1' and resid 359 through 361 No H-bonds generated for 'chain 'S1' and resid 359 through 361' Processing helix chain 'S1' and resid 369 through 371 No H-bonds generated for 'chain 'S1' and resid 369 through 371' 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 463 through 478 Processing helix chain 'S1' and resid 497 through 504 Processing helix chain 'S1' and resid 510 through 516 removed outlier: 4.460A pdb=" N ALAS1 513 " --> pdb=" O GLYS1 510 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYSS1 516 " --> pdb=" O ALAS1 513 " (cutoff:3.500A) 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 566 through 568 No H-bonds generated for 'chain 'S1' and resid 566 through 568' Processing helix chain 'S1' and resid 596 through 606 Processing helix chain 'S1' and resid 616 through 624 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 680 Processing helix chain 'S1' and resid 682 through 692 Processing helix chain 'S2' and resid 8 through 13 Processing helix chain 'S2' and resid 25 through 27 No H-bonds generated for 'chain 'S2' and resid 25 through 27' 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 185 removed outlier: 4.186A 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 280 Processing helix chain 'S2' and resid 293 through 316 Processing helix chain 'S2' and resid 335 through 340 Processing helix chain 'S2' and resid 342 through 353 Processing helix chain 'S2' and resid 394 through 400 Processing helix chain 'S2' and resid 402 through 405 No H-bonds generated for 'chain 'S2' and resid 402 through 405' Processing helix chain 'S2' and resid 411 through 419 Processing helix chain 'S3' and resid 17 through 32 Processing helix chain 'S3' and resid 57 through 65 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: 3.606A pdb=" N ASNS3 128 " --> pdb=" O LYSS3 125 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TRPS3 129 " --> pdb=" O ALAS3 126 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYRS3 130 " --> pdb=" O ALAS3 127 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILES3 134 " --> pdb=" O GLUS3 131 " (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 44 removed outlier: 4.676A pdb=" N SERS7 44 " --> pdb=" O ALAS7 40 " (cutoff:3.500A) Processing helix chain 'S7' and resid 55 through 62 Processing helix chain 'S7' and resid 94 through 104 Proline residue: S7 98 - end of helix 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 28 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 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 23 through 27 Processing helix chain 'S6' and resid 41 through 46 removed outlier: 3.834A pdb=" N ALAS6 45 " --> pdb=" O ILES6 41 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLUS6 46 " --> pdb=" O ASPS6 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'S6' and resid 41 through 46' Processing helix chain 'S4' and resid 19 through 21 No H-bonds generated for 'chain 'S4' and resid 19 through 21' Processing helix chain 'S4' and resid 27 through 31 Processing helix chain 'S4' and resid 90 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 54 through 60 Processing helix chain 'A9' and resid 79 through 84 Processing helix chain 'A9' and resid 109 through 124 Proline residue: A9 114 - end of helix 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 249 Processing helix chain 'A9' and resid 282 through 287 Processing helix chain 'A9' and resid 300 through 303 No H-bonds generated for 'chain 'A9' and resid 300 through 303' 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: 4.455A pdb=" N ALAA5 60 " --> pdb=" O SERA5 56 " (cutoff:3.500A) Processing helix chain 'A5' and resid 64 through 70 Processing helix chain 'A5' and resid 77 through 94 Processing helix chain 'A6' and resid 24 through 39 Processing helix chain 'A6' and resid 42 through 48 Processing helix chain 'A6' and resid 55 through 69 removed outlier: 4.212A 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 119 through 122 No H-bonds generated for 'chain 'A6' and resid 119 through 122' Processing helix chain 'A7' and resid 5 through 14 Processing helix chain 'A7' and resid 58 through 61 Processing helix chain 'AL' and resid 24 through 27 No H-bonds generated for 'chain 'AL' and resid 24 through 27' 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 57 Processing helix chain 'AA' and resid 64 through 68 Processing helix chain 'AA' and resid 73 through 83 Processing helix chain 'AM' and resid 31 through 96 Proline residue: AM 72 - end of helix Processing helix chain 'AM' and resid 130 through 136 Processing helix chain 'AM' and resid 138 through 141 No H-bonds generated for 'chain 'AM' and resid 138 through 141' Processing helix chain 'D3' and resid 2 through 22 Processing helix chain 'D3' and resid 57 through 72 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 45 through 57 Processing helix chain 'D1' and resid 68 through 87 Proline residue: D1 75 - end of helix removed outlier: 4.752A pdb=" N TRPD1 86 " --> pdb=" O ALAD1 82 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ILED1 87 " --> pdb=" O LEUD1 83 " (cutoff:3.500A) Processing helix chain 'D1' and resid 102 through 123 Processing helix chain 'D1' and resid 127 through 141 Processing helix chain 'D1' and resid 145 through 156 removed outlier: 3.762A pdb=" N METD1 156 " --> pdb=" O SERD1 152 " (cutoff:3.500A) Processing helix chain 'D1' and resid 162 through 168 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 180 through 192 Processing helix chain 'D1' and resid 197 through 199 No H-bonds generated for 'chain 'D1' and resid 197 through 199' Processing helix chain 'D1' and resid 210 through 212 No H-bonds generated for 'chain 'D1' and resid 210 through 212' 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 310 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 73 Processing helix chain 'D6' and resid 83 through 85 No H-bonds generated for 'chain 'D6' and resid 83 through 85' Processing helix chain 'D6' and resid 87 through 108 Processing helix chain 'D6' and resid 138 through 144 Processing helix chain 'D6' and resid 151 through 173 removed outlier: 3.712A pdb=" N ILED6 155 " --> pdb=" O THRD6 151 " (cutoff:3.500A) Processing helix chain '4L' and resid 3 through 20 removed outlier: 3.524A pdb=" N VAL4L 14 " --> pdb=" O ALA4L 11 " (cutoff:3.500A) Processing helix chain '4L' and resid 26 through 51 Processing helix chain '4L' and resid 54 through 56 No H-bonds generated for 'chain '4L' and resid 54 through 56' Processing helix chain '4L' and resid 58 through 84 Processing helix chain 'D5' and resid 2 through 13 Processing helix chain 'D5' and resid 17 through 23 Processing helix chain 'D5' and resid 32 through 57 removed outlier: 4.255A 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 88 Processing helix chain 'D5' and resid 90 through 107 Processing helix chain 'D5' and resid 114 through 133 Processing helix chain 'D5' and resid 137 through 155 Processing helix chain 'D5' and resid 162 through 193 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 238 Processing helix chain 'D5' and resid 241 through 249 Processing helix chain 'D5' and resid 255 through 262 removed outlier: 3.557A pdb=" N LEUD5 259 " --> pdb=" O ALAD5 255 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEUD5 260 " --> pdb=" O GLYD5 256 " (cutoff:3.500A) Processing helix chain 'D5' and resid 271 through 291 Processing helix chain 'D5' and resid 298 through 318 Processing helix chain 'D5' and resid 322 through 349 Processing helix chain 'D5' and resid 367 through 379 Processing helix chain 'D5' and resid 387 through 400 removed outlier: 4.245A pdb=" N SERD5 391 " --> pdb=" O THRD5 387 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYSD5 392 " --> pdb=" O GLYD5 388 " (cutoff:3.500A) Processing helix chain 'D5' and resid 408 through 430 Processing helix chain 'D5' and resid 448 through 470 removed outlier: 5.047A pdb=" N GLYD5 465 " --> pdb=" O SERD5 461 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N PHED5 466 " --> pdb=" O LEUD5 462 " (cutoff:3.500A) 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 547 removed outlier: 3.592A pdb=" N TYRD5 529 " --> pdb=" O LEUD5 526 " (cutoff:3.500A) Proline residue: D5 530 - end of helix removed outlier: 3.719A pdb=" N METD5 533 " --> pdb=" O PROD5 530 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HISD5 534 " --> pdb=" O THRD5 531 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARGD5 535 " --> pdb=" O ILED5 532 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N THRD5 537 " --> pdb=" O