Starting phenix.real_space_refine (version: dev) on Sat Dec 17 08:06:41 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc2_4494/12_2022/6qc2_4494_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc2_4494/12_2022/6qc2_4494.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc2_4494/12_2022/6qc2_4494_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/6qc2_4494/12_2022/6qc2_4494_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc2_4494/12_2022/6qc2_4494_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc2_4494/12_2022/6qc2_4494.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc2_4494/12_2022/6qc2_4494.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc2_4494/12_2022/6qc2_4494_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc2_4494/12_2022/6qc2_4494_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= 0.023 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 "D1 ARG 195": "NH1" <-> "NH2" Residue "D6 PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D6 ARG 173": "NH1" <-> "NH2" Residue "AK ARG 19": "NH1" <-> "NH2" Residue "B5 ARG 26": "NH1" <-> "NH2" Residue "AB PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BJ TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AJ ARG 95": "NH1" <-> "NH2" Residue "AJ ARG 305": "NH1" <-> "NH2" Residue "A3 ARG 46": "NH1" <-> "NH2" Residue "C2 ARG 5": "NH1" <-> "NH2" Residue "C2 ARG 120": "NH1" <-> "NH2" Residue "B4 ARG 41": "NH1" <-> "NH2" Residue "AM ARG 26": "NH1" <-> "NH2" Residue "AM ARG 81": "NH1" <-> "NH2" Residue "B9 ARG 92": "NH1" <-> "NH2" Residue "B9 ARG 128": "NH1" <-> "NH2" Residue "B9 ARG 176": "NH1" <-> "NH2" Residue "B8 ARG 70": "NH1" <-> "NH2" Residue "A1 ARG 25": "NH1" <-> "NH2" Residue "a2 ARG 240": "NH1" <-> "NH2" Residue "f1 TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a4 ARG 240": "NH1" <-> "NH2" Residue "b2 ARG 313": "NH1" <-> "NH2" Residue "c2 ARG 139": "NH1" <-> "NH2" Residue "V1 ARG 32": "NH1" <-> "NH2" Residue "V1 ARG 237": "NH1" <-> "NH2" Residue "V1 ARG 423": "NH1" <-> "NH2" Residue "V2 ARG 187": "NH1" <-> "NH2" Residue "S2 TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S7 ARG 174": "NH1" <-> "NH2" Residue "S7 ARG 178": "NH1" <-> "NH2" Residue "S4 ARG 64": "NH1" <-> "NH2" Residue "A9 ARG 97": "NH1" <-> "NH2" Residue "A9 ARG 292": "NH1" <-> "NH2" Residue "A2 ARG 33": "NH1" <-> "NH2" Residue "A6 ARG 22": "NH1" <-> "NH2" Residue "AL ARG 106": "NH1" <-> "NH2" 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: 96938 Number of models: 1 Model: "" Number of chains: 83 Chain: "D3" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 728 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain breaks: 1 Chain: "D1" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2362 Classifications: {'peptide': 296} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 274} Chain breaks: 2 Chain: "D6" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1280 Classifications: {'peptide': 168} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 2, 'TRANS': 162} Chain breaks: 1 Chain: "4L" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 748 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 96} Chain: "D5" Number of atoms: 4805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4805 Classifications: {'peptide': 606} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 26, 'TRANS': 578} Chain: "D4" Number of atoms: 3646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3646 Classifications: {'peptide': 459} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 437} Chain: "D2" Number of atoms: 2724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2724 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 326} Chain: "AK" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1025 Classifications: {'peptide': 140} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 4, 'TRANS': 132} Chain: "B5" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1156 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 128} Chain: "AB" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 702 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain: "A8" Number of atoms: 1404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1404 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 12, 'TRANS': 156} Chain: "BJ" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1441 Classifications: {'peptide': 171} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 159} Chain: "AJ" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2583 Classifications: {'peptide': 319} Link IDs: {'CIS': 6, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 298} Chain: "S5" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 822 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "A3" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 582 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 62} Chain: "B3" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 578 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "C2" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 997 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 10, 'TRANS': 106} Chain: "B4" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1059 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 117} Chain: "AM" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1143 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 131} Chain: "B6" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 797 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 11, '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: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 563 Classifications: {'peptide': 65} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 56} 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: "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: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 164 Classifications: {'peptide': 33} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 32} Link IDs: {'TRANS': 32} Chain breaks: 1 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 33} Unresolved non-hydrogen planarities: 33 Chain: "i1" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 459 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "a3" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3447 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 18, 'TRANS': 425} Chain: "a4" Number of atoms: 3122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3122 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 398} Chain breaks: 1 Chain: "b2" Number of atoms: 3019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3019 Classifications: {'peptide': 378} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 353} Chain: "c2" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1903 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 22, 'TRANS': 215} Chain: "f2" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1514 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "d2" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 888 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "q2" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 631 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 6, 'TRANS': 68} Chain: "h2" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "x2" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 150 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'TRANS': 29} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'UNK:plan-1': 30} Unresolved non-hydrogen planarities: 30 Chain: "i2" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 473 Classifications: {'peptide': 57} Link IDs: {'TRANS': 56} Chain: "V1" Number of atoms: 3312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3312 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 21, 'TRANS': 408} Chain: "V2" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1647 Classifications: {'peptide': 212} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 189} Chain: "S1" Number of atoms: 5275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5275 Classifications: {'peptide': 688} Link IDs: {'CIS': 3, 'PTRANS': 32, 'TRANS': 652} Chain: "S2" Number of atoms: 3435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3435 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 398} Chain breaks: 1 Chain: "S3" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1726 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "S7" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1247 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 145} Chain: "S8" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1414 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 10, 'TRANS': 165} Chain: "V3" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 345 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 3, 'TRANS': 37} Chain: "S6" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 737 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "S4" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1024 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "A9" Number of atoms: 2301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2301 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 14, 'TRANS': 276} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "A2" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 665 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "A5" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 901 Classifications: {'peptide': 111} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 101} Chain: "A6" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 969 Classifications: {'peptide': 114} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 106} Chain: "A7" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 757 Classifications: {'peptide': 95} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 82} Chain breaks: 1 Chain: "AL" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1160 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 11, 'TRANS': 127} 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: "D1" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 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: "D4" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 68 Unusual residues: {'3PE': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Chain: "AB" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Chain: "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: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 194 Unusual residues: {'3PE': 1, 'CDL': 2, 'HEM': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 143 Chain: "c2" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 84 Unusual residues: {'CDL': 1, 'HEC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 59 Chain: "f2" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'3PE': 1, 'FES': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Chain: "V1" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "S1" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "S7" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "S8" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A9" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "AA" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 49838 SG CYSf1 139 136.728 104.721 60.937 1.00135.58 S ATOM 49974 SG CYSf1 158 138.459 101.946 63.402 1.00132.95 S ATOM 65502 SG CYSf2 139 199.940 118.392 52.006 1.00124.88 S ATOM 65638 SG CYSf2 158 197.730 120.251 49.357 1.00118.88 S ATOM 71316 SG CYSV1 365 44.705 164.217 