HISD5 534 " (cutoff:3.500A) Proline residue: D5 538 - end of helix removed outlier: 4.867A pdb=" N ASND5 541 " --> pdb=" O PROD5 538 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEUD5 542 " --> pdb=" O TYRD5 539 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYSD5 547 " --> pdb=" O METD5 544 " (cutoff:3.500A) Processing helix chain 'D5' and resid 555 through 561 Processing helix chain 'D5' and resid 563 through 577 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 Processing helix chain 'D4' and resid 23 through 41 removed outlier: 4.022A pdb=" N LEUD4 41 " --> pdb=" O THRD4 37 " (cutoff:3.500A) Processing helix chain 'D4' and resid 63 through 80 Proline residue: D4 74 - end of helix Processing helix chain 'D4' and resid 89 through 110 Processing helix chain 'D4' and resid 115 through 136 Proline residue: D4 128 - end of helix removed outlier: 3.813A pdb=" N ILED4 131 " --> pdb=" O VALD4 127 " (cutoff:3.500A) Processing helix chain 'D4' and resid 142 through 171 Proline residue: D4 159 - end of helix removed outlier: 4.034A pdb=" N VALD4 162 " --> pdb=" O LEUD4 158 " (cutoff:3.500A) Processing helix chain 'D4' and resid 176 through 181 Processing helix chain 'D4' and resid 191 through 206 Processing helix chain 'D4' and resid 210 through 212 No H-bonds generated for 'chain 'D4' and resid 210 through 212' Processing helix chain 'D4' and resid 214 through 221 removed outlier: 4.646A pdb=" N LYSD4 218 " --> pdb=" O LEUD4 214 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALAD4 219 " --> pdb=" O TRPD4 215 " (cutoff:3.500A) Processing helix chain 'D4' and resid 225 through 248 removed outlier: 4.491A pdb=" N LEUD4 248 " --> pdb=" O METD4 244 " (cutoff:3.500A) Processing helix chain 'D4' and resid 254 through 257 No H-bonds generated for 'chain 'D4' and resid 254 through 257' Processing helix chain 'D4' and resid 259 through 277 removed outlier: 4.072A pdb=" N LEUD4 277 " --> pdb=" O SERD4 273 " (cutoff:3.500A) Processing helix chain 'D4' and resid 282 through 303 removed outlier: 3.748A pdb=" N ILED4 303 " --> pdb=" O ALAD4 300 " (cutoff:3.500A) Processing helix chain 'D4' and resid 306 through 337 Processing helix chain 'D4' and resid 355 through 366 Processing helix chain 'D4' and resid 373 through 389 Processing helix chain 'D4' and resid 393 through 414 removed outlier: 4.196A pdb=" N THRD4 414 " --> pdb=" O METD4 410 " (cutoff:3.500A) Processing helix chain 'D4' and resid 431 through 449 removed outlier: 3.793A pdb=" N LEUD4 442 " --> pdb=" O SERD4 438 " (cutoff:3.500A) 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 41 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 121 removed outlier: 4.252A pdb=" N GLYD2 121 " --> pdb=" O GLUD2 117 " (cutoff:3.500A) Processing helix chain 'D2' and resid 124 through 148 Proline residue: D2 138 - end of helix removed outlier: 3.817A 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 176 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 238 through 252 removed outlier: 3.750A pdb=" N ILED2 242 " --> pdb=" O PROD2 238 " (cutoff:3.500A) Processing helix chain 'D2' and resid 261 through 271 removed outlier: 3.691A pdb=" N METD2 265 " --> pdb=" O METD2 261 " (cutoff:3.500A) Processing helix chain 'D2' and resid 277 through 300 removed outlier: 4.395A pdb=" N LEUD2 290 " --> pdb=" O ALAD2 286 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N TYRD2 291 " --> pdb=" O LEUD2 287 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N PHED2 292 " --> pdb=" O LEUD2 288 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N TYRD2 293 " --> pdb=" O ASND2 289 " (cutoff:3.500A) Processing helix chain 'D2' and resid 311 through 316 removed outlier: 4.897A pdb=" N GLND2 316 " --> pdb=" O LYSD2 312 " (cutoff:3.500A) Processing helix chain 'D2' and resid 326 through 334 Processing helix chain 'D2' and resid 340 through 342 No H-bonds generated for 'chain 'D2' and resid 340 through 342' Processing helix chain 'AK' and resid 2 through 8 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 108 through 130 Processing helix chain 'B5' and resid 16 through 30 Processing helix chain 'B5' and resid 34 through 46 Processing helix chain 'B5' and resid 70 through 79 Processing helix chain 'B5' and resid 83 through 117 Processing helix chain 'B5' and resid 130 through 132 No H-bonds generated for 'chain 'B5' and resid 130 through 132' Processing helix chain 'AB' and resid 8 through 20 Processing helix chain 'AB' and resid 36 through 39 No H-bonds generated for 'chain 'AB' and resid 36 through 39' Processing helix chain 'AB' and resid 44 through 58 Processing helix chain 'AB' and resid 73 through 84 Processing helix chain 'A8' and resid 21 through 33 removed outlier: 4.122A pdb=" N ALAA8 28 " --> pdb=" O LEUA8 24 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N HISA8 29 " --> pdb=" O LYSA8 25 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N HISA8 30 " --> pdb=" O ALAA8 26 " (cutoff:3.500A) Processing helix chain 'A8' and resid 38 through 49 removed outlier: 3.503A pdb=" N TRPA8 47 " --> pdb=" O LEUA8 44 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLUA8 48 " --> pdb=" O CYSA8 45 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLUA8 49 " --> pdb=" O ARGA8 46 " (cutoff:3.500A) Processing helix chain 'A8' and resid 56 through 75 Processing helix chain 'A8' and resid 80 through 88 Processing helix chain 'A8' and resid 101 through 113 Processing helix chain 'BJ' and resid 28 through 56 removed outlier: 4.863A 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 removed outlier: 3.638A pdb=" N PHEBJ 85 " --> pdb=" O VALBJ 81 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLUBJ 86 " --> pdb=" O LEUBJ 82 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 125 through 141 Processing helix chain 'BJ' and resid 152 through 171 Processing helix chain 'AJ' and resid 5 through 10 Processing helix chain 'AJ' and resid 36 through 46 Processing helix chain 'AJ' and resid 56 through 61 removed outlier: 4.129A pdb=" N ALAAJ 59 " --> pdb=" O ILEAJ 56 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 79 through 84 Processing helix chain 'AJ' and resid 94 through 116 Processing helix chain 'AJ' and resid 128 through 140 Processing helix chain 'AJ' and resid 146 through 162 removed outlier: 3.656A pdb=" N VALAJ 160 " --> pdb=" O LYSAJ 156 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N CYSAJ 161 " --> pdb=" O LYSAJ 157 " (cutoff:3.500A) removed outlier: 5.185A 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 231 through 240 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 269 through 272 removed outlier: 3.578A pdb=" N TYRAJ 272 " --> pdb=" O VALAJ 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'AJ' and resid 269 through 272' Processing helix chain 'AJ' and resid 286 through 297 Processing helix chain 'AJ' and resid 306 through 308 No H-bonds generated for 'chain 'AJ' and resid 306 through 308' 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 15 through 17 No H-bonds generated for 'chain 'S5' and resid 15 through 17' Processing helix chain 'S5' and resid 33 through 42 Processing helix chain 'S5' and resid 50 through 53 No H-bonds generated for 'chain 'S5' and resid 50 through 53' Processing helix chain 'S5' and resid 56 through 66 Processing helix chain 'S5' and resid 69 through 88 Processing helix chain 'A3' and resid 16 through 30 Processing helix chain 'A3' and resid 38 through 46 Processing helix chain 'B3' and resid 26 through 38 Processing helix chain 'B3' and resid 49 through 52 No H-bonds generated for 'chain 'B3' and resid 49 through 52' Processing helix chain 'B3' and resid 62 through 66 removed outlier: 3.662A pdb=" N LEUB3 66 " --> pdb=" O PHEB3 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B3' and resid 62 through 66' Processing helix chain 'B3' and resid 68 through 71 removed outlier: 3.778A pdb=" N LYSB3 71 " --> pdb=" O LYSB3 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'B3' and resid 68 through 71' 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 50 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 'B6' and resid 5 through 25 Processing helix chain 'B6' and resid 68 through 91 Proline residue: B6 77 - end of helix removed outlier: 3.694A pdb=" N TYRB6 87 " --> pdb=" O TYRB6 83 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HISB6 88 " --> pdb=" O TYRB6 84 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VALB6 89 " --> pdb=" O LEUB6 85 " (cutoff:3.500A) Processing helix chain 'B7' and resid 3 through 9 Processing