211.725 1.00 46.36 S ATOM 71640 SG CYSV1 405 46.238 166.427 217.817 1.00 44.32 S ATOM 71296 SG CYSV1 362 50.434 164.297 213.547 1.00 59.48 S ATOM 71277 SG CYSV1 359 47.508 170.102 212.616 1.00 39.31 S ATOM 72717 SG CYSV2 103 26.842 174.773 218.462 1.00107.40 S ATOM 72751 SG CYSV2 108 23.830 172.061 219.603 1.00 84.51 S ATOM 73031 SG CYSV2 144 30.333 172.962 221.377 1.00 74.49 S ATOM 73054 SG CYSV2 148 28.362 170.805 223.413 1.00 76.42 S ATOM 74386 SG CYSS1 114 56.973 157.969 194.096 1.00 22.81 S ATOM 74325 SG CYSS1 105 52.201 155.356 190.506 1.00 42.02 S ATOM 74346 SG CYSS1 108 55.446 160.709 188.602 1.00 37.65 S ATOM 74718 SG CYSS1 156 57.159 166.614 201.400 1.00 22.83 S ATOM 74695 SG CYSS1 153 51.580 168.214 198.231 1.00 26.33 S ATOM 74742 SG CYSS1 159 56.484 172.595 198.981 1.00 34.04 S ATOM 75072 SG CYSS1 203 57.034 167.629 195.040 1.00 49.10 S ATOM 73831 SG CYSS1 41 59.345 164.909 207.845 1.00 27.62 S ATOM 73917 SG CYSS1 52 58.859 160.635 208.280 1.00 26.11 S ATOM 73942 SG CYSS1 55 60.200 160.008 212.131 1.00 41.71 S ATOM 74043 SG CYSS1 69 61.116 163.657 213.338 1.00 47.69 S ATOM 84749 SG CYSS7 119 67.255 131.984 166.783 1.00 25.36 S ATOM 84979 SG CYSS7 149 61.733 132.743 169.076 1.00 23.13 S ATOM 84251 SG CYSS7 55 62.340 128.794 163.783 1.00 37.27 S ATOM 84245 SG CYSS7 54 64.142 126.521 169.180 1.00 33.79 S ATOM 86171 SG CYSS8 116 57.721 140.500 168.933 1.00 24.37 S ATOM 86218 SG CYSS8 122 54.301 143.402 173.690 1.00 55.27 S ATOM 85945 SG CYSS8 87 60.859 143.876 173.347 1.00 40.85 S ATOM 86247 SG CYSS8 126 49.797 149.321 176.812 1.00 30.38 S ATOM 85918 SG CYSS8 83 56.068 149.640 174.922 1.00 25.55 S ATOM 85876 SG CYSS8 77 52.080 154.489 173.686 1.00 19.66 S ATOM 85895 SG CYSS8 80 53.501 153.087 179.993 1.00 82.11 S ATOM 87468 SG CYSS6 59 38.163 159.250 182.224 1.00 31.13 S ATOM 87646 SG CYSS6 84 41.675 160.979 182.053 1.00 30.69 S ATOM 87668 SG CYSS6 87 38.937 158.926 180.431 1.00 26.77 S Time building chain proxies: 40.53, per 1000 atoms: 0.42 Number of scatterers: 96938 At special positions: 0 Unit cell: (245, 225.4, 267.4, 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 626 16.00 P 18 15.00 O 17507 8.00 N 16441 7.00 C 62307 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYSAK 17 " - pdb=" SG CYSAK 74 " distance=2.03 Simple disulfide: pdb=" SG CYSAK 94 " - pdb=" SG CYSAK 114 " distance=2.03 Simple disulfide: pdb=" SG CYSA8 35 " - pdb=" SG CYSA8 65 " distance=2.04 Simple disulfide: pdb=" SG CYSA8 45 " - pdb=" SG CYSA8 55 " distance=2.03 Simple disulfide: pdb=" SG CYSA8 77 " - pdb=" SG CYSA8 109 " distance=2.02 Simple disulfide: pdb=" SG CYSA8 87 " - pdb=" SG CYSA8 99 " distance=2.04 Simple disulfide: pdb=" SG CYSBJ 76 " - pdb=" SG CYSBJ 83 " distance=2.03 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=2.03 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 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=2.03 Simple disulfide: pdb=" SG CYSf2 144 " - pdb=" SG CYSf2 160 " distance=2.03 Simple disulfide: pdb=" SG CYSh2 24 " - pdb=" SG CYSh2 68 " distance=2.04 Simple disulfide: pdb=" SG CYSh2 40 " - pdb=" SG CYSh2 54 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=13, symmetry=0 Number of additional bonds: simple=13, symmetry=0 Coordination: Other bonds: Time building additional restraints: 31.73 Conformation dependent library (CDL) restraints added in 11.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FESS1 803 " pdb=" FE2 FESS1 803 " - pdb=" SG CYSS1 55 " pdb=" FE1 FESS1 803 " - pdb=" SG CYSS1 52 " pdb=" FE1 FESS1 803 " - pdb=" SG CYSS1 41 " 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 139 " pdb=" FE2 FESf1 501 " - pdb=" ND1 HISf1 141 " pdb=" FE1 FESf1 501 " - pdb=" SG CYSf1 158 " pdb=" FESf2 202 " pdb=" FE1 FESf2 202 " - pdb=" SG CYSf2 158 " pdb=" FE2 FESf2 202 " - pdb=" ND1 HISf2 161 " pdb=" FE1 FESf2 202 " - pdb=" SG CYSf2 139 " pdb=" FE2 FESf2 202 " - pdb=" ND1 HISf2 141 " pdb=" SF4S1 801 " pdb=" FE3 SF4S1 801 " - pdb=" NE2 HISS1 101 " pdb=" FE1 SF4S1 801 " - pdb=" SG CYSS1 114 " pdb=" FE4 SF4S1 801 " - pdb=" SG CYSS1 108 " pdb=" FE2 SF4S1 801 " - pdb=" SG CYSS1 105 " pdb=" SF4S1 802 " pdb=" FE4 SF4S1 802 " - pdb=" SG CYSS1 203 " pdb=" FE1 SF4S1 802 " - pdb=" SG CYSS1 156 " pdb=" FE2 SF4S1 802 " - pdb=" SG CYSS1 153 " pdb=" FE3 SF4S1 802 " - pdb=" SG CYSS1 159 " pdb=" SF4S7 300 " pdb=" FE1 SF4S7 300 " - pdb=" SG CYSS7 119 " pdb=" FE4 SF4S7 300 " - pdb=" SG CYSS7 54 " pdb=" FE3 SF4S7 300 " - pdb=" SG CYSS7 55 " pdb=" FE2 SF4S7 300 " - pdb=" SG CYSS7 149 " pdb=" SF4S8 201 " pdb=" FE2 SF4S8 201 " - pdb=" SG CYSS8 116 " pdb=" FE4 SF4S8 201 " - pdb=" SG CYSS8 87 " pdb=" FE3 SF4S8 201 " - pdb=" SG CYSS8 122 " pdb=" FE1 SF4S8 201 " - pdb=" SG CYSS8 119 " pdb=" FE2 SF4S8 201 " - pdb=" NE2 HISS8 65 " pdb=" SF4S8 202 " pdb=" FE4 SF4S8 202 " - pdb=" SG CYSS8 80 " pdb=" FE3 SF4S8 202 " - pdb=" SG CYSS8 77 " pdb=" FE1 SF4S8 202 " - pdb=" SG CYSS8 126 " pdb=" FE2 SF4S8 202 " - pdb=" SG CYSS8 83 " pdb=" SF4V1 500 " pdb=" FE2 SF4V1 500 " - pdb=" SG CYSV1 405 " pdb=" FE1 SF4V1 500 " - pdb=" SG CYSV1 365 " pdb=" FE4 SF4V1 500 " - pdb=" SG CYSV1 359 " pdb=" FE3 SF4V1 500 " - pdb=" SG CYSV1 362 " Number of angles added : 87 Zn2+ tetrahedral coordination pdb=" ZNS6 300 " pdb="ZN ZNS6 300 " - pdb=" NE2 HISS6 68 " pdb="ZN ZNS6 300 " - pdb=" SG CYSS6 87 " pdb="ZN ZNS6 300 " - pdb=" SG CYSS6 59 " pdb="ZN ZNS6 300 " - pdb=" SG CYSS6 84 " Number of angles added : 3 23696 Ramachandran restraints generated. 