helix chain 'B7' and resid 42 through 48 Processing helix chain 'B7' and resid 60 through 71 Processing helix chain 'B7' and resid 81 through 117 Processing helix chain 'B9' and resid 11 through 29 Processing helix chain 'B9' and resid 34 through 47 Processing helix chain 'B9' and resid 57 through 71 Processing helix chain 'B9' and resid 108 through 113 Processing helix chain 'B9' and resid 115 through 131 Processing helix chain 'B9' and resid 133 through 142 Processing helix chain 'B9' and resid 167 through 170 No H-bonds generated for 'chain 'B9' and resid 167 through 170' Processing helix chain 'B2' and resid 19 through 40 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 16 through 26 removed outlier: 3.805A pdb=" N ARGB8 20 " --> pdb=" O THRB8 16 " (cutoff:3.500A) Processing helix chain 'B8' and resid 99 through 121 Processing helix chain 'BK' and resid 53 through 63 Processing helix chain 'BK' and resid 70 through 78 Processing helix chain 'BK' and resid 86 through 102 Processing helix chain 'C1' and resid 16 through 45 Processing helix chain 'B1' and resid 12 through 33 removed outlier: 3.921A pdb=" N LEUB1 15 " --> pdb=" O ILEB1 12 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N VALB1 16 " --> pdb=" O HISB1 13 " (cutoff:3.500A) Proline residue: B1 17 - end of helix 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 30 Proline residue: A1 19 - end of helix Processing helix chain 'A1' and resid 42 through 53 Processing helix chain 'A1' and resid 60 through 62 No H-bonds generated for 'chain 'A1' and resid 60 through 62' Processing sheet with id= A, first strand: chain 'a1' and resid 15 through 19 removed outlier: 6.711A pdb=" N METa1 195 " --> pdb=" O ARGa1 24 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ALAa1 26 " --> pdb=" O METa1 195 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEUa1 197 " --> pdb=" O ALAa1 26 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N GLUa1 28 " --> pdb=" O LEUa1 197 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALAa1 199 " --> pdb=" O GLUa1 28 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'a1' and resid 240 through 244 removed outlier: 6.221A pdb=" N VALa1 422 " --> pdb=" O ILEa1 241 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N HISa1 243 " --> pdb=" O VALa1 422 " (cutoff:3.500A) removed outlier: 6.711A 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 246 Processing sheet with id= E, first strand: chain 'f1' and resid 74 through 77 Processing sheet with id= F, first strand: chain 'f1' and resid 85 through 91 Processing sheet with id= G, first strand: chain 'a3' and resid 15 through 19 Processing sheet with id= H, first strand: chain 'a3' and resid 239 through 244 Processing sheet with id= I, first strand: chain 'a4' and resid 25 through 29 Processing sheet with id= J, first strand: chain 'a4' and resid 242 through 247 Processing sheet with id= K, first strand: chain 'b2' and resid 22 through 24 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 85 through 88 Processing sheet with id= N, first strand: chain 'V1' and resid 221 through 224 removed outlier: 6.830A pdb=" N ALAV1 133 " --> pdb=" O LEUV1 93 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N VALV1 95 " --> pdb=" O ALAV1 133 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N TYRV1 135 " --> pdb=" O VALV1 95 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ALAV1 97 " --> pdb=" O TYRV1 135 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N TYRV1 137 " --> pdb=" O ALAV1 97 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'V1' and resid 253 through 258 Processing sheet with id= P, first strand: chain 'V1' and resid 294 through 298 removed outlier: 6.830A pdb=" N METV1 337 " --> pdb=" O LEUV1 295 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N VALV1 297 " --> pdb=" O ILEV1 335 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILEV1 335 " --> pdb=" O VALV1 297 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'V2' and resid 137 through 142 removed outlier: 6.604A pdb=" N TYRV2 98 " --> pdb=" O THRV2 138 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ILEV2 140 " --> pdb=" O TYRV2 98 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ILEV2 100 " --> pdb=" O ILEV2 140 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VALV2 142 " --> pdb=" O ILEV2 100 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VALV2 102 " --> pdb=" O VALV2 142 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'S1' and resid 16 through 20 removed outlier: 6.280A pdb=" N TRPS1 77 " --> pdb=" O PHES1 12 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'S1' and resid 146 through 148 Processing sheet with id= T, first strand: chain 'S1' and resid 173 through 177 Processing sheet with id= U, first strand: chain 'S1' and resid 223 through 228 Processing sheet with id= V, first strand: chain 'S1' and resid 342 through 344 removed outlier: 6.564A pdb=" N METS1 521 " --> pdb=" O ALAS1 316 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ILES1 318 " --> pdb=" O METS1 521 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHES1 523 " --> pdb=" O ILES1 318 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N PHES1 542 " --> pdb=" O LEUS1 522 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEUS1 524 " --> pdb=" O PHES1 542 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VALS1 544 " --> pdb=" O LEUS1 524 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N VALS1 559 " --> pdb=" O TYRS1 545 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLYS1 547 " --> pdb=" O VALS1 559 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEUS1 561 " --> pdb=" O GLYS1 547 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'S1' and resid 405 through 409 Processing sheet with id= X, first strand: chain 'S1' and resid 572 through 574 Processing sheet with id= Y, first strand: chain 'S2' and resid 47 through 51 Processing sheet with id= Z, first strand: chain 'S2' and resid 361 through 369 Processing sheet with id= AA, first strand: chain 'S3' and resid 39 through 42 Processing sheet with id= AB, first strand: chain 'S3' and resid 173 through 177 Processing sheet with id= AC, first strand: chain 'S7' and resid 85 through 89 removed outlier: 6.529A pdb=" N TYRS7 112 " --> pdb=" O METS7 86 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VALS7 88 " --> pdb=" O TYRS7 112 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VALS7 114 " --> pdb=" O VALS7 88 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILES7 144 " --> pdb=" O SERS7 115 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'S8' and resid 92 through 95 Processing sheet with id= AE, first strand: chain 'S6' and resid 56 through 59 Processing sheet with id= AF, first strand: chain 'S4' and resid 103 through 105 removed outlier: 6.743A pdb=" N ALAS4 35 " --> pdb=" O ASPS4 104 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'A9' and resid 228 through 230 removed outlier: 6.637A pdb=" N VALA9 91 " --> pdb=" O ILEA9 130 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N ILEA9 132 " --> pdb=" O VALA9 91 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ASNA9 93 " --> pdb=" O ILEA9 132 " (cutoff:3.500A) removed outlier: 9.252A pdb=" N HISA9 134 " --> pdb=" O ASNA9 93 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N GLNA9 44 " --> pdb=" O ALAA9 21 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VALA9 23 " --> pdb=" O GLNA9 44 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILEA9 46 " --> pdb=" O VALA9 23 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ILEA9 69 " --> pdb=" O VALA9 47 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'A2' and resid 52 through 56 removed outlier: 6.704A pdb=" N ILEA2 18 " --> pdb=" O LEUA2 53 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ARGA2 55 " --> pdb=" O ILEA2 18 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILEA2 20 " --> pdb=" O ARGA2 55 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'AL' and resid 40 through 42 Processing sheet with id= AJ, first strand: chain 'D5' and resid 61 through 68 removed outlier: 4.850A pdb=" N HISD5 67 " --> pdb=" O LEUD5 76 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEUD5 76 " --> pdb=" O HISD5 67 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'D4' and resid 50 through 52 Processing sheet with id= AL, first strand: chain 'AJ' and resid 122 through 124 removed outlier: 6.325A pdb=" N VALAJ 168 " --> pdb=" O THRAJ 26 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ASPAJ 28 " --> pdb=" O VALAJ 168 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ILEAJ 170 " --> pdb=" O ASPAJ 28 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLUAJ 219 " --> pdb=" O VALAJ 169 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N TYRAJ 171 " --> pdb=" O GLUAJ 219 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LEUAJ 221 " --> pdb=" O TYRAJ 171 " (cutoff:3.500A) 4289 hydrogen bonds defined for protein. 12267 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: 40.15 Time building geometry restraints manager: 35.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 41644 1.42 - 1.64: 56761 1.64 - 1.86: 1007 1.86 - 2.08: 24 2.08 - 2.31: 88 Bond restraints: 99524 Sorted by residual: bond pdb=" C2D HECc2 501 " pdb=" C3D HECc2 501 " ideal model delta sigma weight residual 1.544 1.321 0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" C2D HECc1 501 " pdb=" C3D HECc1 501 " ideal model delta sigma weight residual 1.544 1.323 0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" CAC HECc2 501 " pdb=" CBC HECc2 501 " ideal model delta sigma weight residual 1.544 1.362 0.182 2.00e-02 2.50e+03 8.33e+01 bond pdb=" CAC HECc1 501 " pdb=" CBC HECc1 501 " ideal model delta sigma weight residual 1.544 1.366 0.178 2.00e-02 2.50e+03 7.94e+01 bond pdb=" CAB HECc2 501 " pdb=" CBB HECc2 501 " ideal model delta sigma weight residual 1.544 1.400 0.144 2.00e-02 2.50e+03 5.19e+01 ... (remaining 99519 not shown) Histogram of bond angle deviations from ideal: 70.29 - 92.08: 111 92.08 - 113.87: 58917 113.87 - 135.67: 76066 135.67 - 157.46: 7 157.46 - 179.25: 12 Bond angle restraints: 135113 Sorted by residual: angle pdb=" PA NDPA9 401 " pdb=" O3 NDPA9 401 " pdb=" PN NDPA9 401 " ideal model delta sigma weight residual 107.74 132.90 -25.16 1.95e+00 2.62e-01 1.66e+02 angle pdb=" S1 FESf2 501 " pdb=" FE2 FESf2 501 " pdb=" S2 FESf2 501 " ideal model delta sigma weight residual 104.33 90.18 14.15 1.14e+00 7.69e-01 1.54e+02 angle pdb=" FE1 FESf2 501 " pdb=" S2 FESf2 501 " pdb=" FE2 FESf2 501 " ideal model delta sigma weight residual 75.66 89.73 -14.07 1.14e+00 7.69e-01 1.52e+02 angle pdb=" S1 FESf1 501 " pdb=" FE2 FESf1 501 " pdb=" S2 FESf1 501 " ideal model delta sigma weight residual 104.33 90.72 13.61 1.14e+00 7.69e-01 1.43e+02 angle pdb=" FE1 FESf2 501 " pdb=" S1 FESf2 501 " pdb=" FE2 FESf2 501 " ideal model delta sigma weight residual 75.66 89.88 -14.22 1.20e+00 6.94e-01 1.40e+02 ... (remaining 135108 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.33: 58185 27.33 - 54.67: 1190 54.67 - 82.00: 109 82.00 - 109.33: 16 109.33 - 136.66: 3 Dihedral angle restraints: 59503 sinusoidal: 24285 harmonic: 35218 Sorted by residual: dihedral pdb=" CA PHEAJ 278 " pdb=" C PHEAJ 278 " pdb=" N LEUAJ 279 " pdb=" CA LEUAJ 279 " ideal model delta harmonic sigma weight residual 180.00 120.22 59.78 0 5.00e+00 4.00e-02 1.43e+02 dihedral pdb=" CA LYSB3 22 " pdb=" C LYSB3 22 " pdb=" N ILEB3 23 " pdb=" CA ILEB3 23 " ideal model delta harmonic sigma weight residual 180.00 -122.01 -57.99 0 5.00e+00 4.00e-02 1.35e+02 dihedral pdb=" CA SERD4 53 " pdb=" C SERD4 53 " pdb=" N LEUD4 54 " pdb=" CA LEUD4 54 " ideal model delta harmonic sigma weight residual -180.00 -124.34 -55.66 0 5.00e+00 4.00e-02 1.24e+02 ... (remaining 59500 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.229: 14808 4.229 - 8.458: 0 8.458 - 12.687: 0 12.687 - 16.916: 0 16.916 - 21.145: 24 Chirality restraints: 14832 Sorted by residual: 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 -10.59 21.15 2.00e-01 2.50e+01 1.12e+04 chirality pdb=" FE1 SF4S8 202 " pdb=" S2 SF4S8 202 " pdb=" S3 SF4S8 202 " pdb=" S4 SF4S8 202 " 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=" FE4 SF4V1 500 " pdb=" S1 SF4V1 500 " pdb=" S2 SF4V1 500 " pdb=" S3 SF4V1 500 " both_signs ideal model delta sigma weight residual False 10.55 -10.57 21.12 2.00e-01 2.50e+01 1.12e+04 ... (remaining 14829 not shown) Planarity restraints: 17157 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMNV1 501 " 0.117 2.00e-02 2.50e+03 5.42e-02 1.39e+02 pdb=" C10 FMNV1 501 " -0.039 2.00e-02 2.50e+03 pdb=" C2 FMNV1 501 " 0.017 2.00e-02 2.50e+03 pdb=" C4 FMNV1 501 " 0.011 2.00e-02 2.50e+03 pdb=" C4A FMNV1 501 " -0.025 2.00e-02 2.50e+03 pdb=" C5A FMNV1 501 " -0.058 2.00e-02 2.50e+03 pdb=" C6 FMNV1 501 " -0.008 2.00e-02 2.50e+03 pdb=" C7 FMNV1 501 " 0.022 2.00e-02 2.50e+03 pdb=" C7M FMNV1 501 " 0.092 2.00e-02 2.50e+03 pdb=" C8 FMNV1 501 " -0.013 2.00e-02 2.50e+03 pdb=" C8M FMNV1 501 " 0.057 2.00e-02 2.50e+03 pdb=" C9 FMNV1 501 " -0.085 2.00e-02 2.50e+03 pdb=" C9A FMNV1 501 " -0.089 2.00e-02 2.50e+03 pdb=" N1 FMNV1 501 " -0.019 2.00e-02 2.50e+03 pdb=" N10 FMNV1 501 " -0.056 2.00e-02 2.50e+03 pdb=" N3 FMNV1 501 " 0.030 2.00e-02 2.50e+03 pdb=" N5 FMNV1 501 " -0.031 2.00e-02 2.50e+03 pdb=" O2 FMNV1 501 " 0.046 2.00e-02 2.50e+03 pdb=" O4 FMNV1 501 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VALS1 489 " -0.038 2.00e-02 2.50e+03 7.54e-02 5.68e+01 pdb=" C VALS1 489 " 0.130 2.00e-02 2.50e+03 pdb=" O VALS1 489 " -0.047 2.00e-02 2.50e+03 pdb=" N METS1 490 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VALS2 73 " -0.029 2.00e-02 2.50e+03 5.74e-02 3.29e+01 pdb=" C VALS2 73 " 0.099 2.00e-02 2.50e+03 pdb=" O VALS2 73 " -0.037 2.00e-02 2.50e+03 pdb=" N ARGS2 74 " -0.033 2.00e-02 2.50e+03 ... (remaining 17154 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 791 2.58 - 3.16: 77779 3.16 - 3.74: 154878 3.74 - 4.32: 204263 4.32 - 4.90: 329697 Nonbonded interactions: 767408 Sorted by model distance: nonbonded pdb=" NE2 HISb2 182 " pdb="FE HEMb2 401 " model vdw 1.997 3.080 nonbonded pdb=" O GLNS3 38 " pdb=" CA SERA7 70 " model vdw 1.997 3.470 nonbonded pdb=" NE2 HISb2 97 " pdb="FE HEMb2 402 " model vdw 2.018 3.080 nonbonded pdb=" NE2 HISb1 182 " pdb="FE HEMb1 401 " model vdw 2.034 3.080 nonbonded pdb=" O ARGc1 237 " pdb=" CA HISq1 12 " model vdw 2.146 3.470 ... (remaining 767403 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 239 or resid 501)) selection = chain 'c2' } 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' selection = (chain 'x2' and (resid 4 through 7 or (resid 8 and (name N or name CA or name C \ or name O )) or resid 9 through 26)) } 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 9 5.49 5 S 628 5.16 5 C 62395 2.51 5 N 16481 2.21 5 O 17497 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: 7.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 34.960 Check model and map are aligned: 1.120 Convert atoms to be neutral: 0.670 Process input model: 237.590 Find NCS groups from input model: 4.620 Set up NCS constraints: 0.640 Set refine NCS operators: 0.000 Set scattering table: 0.050 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 290.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.223 99524 Z= 0.448 Angle : 1.163 25.159 135113 Z= 0.617 Chirality : 0.850 21.145 14832 Planarity : 0.009 0.089 17157 Dihedral : 11.426 136.663 36741 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.24 % Favored : 88.63 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.77 % Cis-general : 0.18 % Twisted Proline : 1.33 % Twisted General : 0.30 % 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: -3.98 (0.06), residues: 11903 helix: -1.98 (0.05), residues: 6060 sheet: -1.76 (0.19), residues: 693 loop : -3.59 (0.07), residues: 5150 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23806 Ramachandran restraints generated. 11903 Oldfield, 0 Emsley, 11903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23806 Ramachandran restraints generated. 11903 Oldfield, 0 Emsley, 11903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4163 residues out of total 10431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 4121 time to evaluate : 9.083 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 outliers start: 42 outliers final: 8 residues processed: 4148 average time/residue: 0.9246 time to fit residues: 6493.2268 Evaluate side-chains 2218 residues out of total 10431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 2210 time to evaluate : 9.045 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.6851 time to fit residues: 22.6404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1177 random chunks: chunk 993 optimal weight: 0.0270 chunk 892 optimal weight: 4.9990 chunk 495 optimal weight: 5.9990 chunk 304 optimal weight: 8.9990 chunk 601 optimal weight: 10.0000 chunk 476 optimal weight: 1.9990 chunk 922 optimal weight: 0.8980 chunk 356 optimal weight: 8.9990 chunk 560 optimal weight: 3.9990 chunk 686 optimal weight: 3.9990 chunk 1068 optimal weight: 5.9990 overall best weight: 2.