11848 Oldfield, 0 Emsley, 11848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 22650 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 457 helices and 39 sheets defined 48.6% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.62 Creating SS restraints... Processing helix chain 'D3' and resid 2 through 23 Processing helix chain 'D3' and resid 53 through 78 removed outlier: 3.843A pdb=" N VALD3 58 " --> pdb=" O LYSD3 54 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALAD3 59 " --> pdb=" O PHED3 55 " (cutoff:3.500A) Proline residue: D3 74 - end of helix removed outlier: 5.638A pdb=" N TRPD3 77 " --> pdb=" O LEUD3 73 " (cutoff:3.500A) Processing helix chain 'D3' and resid 84 through 107 Processing helix chain 'D1' and resid 2 through 10 Processing helix chain 'D1' and resid 12 through 31 Processing helix chain 'D1' and resid 46 through 57 Processing helix chain 'D1' and resid 68 through 86 Proline residue: D1 75 - end of helix removed outlier: 4.943A pdb=" N TRPD1 86 " --> pdb=" O ALAD1 82 " (cutoff:3.500A) Processing helix chain 'D1' and resid 102 through 123 Processing helix chain 'D1' and resid 126 through 155 removed outlier: 4.552A pdb=" N TYRD1 142 " --> pdb=" O GLND1 138 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLUD1 143 " --> pdb=" O THRD1 139 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VALD1 144 " --> pdb=" O ILED1 140 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N THRD1 145 " --> pdb=" O SERD1 141 " (cutoff:3.500A) Processing helix chain 'D1' and resid 163 through 170 removed outlier: 4.596A pdb=" N GLUD1 170 " --> pdb=" O ILED1 166 " (cutoff:3.500A) Processing helix chain 'D1' and resid 179 through 192 Processing helix chain 'D1' and resid 220 through 242 Processing helix chain 'D1' and resid 253 through 276 removed outlier: 4.416A pdb=" N SERD1 276 " --> pdb=" O TRPD1 272 " (cutoff:3.500A) Processing helix chain 'D1' and resid 282 through 306 Proline residue: D1 295 - end of helix Processing helix chain 'D6' and resid 5 through 21 Processing helix chain 'D6' and resid 26 through 46 Processing helix chain 'D6' and resid 52 through 59 removed outlier: 3.565A pdb=" N LEUD6 58 " --> pdb=" O LEUD6 54 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILED6 59 " --> pdb=" O METD6 55 " (cutoff:3.500A) Processing helix chain 'D6' and resid 65 through 73 Processing helix chain 'D6' and resid 87 through 108 Processing helix chain 'D6' and resid 138 through 143 Processing helix chain 'D6' and resid 151 through 171 removed outlier: 3.527A pdb=" N ILED6 155 " --> pdb=" O THRD6 151 " (cutoff:3.500A) Processing helix chain '4L' and resid 4 through 20 Processing helix chain '4L' and resid 27 through 51 Processing helix chain '4L' and resid 59 through 84 Processing helix chain 'D5' and resid 2 through 15 removed outlier: 4.003A pdb=" N LEUD5 15 " --> pdb=" O THRD5 11 " (cutoff:3.500A) Processing helix chain 'D5' and resid 17 through 23 Processing helix chain 'D5' and resid 32 through 56 removed outlier: 4.576A pdb=" N ILED5 49 " --> pdb=" O ILED5 45 " (cutoff:3.500A) Proline residue: D5 50 - end of helix Processing helix chain 'D5' and resid 84 through 107 removed outlier: 4.568A pdb=" N VALD5 90 " --> pdb=" O SERD5 86 " (cutoff:3.500A) Proline residue: D5 91 - end of helix Processing helix chain 'D5' and resid 114 through 133 Processing helix chain 'D5' and resid 137 through 157 Processing helix chain 'D5' and resid 162 through 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 230 through 238 Proline residue: D5 234 - end of helix Processing helix chain 'D5' and resid 241 through 249 Processing helix chain 'D5' and resid 258 through 262 Processing helix chain 'D5' and resid 264 through 267 No H-bonds generated for 'chain 'D5' and resid 264 through 267' Processing helix chain 'D5' and resid 271 through 292 Processing helix chain 'D5' and resid 298 through 318 Processing helix chain 'D5' and resid 322 through 350 Processing helix chain 'D5' and resid 367 through 379 Processing helix chain 'D5' and resid 387 through 400 removed outlier: 4.625A pdb=" N SERD5 391 " --> pdb=" O THRD5 387 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LYSD5 392 " --> pdb=" O GLYD5 388 " (cutoff:3.500A) Processing helix chain 'D5' and resid 408 through 431 Processing helix chain 'D5' and resid 448 through 462 Processing helix chain 'D5' and resid 464 through 470 Processing helix chain 'D5' and resid 488 through 508 Processing helix chain 'D5' and resid 519 through 524 Processing helix chain 'D5' and resid 526 through 546 removed outlier: 3.836A pdb=" N TYRD5 529 " --> pdb=" O LEUD5 526 " (cutoff:3.500A) Proline residue: D5 530 - end of helix removed outlier: 3.698A pdb=" N METD5 533 " --> pdb=" O PROD5 530 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N HISD5 534 " --> pdb=" O THRD5 531 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N THRD5 537 " --> pdb=" O HISD5 534 " (cutoff:3.500A) Proline residue: D5 538 - end of helix removed outlier: 3.648A pdb=" N LEUD5 542 " --> pdb=" O TYRD5 539 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLND5 546 " --> pdb=" O THRD5 543 " (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 585 through 599 Processing helix chain 'D4' and resid 2 through 10 Proline residue: D4 7 - end of helix Processing helix chain 'D4' and resid 12 through 16 removed outlier: 4.176A pdb=" N TRPD4 16 " --> pdb=" O METD4 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'D4' and resid 12 through 16' Processing helix chain 'D4' and resid 23 through 41 removed outlier: 3.965A pdb=" N LEUD4 41 " --> pdb=" O THRD4 37 " (cutoff:3.500A) Processing helix chain 'D4' and resid 63 through 79 Proline residue: D4 74 - end of helix Processing helix chain 'D4' and resid 89 through 110 Processing helix chain 'D4' and resid 115 through 135 Proline residue: D4 128 - end of helix removed outlier: 3.947A 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: 3.998A pdb=" N VALD4 162 " --> pdb=" O LEUD4 158 " (cutoff:3.500A) Processing helix chain 'D4' and resid 176 through 179 No H-bonds generated for 'chain 'D4' and resid 176 through 