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a1 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a1 29 GLN a1 52 ASN ** a1 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a1 173 ASN a1 215 HIS ** a1 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a1 267 ASN a1 363 ASN a1 418 GLN ** a2 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a2 104 ASN a2 125 ASN a2 164 HIS a2 385 GLN ** b1 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b1 54 HIS b1 85 ASN b1 267 HIS ** b1 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b1 322 GLN b1 374 ASN c1 50 HIS c1 97 ASN c1 199 HIS f1 53 ASN ** f1 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d1 79 GLN q1 28 HIS ** h1 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h1 71 HIS a3 21 ASN a3 29 GLN ** a3 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a3 189 HIS ** a3 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a3 328 HIS ** a3 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a3 341 GLN a3 418 GLN a4 67 HIS a4 104 ASN a4 141 GLN a4 343 GLN a4 385 GLN b2 85 ASN ** b2 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b2 137 GLN b2 322 GLN ** c2 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c2 71 GLN c2 105 ASN c2 121 HIS c2 197 HIS f2 53 ASN f2 179 ASN q2 23 GLN q2 73 ASN ** i2 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V1 165 ASN ** V1 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V1 416 GLN V1 431 GLN V2 16 ASN V2 42 HIS V2 99 HIS V2 112 ASN V2 150 ASN S1 7 ASN S1 28 GLN S1 36 GLN S1 43 HIS ** S1 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 421 HIS S1 494 HIS ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1 665 GLN S2 84 HIS ** S2 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 280 GLN S2 316 ASN ** S2 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 19 HIS ** S7 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S8 157 ASN V3 44 HIS ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 43 ASN A9 44 GLN ** A9 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A9 288 HIS A5 49 GLN A6 98 GLN A7 8 GLN A7 24 GLN AL 31 ASN ** AL 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 74 GLN D1 5 ASN ** D1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 205 ASN ** D5 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 323 HIS D5 400 ASN D5 484 HIS D4 192 ASN D4 304 GLN ** D2 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 63 GLN ** D2 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 150 ASN D2 235 ASN D2 316 GLN AK 18 HIS B5 86 ASN B5 135 HIS ** A8 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A8 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 27 ASN ** BJ 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 122 GLN AJ 76 ASN AJ 97 GLN AJ 114 HIS ** AJ 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 154 GLN AJ 200 GLN ** AJ 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 251 GLN ** AJ 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 309 ASN S5 24 GLN ** A3 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 68 HIS B4 74 ASN B4 78 ASN B4 82 ASN B9 32 HIS B9 77 GLN ** B2 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B8 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B8 78 HIS BK 27 GLN BK 57 ASN B1 30 ASN A1 44 GLN A1 68 ASN Total number of N/Q/H flips: 111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.320 99524 Z= 0.514 Angle : 1.452 51.266 135113 Z= 0.904 Chirality : 0.254 6.399 14832 Planarity : 0.006 0.096 17157 Dihedral : 8.093 129.353 13386 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.52 % Favored : 90.44 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.77 % Cis-general : 0.18 % Twisted Proline : 0.44 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.07), residues: 11903 helix: -0.57 (0.06), residues: 6111 sheet: -1.50 (0.19), residues: 692 loop : -3.28 (0.08), residues: 5100 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23806 Ramachandran restraints generated. 11903 Oldfield, 0 Emsley, 11903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23806 Ramachandran restraints generated. 11903 Oldfield, 0 Emsley, 11903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2882 residues out of total 10431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 2858 time to evaluate : 10.216 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 outliers start: 24 outliers final: 7 residues processed: 2874 average time/residue: 0.8470 time to fit residues: 4201.1439 Evaluate side-chains 2032 residues out of total 10431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 2025 time to evaluate : 8.966 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.6864 time to fit residues: 20.9519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1177 random chunks: chunk 594 optimal weight: 9.9990 chunk 331 optimal weight: 20.0000 chunk 889 optimal weight: 2.9990 chunk 727 optimal weight: 0.3980 chunk 294 optimal weight: 0.0000 chunk 1070 optimal weight: 7.9990 chunk 1156 optimal weight: 0.9990 chunk 953 optimal weight: 6.9990 chunk 1061 optimal weight: 9.9990 chunk 365 optimal weight: 0.9990 chunk 859 optimal weight: 7.9990 overall best weight: 1.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a1 15 GLN a1 141 ASN a1 159 GLN a1 189 HIS ** a1 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a2 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b1 267 HIS b1 312 GLN c1 197 HIS ** h1 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a4 20 HIS a4 158 HIS b2 85 ASN b2 137 GLN ** c2 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d2 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q2 23 GLN ** i2 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V1 373 ASN ** V1 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 7 ASN S1 179 ASN ** S1 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 347 HIS ** S3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A9 148 ASN A9 321 HIS ** A5 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A7 20 GLN ** D1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 139 GLN D5 226 GLN ** D5 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 580 GLN D4 83 HIS D4 180 GLN D4 279 GLN ** D4 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 150 ASN D2 174 GLN D2 235 ASN AK 18 HIS B5 86 ASN ** B5 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A8 30 HIS ** A8 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A8 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A8 72 GLN ** BJ 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 92 ASN ** AJ 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S5 26 HIS A3 45 ASN A3 68 HIS ** C2 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 82 ASN ** B6 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B8 72 ASN B1 30 ASN A1 44 GLN A1 68 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.267 99524 Z= 0.490 Angle : 1.418 50.668 135113 Z= 0.887 Chirality : 0.258 6.459 14832 Planarity : 0.006 0.098 17157 Dihedral : 7.596 126.858 13386 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.34 % Favored : 90.63 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.77 % Cis-general : 0.18 % Twisted Proline : 0.29 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.07), residues: 11903 helix: -0.01 (0.06), residues: 6148 sheet: -1.40 (0.19), residues: 716 loop : -3.06 (0.08), residues: 5039 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23806 Ramachandran restraints generated. 11903 Oldfield, 0 Emsley, 11903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23806 Ramachandran restraints generated. 11903 Oldfield, 0 Emsley, 11903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2741 residues out of total 10431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 2725 time to evaluate : 9.028 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 outliers start: 16 outliers final: 5 residues processed: 2739 average time/residue: 0.8551 time to fit residues: 4058.0739 Evaluate side-chains 1976 residues out of total 10431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1971 time to evaluate : 10.538 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.6986 time to fit residues: 18.5344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1177 random chunks: chunk 1057 optimal weight: 20.0000 chunk 805 optimal weight: 0.9980 chunk 555 optimal weight: 8.9990 chunk 118 optimal weight: 5.9990 chunk 511 optimal weight: 0.9990 chunk 719 optimal weight: 20.0000 chunk 1074 optimal weight: 10.0000 chunk 1137 optimal weight: 3.9990 chunk 561 optimal weight: 8.9990 chunk 1018 optimal weight: 0.8980 chunk 306 optimal weight: 10.