179' Processing helix chain 'D4' and resid 190 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: 4.429A pdb=" N LYSD4 218 " --> pdb=" O LEUD4 214 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALAD4 219 " --> pdb=" O TRPD4 215 " (cutoff:3.500A) Processing helix chain 'D4' and resid 225 through 248 removed outlier: 4.865A pdb=" N LEUD4 248 " --> pdb=" O METD4 244 " (cutoff:3.500A) Processing helix chain 'D4' and resid 251 through 257 removed outlier: 4.170A pdb=" N ASPD4 255 " --> pdb=" O ASND4 251 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N PHED4 256 " --> pdb=" O PROD4 252 " (cutoff:3.500A) Processing helix chain 'D4' and resid 259 through 277 removed outlier: 3.790A pdb=" N METD4 263 " --> pdb=" O TYRD4 259 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEUD4 277 " --> pdb=" O SERD4 273 " (cutoff:3.500A) Processing helix chain 'D4' and resid 282 through 302 removed outlier: 3.728A pdb=" N ILED4 286 " --> pdb=" O LYSD4 283 " (cutoff:3.500A) Processing helix chain 'D4' and resid 306 through 336 Processing helix chain 'D4' and resid 353 through 366 removed outlier: 3.569A pdb=" N ALAD4 362 " --> pdb=" O TRPD4 359 " (cutoff:3.500A) Processing helix chain 'D4' and resid 373 through 388 Processing helix chain 'D4' and resid 393 through 414 removed outlier: 3.589A pdb=" N THRD4 414 " --> pdb=" O METD4 410 " (cutoff:3.500A) Processing helix chain 'D4' and resid 431 through 441 Processing helix chain 'D4' and resid 443 through 449 Processing helix chain 'D2' and resid 3 through 22 Processing helix chain 'D2' and resid 26 through 43 Proline residue: D2 42 - end of helix Processing helix chain 'D2' and resid 50 through 79 Processing helix chain 'D2' and resid 92 through 105 Processing helix chain 'D2' and resid 109 through 111 No H-bonds generated for 'chain 'D2' and resid 109 through 111' Processing helix chain 'D2' and resid 113 through 120 removed outlier: 4.173A pdb=" N GLUD2 117 " --> pdb=" O PHED2 113 " (cutoff:3.500A) Processing helix chain 'D2' and resid 124 through 148 Proline residue: D2 138 - end of helix removed outlier: 3.731A pdb=" N VALD2 141 " --> pdb=" O ALAD2 137 " (cutoff:3.500A) Proline residue: D2 147 - end of helix Processing helix chain 'D2' and resid 151 through 167 Processing helix chain 'D2' and resid 175 through 191 Processing helix chain 'D2' and resid 198 through 219 Processing helix chain 'D2' and resid 228 through 236 Processing helix chain 'D2' and resid 239 through 252 Processing helix chain 'D2' and resid 261 through 271 removed outlier: 3.654A pdb=" N METD2 265 " --> pdb=" O METD2 261 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILED2 266 " --> pdb=" O PROD2 262 " (cutoff:3.500A) Processing helix chain 'D2' and resid 277 through 300 removed outlier: 3.919A pdb=" N LEUD2 290 " --> pdb=" O ALAD2 286 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N TYRD2 291 " --> pdb=" O LEUD2 287 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N PHED2 292 " --> pdb=" O LEUD2 288 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYRD2 293 " --> pdb=" O ASND2 289 " (cutoff:3.500A) Processing helix chain 'D2' and resid 311 through 314 No H-bonds generated for 'chain 'D2' and resid 311 through 314' Processing helix chain 'D2' and resid 327 through 333 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 10 Processing helix chain 'AK' and resid 19 through 41 Processing helix chain 'AK' and resid 48 through 80 Processing helix chain 'AK' and resid 87 through 103 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 116 Processing helix chain 'AB' and resid 8 through 21 Processing helix chain 'AB' and resid 44 through 58 Processing helix chain 'AB' and resid 73 through 83 Processing helix chain 'A8' and resid 22 through 26 Processing helix chain 'A8' and resid 28 through 33 Processing helix chain 'A8' and resid 39 through 48 Processing helix chain 'A8' and resid 56 through 74 Processing helix chain 'A8' and resid 80 through 89 Processing helix chain 'A8' and resid 101 through 113 Processing helix chain 'BJ' and resid 28 through 55 removed outlier: 4.928A 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: 3.991A 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 143 through 145 No H-bonds generated for 'chain 'BJ' and resid 143 through 145' 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 71 through 74 No H-bonds generated for 'chain 'AJ' and resid 71 through 74' Processing helix chain 'AJ' and resid 79 through 84 Processing helix chain 'AJ' and resid 94 through 116 Processing helix chain 'AJ' and resid 128 through 140 Processing helix chain 'AJ' and resid 146 through 162 removed outlier: 4.039A pdb=" N CYSAJ 161 " --> pdb=" O LYSAJ 157 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLUAJ 162 " --> pdb=" O VALAJ 158 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 176 through 184 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 197 through 208 Processing helix chain 'AJ' and resid 210 through 214 Processing helix chain 'AJ' and resid 232 through 240 Processing helix chain 'AJ' and resid 254 through 263 Processing helix chain 'AJ' and resid 267 through 272 removed outlier: 5.071A pdb=" N TYRAJ 272 " --> pdb=" O GLUAJ 268 " (cutoff:3.500A) 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 33 through 42 Processing helix chain 'S5' and resid 50 through 54 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 46 through 52 removed outlier: 3.893A pdb=" N ALAB3 49 " --> pdb=" O ARGB3 46 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N TRPB3 50 " --> pdb=" O ASNB3 47 " (cutoff:3.500A) Processing helix chain 'B3' and resid 62 through 69 removed outlier: 4.505A pdb=" N LEUB3 66 " --> pdb=" O PHEB3 62 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLYB3 69 " --> pdb=" O ALAB3 