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a1 159 GLN ** a1 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a1 279 HIS a2 164 HIS a2 248 ASN a2 284 HIS ** b1 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b1 267 HIS ** h1 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a3 418 GLN a4 20 HIS a4 158 HIS b2 148 ASN ** d2 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q2 23 GLN h2 49 GLN ** i2 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V1 373 ASN ** V1 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V2 150 ASN S1 7 ASN ** S1 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 494 HIS ** S1 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 95 ASN ** S7 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S8 123 GLN ** S8 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A9 148 ASN A5 85 ASN AM 60 GLN ** D1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 304 HIS D5 226 GLN ** D5 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D5 309 GLN D5 446 ASN D4 82 HIS D4 180 GLN D4 279 GLN ** D4 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 150 ASN D2 235 ASN AK 18 HIS B5 69 HIS B5 86 ASN ** A8 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A8 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 151 HIS ** AJ 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S5 26 HIS ** B4 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 82 ASN B9 17 GLN B9 77 GLN BK 103 HIS B1 30 ASN A1 68 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.276 99524 Z= 0.506 Angle : 1.427 50.949 135113 Z= 0.891 Chirality : 0.257 6.408 14832 Planarity : 0.005 0.101 17157 Dihedral : 7.360 125.559 13386 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.01 % Favored : 89.96 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.77 % Cis-general : 0.18 % Twisted Proline : 0.29 % Twisted General : 0.08 % 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: -1.77 (0.08), residues: 11903 helix: 0.19 (0.06), residues: 6135 sheet: -1.28 (0.19), residues: 743 loop : -2.98 (0.08), residues: 5025 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23806 Ramachandran restraints generated. 11903 Oldfield, 0 Emsley, 11903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23806 Ramachandran restraints generated. 11903 Oldfield, 0 Emsley, 11903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2571 residues out of total 10431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 2561 time to evaluate : 9.151 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 outliers start: 10 outliers final: 3 residues processed: 2569 average time/residue: 0.8730 time to fit residues: 3906.5897 Evaluate side-chains 1907 residues out of total 10431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1904 time to evaluate : 9.036 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.7332 time to fit residues: 15.9634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1177 random chunks: chunk 947 optimal weight: 0.9980 chunk 645 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 chunk 847 optimal weight: 3.9990 chunk 469 optimal weight: 9.9990 chunk 970 optimal weight: 3.9990 chunk 786 optimal weight: 4.9990 chunk 1 optimal weight: 0.0060 chunk 580 optimal weight: 10.0000 chunk 1021 optimal weight: 7.9990 chunk 287 optimal weight: 0.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a1 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a2 164 HIS ** b1 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b1 267 HIS ** c1 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h1 63 HIS ** a3 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a4 20 HIS ** b2 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d2 38 HIS ** d2 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q2 23 GLN ** i2 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V1 283 HIS V1 373 ASN ** V1 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 7 ASN S1 494 HIS ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S3 71 GLN S7 38 ASN S8 123 GLN ** S8 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V3 43 HIS ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A9 115 GLN A9 148 ASN A5 85 ASN ** A7 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D6 46 ASN D5 116 GLN ** D5 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 447 ASN D4 82 HIS D4 83 HIS ** D4 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4 279 GLN ** D2 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 186 HIS D2 235 ASN AK 18 HIS B5 86 ASN ** B5 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A8 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A8 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S5 26 HIS ** B4 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 82 ASN ** B6 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B9 77 GLN C1 9 HIS B1 30 ASN ** A1 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.262 99524 Z= 0.491 Angle : 1.415 50.688 135113 Z= 0.885 Chirality : 0.257 6.423 14832 Planarity : 0.005 0.085 17157 Dihedral : 7.213 128.617 13386 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.38 % Favored : 90.60 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.77 % Cis-general : 0.18 % Twisted Proline : 0.29 % Twisted General : 0.08 % 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: -1.54 (0.08), residues: 11903 helix: 0.39 (0.07), residues: 6089 sheet: -1.23 (0.19), residues: 747 loop : -2.87 (0.08), residues: 5067 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23806 Ramachandran restraints generated. 11903 Oldfield, 0 Emsley, 11903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23806 Ramachandran restraints generated. 11903 Oldfield, 0 Emsley, 11903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2590 residues out of total 10431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 2584 time to evaluate : 9.755 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 outliers start: 6 outliers final: 1 residues processed: 2589 average time/residue: 0.8561 time to fit residues: 3862.5644 Evaluate side-chains 1940 residues out of total 10431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1939 time to evaluate : 9.173 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.6695 time to fit residues: 13.3713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1177 random chunks: chunk 382 optimal weight: 8.9990 chunk 1024 optimal weight: 8.9990 chunk 224 optimal weight: 6.9990 chunk 667 optimal weight: 0.0870 chunk 280 optimal weight: 0.0570 chunk 1138 optimal weight: 4.9990 chunk 945 optimal weight: 7.9990 chunk 527 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 376 optimal weight: 0.6980 chunk 597 optimal weight: 0.9980 overall best weight: 1.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a1 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b1 267 HIS b1 374 ASN ** a3 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a3 301 ASN a4 20 HIS b2 312 GLN d2 56 ASN q2 23 GLN h2 71 HIS ** V1 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V1 373 ASN V1 398 GLN S1 7 ASN S1 494 HIS ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 157 HIS ** S7 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S8 123 GLN S8 157 ASN ** S8 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A9 44 GLN ** A9 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A9 148 ASN A5 85 ASN A7 20 GLN ** D3 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 304 HIS ** D5 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 82 HIS D4 180 GLN ** D2 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 150 ASN D2 235 ASN AK 18 HIS B5 63 HIS B5 86 ASN ** B5 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A8 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A8 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S5 26 HIS ** B4 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 82 ASN B9 61 GLN B1 30 ASN A1 68 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.268 99524 Z= 0.490 Angle : 1.412 50.672 135113 Z= 0.884 Chirality : 0.257 6.431 14832 Planarity : 0.005 0.105 17157 Dihedral : 7.065 136.058 13386 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.43 % Favored : 90.54 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.77 % Cis-general : 0.18 % Twisted Proline : 0.15 % Twisted General : 0.07 % 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: -1.39 (0.08), residues: 11903 helix: 0.51 (0.07), residues: 6061 sheet: -1.10 (0.19), residues: 735 loop : -2.78 (0.08), residues: 5107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23806 Ramachandran restraints generated. 