65 " (cutoff:3.500A) Processing helix chain 'B3' and resid 74 through 82 Processing helix chain 'C2' and resid 17 through 19 No H-bonds generated for 'chain 'C2' and resid 17 through 19' Processing helix chain 'C2' and resid 29 through 48 Processing helix chain 'C2' and resid 58 through 96 Processing helix chain 'C2' and resid 98 through 100 No H-bonds generated for 'chain 'C2' and resid 98 through 100' Processing helix chain 'B4' and resid 26 through 48 Processing helix chain 'B4' and resid 62 through 72 Processing helix chain 'B4' and resid 83 through 117 removed outlier: 3.545A pdb=" N ILEB4 94 " --> pdb=" O ALAB4 90 " (cutoff:3.500A) Proline residue: B4 96 - end of helix Processing helix chain 'AM' and resid 31 through 96 removed outlier: 3.607A pdb=" N METAM 71 " --> pdb=" O ARGAM 67 " (cutoff:3.500A) Proline residue: AM 72 - end of helix Processing helix chain 'AM' and resid 130 through 136 Processing helix chain 'B6' and resid 5 through 24 Processing helix chain 'B6' and resid 68 through 91 Proline residue: B6 77 - end of helix removed outlier: 4.001A pdb=" N TYRB6 87 " --> pdb=" O TYRB6 83 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N HISB6 88 " --> pdb=" O TYRB6 84 " (cutoff:3.500A) removed outlier: 5.198A 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 47 Processing helix chain 'B7' and resid 59 through 71 Processing helix chain 'B7' and resid 81 through 118 Processing helix chain 'B9' and resid 11 through 29 Processing helix chain 'B9' and resid 34 through 48 Processing helix chain 'B9' and resid 56 through 72 Processing helix chain 'B9' and resid 92 through 96 removed outlier: 3.979A pdb=" N CYSB9 95 " --> pdb=" O ARGB9 92 " (cutoff:3.500A) Processing helix chain 'B9' and resid 108 through 112 Processing helix chain 'B9' and resid 115 through 130 Processing helix chain 'B9' and resid 134 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 41 Processing helix chain 'B8' and resid 5 through 7 No H-bonds generated for 'chain 'B8' and resid 5 through 7' Processing helix chain 'B8' and resid 18 through 27 Processing helix chain 'B8' and resid 81 through 83 No H-bonds generated for 'chain 'B8' and resid 81 through 83' Processing helix chain 'B8' and resid 99 through 121 Processing helix chain 'BK' and resid 51 through 64 removed outlier: 3.881A pdb=" N VALBK 55 " --> pdb=" O PROBK 51 " (cutoff:3.500A) Processing helix chain 'BK' and resid 70 through 78 Processing helix chain 'BK' and resid 87 through 102 Processing helix chain 'C1' and resid 15 through 45 Processing helix chain 'B1' and resid 12 through 34 removed outlier: 3.585A pdb=" N LEUB1 15 " --> pdb=" O ILEB1 12 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N VALB1 16 " --> pdb=" O HISB1 13 " (cutoff:3.500A) Proline residue: B1 17 - end of helix removed outlier: 3.538A pdb=" N VALB1 21 " --> pdb=" O VALB1 18 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEUB1 34 " --> pdb=" O ASPB1 31 " (cutoff:3.500A) 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 31 Proline residue: A1 19 - end of helix removed outlier: 3.741A pdb=" N ASNA1 31 " --> pdb=" O HISA1 27 " (cutoff:3.500A) Processing helix chain 'A1' and resid 42 through 54 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 81 Processing helix chain 'a1' and resid 103 through 118 Proline residue: a1 107 - end of helix removed outlier: 3.543A pdb=" N LEUa1 112 " --> pdb=" O ALAa1 109 " (cutoff:3.500A) removed outlier: 3.711A 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 175 Processing helix chain 'a1' and resid 179 through 189 Processing helix chain 'a1' and resid 206 through 215 Processing helix chain 'a1' and resid 266 through 276 Processing helix chain 'a1' and resid 293 through 300 Processing helix chain 'a1' and resid 328 through 347 removed outlier: 3.808A pdb=" N ILEa1 331 " --> pdb=" O HISa1 328 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ASPa1 332 " --> pdb=" O METa1 329 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASPa1 333 " --> pdb=" O SERa1 330 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VALa1 337 " --> pdb=" O METa1 334 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THRa1 347 " --> pdb=" O ARGa1 344 " (cutoff:3.500A) Processing helix chain 'a1' and resid 352 through 368 Processing helix chain 'a1' and resid 373 through 385 removed outlier: 3.508A pdb=" N THRa1 385 " --> pdb=" O ARGa1 381 " (cutoff:3.500A) 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 439 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 65 through 70 Processing helix chain 'a2' and resid 82 through 92 Processing helix chain 'a2' and resid 116 through 128 Processing helix chain 'a2' and resid 134 through 152 Processing helix chain 'a2' and resid 155 through 166 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 196 Processing helix chain 'a2' and resid 213 through 222 Processing helix chain 'a2' and resid 267 through 279 Processing helix chain 'a2' and resid 294 through 302 Processing helix chain 'a2' and resid 334 through 348 Processing helix chain 'a2' and resid 354 through 370 Processing helix chain 'a2' and resid 375 through 387 Processing helix chain 'a2' and resid 395 through 404 Processing helix chain 'a2' and resid 407 through 418 Processing helix chain 'b1' and resid 9 through 18 removed outlier: 3.951A pdb=" N ILEb1 13 " --> pdb=" O PROb1 9 " (cutoff:3.500A) Processing helix chain 'b1' and resid 29 through 54 removed outlier: 4.159A pdb=" N PHEb1 33 " --> pdb=" O TRPb1 30 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLYb1 34 " --> pdb=" O TRPb1 31 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SERb1 35 " --> pdb=" O ASNb1 32 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEUb1 36 " --> pdb=" O PHEb1 33 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THRb1 47 " --> pdb=" O GLNb1 44 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLYb1 48 " --> pdb=" O ILEb1 45 " (cutoff:3.500A) Processing helix chain 'b1' and resid 62 through 71 Processing helix chain 'b1' and resid 76 through 103 Processing helix chain 'b1' and resid 106 through 108 No H-bonds generated for 'chain 'b1' and resid 106 through 108' Processing helix chain 'b1' and resid 111 through 133 Processing helix chain 'b1' and resid 137 through 152 Processing helix chain 'b1' and resid 158 through 165 Processing helix chain 'b1' and resid 172 through 203 Proline residue: b1 186 - end of helix Processing helix chain 'b1' and resid 224 through 244 Processing helix chain 'b1' and resid 254 through 256 No H-bonds generated for 'chain 'b1' and resid 254 through 256' Processing helix chain 'b1' and resid 272 through 282 removed outlier: 4.694A pdb=" N PHEb1 276 " --> pdb=" O TYRb1 273 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILEb1 280 " --> pdb=" O ALAb1 277 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARGb1 282 " --> pdb=" O ALAb1 279 " (cutoff:3.500A) Processing helix chain 'b1' and resid 287 through 307 Proline residue: b1 305 - end of helix Processing helix chain 'b1' and resid 319 through 339 Processing helix chain 'b1' and resid 345 through 376 removed outlier: 4.872A pdb=" N METb1 366 " --> pdb=" O ILEb1 362 " (cutoff:3.500A) Proline residue: b1 367 - end of helix 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 51 Processing helix chain 'c1' and resid 58 through 66 Processing helix chain 'c1' and resid 98 through 102 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: 4.435A pdb=" N VALc1 228 " --> pdb=" O HISc1 224 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LEUc1 229 " --> pdb=" O LYSc1 225 " (cutoff:3.500A) Processing helix chain 'f1' and resid 28 through 61 removed outlier: 3.697A pdb=" N ARGf1 32 " --> pdb=" O SERf1 28 " (cutoff:3.500A) Processing helix chain 'f1' and resid 66 through 69 No H-bonds generated for 'chain 'f1' and resid 66 through 69' Processing helix chain 'f1' and resid 103 through 110 Processing helix chain 'd1' and resid 12 through 22 Processing helix chain 'd1' and resid 26 through 29 No H-bonds generated for 'chain 'd1' and resid 26 through 29' 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 83 through 85 No H-bonds generated for 'chain 'd1' and resid 83 through 85' Processing helix chain 'd1' and resid 91 through 108 Processing helix chain 'q1' and resid 30 through 42 removed outlier: 3.527A pdb=" N ILEq1 34 " --> pdb=" O PHEq1 30 " (cutoff:3.500A) Proline residue: q1 35 - end of helix Processing helix chain 'q1' and resid 45 through 69 Proline residue: q1 50 - end of helix removed outlier: 4.268A pdb=" N VALq1 54 " --> pdb=" O PROq1 50 " (cutoff:3.500A) Processing helix chain 'h1' and resid 16 through 26 removed outlier: 4.193A pdb=" N GLUh1 25 " --> pdb=" O ARGh1 21 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N GLNh1 26 " --> pdb=" O GLUh1 22 " (cutoff:3.500A) Processing helix chain 'h1' and resid 28 through 46 Processing helix chain 'h1' and resid 56 through 72 removed outlier: 3.534A pdb=" N LYSh1 72 " --> pdb=" O CYSh1 68 " (cutoff:3.500A) Processing helix chain 'i1' and resid 6 through 13 Processing helix chain 'i1' and resid 17 through 46 Processing helix chain 'i1' and resid 52 through 57 Processing helix chain 'a3' and resid 4 through 10 removed outlier: 3.523A pdb=" N SERa3 10 " --> pdb=" O GLNa3 6 " (cutoff:3.500A) Processing helix chain 'a3' and resid 55 through 62 Processing helix chain 'a3' and resid 74 through 82 Processing helix chain 'a3' and resid 103 through 118 removed outlier: 3.790A pdb=" N LEUa3 106 " --> pdb=" O SERa3 103 " (cutoff:3.500A) Proline residue: a3 107 - end of helix removed outlier: 4.339A pdb=" N GLNa3 118 " --> pdb=" O ASPa3 115 " (cutoff:3.500A) 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 179 through 189 Processing helix chain 'a3' and resid 192 through 194 No H-bonds generated for 'chain 'a3' and resid 192 through 194' Processing helix chain 'a3' and resid 205 through 215 Processing helix chain 'a3' and resid 266 through 277 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 301 Processing helix chain 'a3' and resid 331 through 347 Processing helix chain 'a3' and resid 352 through 368 Processing helix chain 'a3' and resid 373 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 60 through 62 No H-bonds generated for 'chain 'a4' and resid 60 through 62' Processing helix chain 'a4' and resid 66 through 70 Processing helix chain 'a4' and resid 82 through 92 Processing helix chain 'a4' and resid 113 through 128 removed outlier: 3.997A pdb=" N VALa4 116 " --> pdb=" O ARGa4 113 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ASPa4 117 " --> pdb=" O ASPa4 114 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILEa4 118 " --> pdb=" O ASPa4 115 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEUa4 119 " --> pdb=" O VALa4 116 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THRa4 128 " --> pdb=" O ASNa4 125 " (cutoff:3.500A) Processing helix chain 'a4' and resid 134 through 152 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 196 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 223 Processing helix chain 'a4' and resid 267 through 279 Processing helix chain 'a4' and resid 294 through 302 Processing helix chain 'a4' and resid 334 through 348 Processing helix chain 'a4' and resid 354 through 370 Processing helix chain 'a4' and resid 375 through 388 Processing helix chain 'a4' and resid 395 through 403 Processing helix chain 'a4' and resid 407 through 419 Processing helix chain 'b2' and resid 4 through 6 No H-bonds generated for 'chain 'b2' and resid 4 through 6' Processing helix chain 'b2' and