11903 Oldfield, 0 Emsley, 11903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23806 Ramachandran restraints generated. 11903 Oldfield, 0 Emsley, 11903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2536 residues out of total 10431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 2533 time to evaluate : 9.221 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 outliers start: 3 outliers final: 1 residues processed: 2536 average time/residue: 0.8560 time to fit residues: 3795.6137 Evaluate side-chains 1896 residues out of total 10431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1895 time to evaluate : 9.040 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.7682 time to fit residues: 13.3025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1177 random chunks: chunk 1097 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 648 optimal weight: 7.9990 chunk 831 optimal weight: 5.9990 chunk 644 optimal weight: 3.9990 chunk 958 optimal weight: 6.9990 chunk 635 optimal weight: 10.0000 chunk 1134 optimal weight: 10.0000 chunk 709 optimal weight: 9.9990 chunk 691 optimal weight: 8.9990 chunk 523 optimal weight: 0.3980 overall best weight: 4.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a1 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a1 119 ASN ** a1 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a1 289 HIS ** a1 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a2 162 ASN a2 164 HIS b1 32 ASN b1 68 HIS b1 85 ASN ** b1 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b1 267 HIS q1 12 HIS a3 61 HIS ** a3 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b2 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q2 23 GLN ** q2 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V1 373 ASN V2 27 ASN S1 7 ASN ** S1 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 494 HIS S1 682 GLN ** S2 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 190 HIS S8 157 ASN S8 168 ASN V3 42 GLN V3 65 GLN V3 75 HIS S6 47 GLN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S6 94 GLN ** A9 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A9 148 ASN A9 296 HIS A7 20 GLN ** AL 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3 80 GLN ** D1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 59 GLN D5 116 GLN ** D5 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D5 446 ASN ** D4 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4 279 GLN ** D4 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 235 ASN ** AK 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B5 86 ASN ** A8 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A8 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 99 GLN ** BJ 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 154 GLN ** AJ 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 82 ASN B9 61 GLN B9 138 GLN B2 16 GLN B8 104 HIS B1 30 ASN ** A1 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.5147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.264 99524 Z= 0.561 Angle : 1.477 50.954 135113 Z= 0.913 Chirality : 0.257 6.382 14832 Planarity : 0.006 0.100 17157 Dihedral : 7.369 139.815 13386 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 20.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.08 % Favored : 88.89 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.77 % Cis-general : 0.18 % Twisted Proline : 0.29 % Twisted General : 0.08 % 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: -1.61 (0.08), residues: 11903 helix: 0.26 (0.07), residues: 6065 sheet: -1.09 (0.19), residues: 737 loop : -2.80 (0.08), residues: 5101 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23806 Ramachandran restraints generated. 11903 Oldfield, 0 Emsley, 11903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23806 Ramachandran restraints generated. 11903 Oldfield, 0 Emsley, 11903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2356 residues out of total 10431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 2351 time to evaluate : 9.702 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 outliers start: 5 outliers final: 1 residues processed: 2355 average time/residue: 0.8522 time to fit residues: 3519.4998 Evaluate side-chains 1785 residues out of total 10431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1784 time to evaluate : 9.050 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.7849 time to fit residues: 13.3116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1177 random chunks: chunk 701 optimal weight: 0.0170 chunk 453 optimal weight: 5.9990 chunk 677 optimal weight: 4.9990 chunk 341 optimal weight: 10.0000 chunk 222 optimal weight: 5.9990 chunk 219 optimal weight: 7.9990 chunk 721 optimal weight: 20.0000 chunk 772 optimal weight: 2.9990 chunk 560 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 891 optimal weight: 0.9990 overall best weight: 2.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a1 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a1 279 HIS ** a1 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a2 141 GLN a2 164 HIS b1 85 ASN ** b1 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b1 267 HIS ** b1 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a3 61 HIS ** a3 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a3 87 ASN a4 20 HIS ** b2 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 201 HIS b2 312 GLN c2 224 HIS q2 23 GLN ** q2 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V1 37 GLN ** V1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V1 373 ASN S1 7 ASN S1 36 GLN S1 401 HIS S1 494 HIS ** S2 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V3 75 HIS ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A9 87 HIS ** A9 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A9 148 ASN ** A9 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A6 98 GLN D1 97 ASN ** D1 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 304 HIS D5 139 GLN ** D5 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D5 328 HIS ** D5 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 82 HIS ** D4 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2 48 HIS D2 150 ASN D2 235 ASN ** AK 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B5 86 ASN ** A8 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A8 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 82 ASN B9 61 GLN B2 16 GLN B8 104 HIS B8 137 ASN B1 30 ASN A1 68 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.5300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.270 99524 Z= 0.511 Angle : 1.440 50.816 135113 Z= 0.896 Chirality : 0.258 6.535 14832 Planarity : 0.005 0.112 17157 Dihedral : 7.227 145.197 13386 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.85 % Favored : 90.12 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.77 % Cis-general : 0.18 % Twisted Proline : 0.29 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.08), residues: 11903 helix: 0.38 (0.07), residues: 6054 sheet: -1.17 (0.19), residues: 754 loop : -2.74 (0.08), residues: 5095 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23806 Ramachandran restraints generated. 11903 Oldfield, 0 Emsley, 11903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23806 Ramachandran restraints generated. 11903 Oldfield, 0 Emsley, 11903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2339 residues out of total 10431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 2336 time to evaluate : 9.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 3 outliers final: 0 residues processed: 2338 average time/residue: 0.8467 time to fit residues: 3473.5332 Evaluate side-chains 1820 residues out of total 10431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1820 time to evaluate : 9.052 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 11.7175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1177 random chunks: chunk 1031 optimal weight: 6.9990 chunk 1086 optimal weight: 9.9990 chunk 991 optimal weight: 9.9990 chunk 1057 optimal weight: 9.9990 chunk 636 optimal weight: 7.9990 chunk 460 optimal weight: 3.9990 chunk 830 optimal weight: 10.0000 chunk 324 optimal weight: 0.8980 chunk 955 optimal weight: 0.8980 chunk 999 optimal weight: 0.0670 chunk 1053 optimal weight: 5.9990 overall best weight: 2.3722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a1 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b1 85 ASN ** b1 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b1 267 HIS ** b1 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b2 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q2 23 GLN ** q2 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V1 373 ASN S1 7 ASN ** S1 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 94 ASN S8 123 GLN ** S8 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V3 43 HIS ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A9 148 ASN A9 321 HIS A7 8 GLN AL 46 ASN D1 97 ASN D1 138 GLN ** D1 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D6 46 ASN D6 175 ASN D5 116 GLN ** D5 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4 82 HIS ** D4 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 48 HIS D2 63 GLN ** D2 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 172 GLN D2 186 HIS D2 222 ASN D2 235 ASN ** AK 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B5 86 ASN ** A8 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A8 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2 117 HIS ** B4 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 82 ASN B9 61 GLN B8 72 ASN B8 104 HIS B8 137 ASN B1 30 ASN ** A1 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.5461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.265 99524 Z= 0.505 Angle : 1.443 50.687 135113 Z= 0.896 Chirality : 0.257 6.462 14832 Planarity : 0.005 0.106 17157 Dihedral : 7.160 149.423 13386 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 18.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.35 % Favored : 89.62 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.77 % Cis-general : 0.18 % Twisted Proline : 0.29 % Twisted General : 0.08 % 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: -1.44 (0.08), residues: 11903 helix: 0.42 (0.07), residues: 6066 sheet: -1.16 (0.18), residues: 766 loop : -2.72 (0.08), residues: 5071 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23806 Ramachandran restraints generated. 11903 Oldfield, 0 Emsley, 11903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23806 Ramachandran restraints generated. 11903 Oldfield, 0 Emsley, 11903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2351 residues out of total 10431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 2344 time to evaluate : 9.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 2348 average time/residue: 0.8631 time to fit residues: 3570.0246 Evaluate side-chains 1810 residues out of total 10431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1809 time to evaluate : 9.087 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.7675 time to fit residues: 13.2849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1177 random chunks: chunk 694 optimal weight: 10.0000 chunk 1117 optimal weight: 1.9990 chunk 682 optimal weight: 0.3980 chunk 530 optimal weight: 4.9990 chunk 777 optimal weight: 0.9990 chunk 1172 optimal weight: 0.8980 chunk 1079 optimal weight: 5.9990 chunk 933 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 chunk 721 optimal weight: 10.0000 chunk 572 optimal weight: 10.0000 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a1 85 HIS ** a1 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a2 164 HIS b1 267 HIS ** b1 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a3 85 HIS a3 87 ASN a4 174 ASN ** b2 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 312 GLN c2 71 GLN q2 23 GLN ** V1 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V1 373 ASN S1 7 ASN ** S1 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S8 123 GLN S8 157 ASN V3 43 HIS ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 44 ASN ** A9 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A9 148 ASN A9 296 HIS AM 89 ASN D1 194 ASN ** D1 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D6 175 ASN ** D5 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2 48 HIS D2 63 GLN D2 174 GLN D2 222 ASN D2 235 ASN ** AK 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B5 86 ASN ** A8 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A8 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A8 162 HIS ** BJ 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 82 ASN B9 61 GLN B8 72 ASN B8 137 ASN BK 41 ASN C1 35 HIS B1 30 ASN A1 68 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.5616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.262 99524 Z= 0.500 Angle : 1.440 50.648 135113 Z= 0.895 Chirality : 0.257 6.446 14832 Planarity : 0.005 0.089 17157 Dihedral : 7.113 153.384 13386 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.83 % Favored : 90.14 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.77 % Cis-general : 0.18 % Twisted Proline : 0.29 % Twisted General : 0.07 % 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: -1.37 (0.08), residues: 11903 helix: 0.47 (0.07), residues: 6066 sheet: -0.99 (0.19), residues: 736 loop : -2.70 (0.08), residues: 5101 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23806 Ramachandran restraints generated. 11903 Oldfield, 0 Emsley, 11903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23806 Ramachandran restraints generated. 11903 Oldfield, 0 Emsley, 11903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2322 residues out of total 10431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 2318 time to evaluate : 8.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 2321 average time/residue: 0.8357 time to fit residues: 3421.2062 Evaluate side-chains 1828 residues out of total 10431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1828 time to evaluate : 9.000 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 11.8920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1177 random chunks: chunk 741 optimal weight: 0.9990 chunk 994 optimal weight: 4.9990 chunk 286 optimal weight: 8.9990 chunk 860 optimal weight: 0.8980 chunk 137 optimal weight: 0.0470 chunk 259 optimal weight: 9.9990 chunk 935 optimal weight: 9.9990 chunk 391 optimal weight: 0.0670 chunk 960 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 chunk 172 optimal weight: 8.9990 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a1 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b1 267 HIS ** b1 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a3 274 ASN ** b2 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 312 GLN f2 53 ASN q2 23 GLN ** V1 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V1 373 ASN S1 7 ASN ** S1 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S8 157 ASN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 44 ASN A9 36 ASN ** A9 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A9 148 ASN A9 296 HIS D1 138 GLN ** D1 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D6 175 ASN ** D5 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 170 GLN ** D5 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 580 GLN ** D4 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2 48 HIS D2 172 GLN D2 222 ASN D2 235 ASN ** AK 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A8 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A8 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 113 GLN ** BJ 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 82 ASN BK 41 ASN B1 30 ASN A1 68 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.113262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.102980 restraints weight = 317154.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.104417 restraints weight = 204065.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.106077 restraints weight = 147254.528| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.5763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.254 99524 Z= 0.491 Angle : 1.433 50.565 135113 Z= 0.890 Chirality : 0.257 6.486 14832 Planarity : 0.005 0.125 17157 Dihedral : 6.951 156.852 13386 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.38 % Favored : 90.60 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.77 % Cis-general : 0.18 % Twisted Proline : 0.29 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.08), residues: 11903 helix: 0.58 (0.07), residues: 6066 sheet: -1.05 (0.18), residues: 773 loop : -2.65 (0.08), residues: 5064 =============================================================================== Job complete usr+sys time: 46680.79 seconds wall clock time: 806 minutes 30.07 seconds (48390.07 seconds total)