resid 9 through 18 removed outlier: 3.565A pdb=" N ILEb2 13 " --> pdb=" O PROb2 9 " (cutoff:3.500A) Processing helix chain 'b2' and resid 32 through 54 Processing helix chain 'b2' and resid 62 through 72 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 110 through 133 Processing helix chain 'b2' and resid 137 through 152 Processing helix chain 'b2' and resid 158 through 164 Processing helix chain 'b2' and resid 172 through 203 Proline residue: b2 186 - end of helix Processing helix chain 'b2' and resid 223 through 244 Processing helix chain 'b2' and resid 272 through 282 removed outlier: 5.570A pdb=" N PHEb2 276 " --> pdb=" O TYRb2 273 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYRb2 278 " --> pdb=" O LEUb2 275 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALAb2 279 " --> pdb=" O PHEb2 276 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARGb2 282 " --> pdb=" O ALAb2 279 " (cutoff:3.500A) Processing helix chain 'b2' and resid 287 through 302 Processing helix chain 'b2' and resid 305 through 307 No H-bonds generated for 'chain 'b2' and resid 305 through 307' Processing helix chain 'b2' and resid 319 through 339 Processing helix chain 'b2' and resid 345 through 363 Processing helix chain 'b2' and resid 365 through 377 removed outlier: 4.661A pdb=" N LEUb2 377 " --> pdb=" O GLUb2 373 " (cutoff:3.500A) Processing helix chain 'c2' and resid 23 through 35 Processing helix chain 'c2' and resid 48 through 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 178 through 193 Processing helix chain 'c2' and resid 197 through 225 removed outlier: 3.770A pdb=" N LEUc2 215 " --> pdb=" O METc2 211 " (cutoff:3.500A) Proline residue: c2 216 - end of helix Processing helix chain 'c2' and resid 227 through 231 Processing helix chain 'f2' and resid 27 through 61 removed outlier: 3.970A pdb=" N ALAf2 31 " --> pdb=" O GLUf2 27 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARGf2 32 " --> pdb=" O SERf2 28 " (cutoff:3.500A) Processing helix chain 'f2' and resid 103 through 109 Processing helix chain 'd2' and resid 10 through 24 removed outlier: 4.271A pdb=" N GLYd2 15 " --> pdb=" O LYSd2 11 " (cutoff:3.500A) Processing helix chain 'd2' and resid 33 through 35 No H-bonds generated for 'chain 'd2' and resid 33 through 35' Processing helix chain 'd2' and resid 41 through 48 Processing helix chain 'd2' and resid 52 through 70 Processing helix chain 'd2' and resid 77 through 79 No H-bonds generated for 'chain 'd2' and resid 77 through 79' Processing helix chain 'd2' and resid 90 through 108 Processing helix chain 'q2' and resid 33 through 42 Processing helix chain 'q2' and resid 45 through 70 Proline residue: q2 50 - end of helix removed outlier: 3.683A pdb=" N VALq2 54 " --> pdb=" O PROq2 50 " (cutoff:3.500A) Processing helix chain 'h2' and resid 17 through 24 Processing helix chain 'h2' and resid 29 through 45 Processing helix chain 'h2' and resid 56 through 71 Processing helix chain 'h2' and resid 74 through 76 No H-bonds generated for 'chain 'h2' and resid 74 through 76' Processing helix chain 'i2' and resid 4 through 13 Processing helix chain 'i2' and resid 18 through 47 removed outlier: 3.609A pdb=" N ASNi2 47 " --> pdb=" O TYRi2 43 " (cutoff:3.500A) Processing helix chain 'i2' and resid 53 through 57 Processing helix chain 'V1' and resid 33 through 39 Processing helix chain 'V1' and resid 46 through 49 No H-bonds generated for 'chain 'V1' and resid 46 through 49' Processing helix chain 'V1' and resid 53 through 62 Processing helix chain 'V1' and resid 75 through 81 Processing helix chain 'V1' and resid 106 through 113 removed outlier: 4.058A pdb=" N ILEV1 110 " --> pdb=" O LYSV1 106 " (cutoff:3.500A) Processing helix chain 'V1' and resid 115 through 127 Processing helix chain 'V1' and resid 143 through 158 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 215 through 217 No H-bonds generated for 'chain 'V1' and resid 215 through 217' Processing helix chain 'V1' and resid 225 through 236 Proline residue: V1 232 - end of helix removed outlier: 3.545A pdb=" N CYSV1 235 " --> pdb=" O SERV1 231 " (cutoff:3.500A) Processing helix chain 'V1' and resid 242 through 244 No H-bonds generated for 'chain 'V1' and resid 242 through 244' Processing helix chain 'V1' and resid 276 through 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 314 removed outlier: 4.158A pdb=" N THRV1 314 " --> pdb=" O SERV1 310 " (cutoff:3.500A) 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 386 through 399 Processing helix chain 'V1' and resid 407 through 421 Proline residue: V1 414 - end of helix Processing helix chain 'V1' and resid 423 through 437 Processing helix chain 'V2' and resid 25 through 37 Processing helix chain 'V2' and resid 43 through 57 removed outlier: 3.844A pdb=" N VALV2 47 " --> pdb=" O ALAV2 44 " (cutoff:3.500A) removed outlier: 3.887A 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 78 through 86 Processing helix chain 'V2' and resid 107 through 110 No H-bonds generated for 'chain 'V2' and resid 107 through 110' Processing helix chain 'V2' and resid 113 through 124 Processing helix chain 'V2' and resid 166 through 176 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: 3.709A 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 265 through 268 No H-bonds generated for 'chain 'S1' and resid 265 through 268' Processing helix chain 'S1' and resid 273 through 275 No H-bonds generated for 'chain 'S1' and resid 273 through 275' Processing helix chain 'S1' and resid 296 through 308 Processing helix chain 'S1' and resid 326 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 370 through 373 Processing helix chain 'S1' and resid 389 through 401 Processing helix chain 'S1' and resid 426 through 433 Processing helix chain 'S1' and resid 438 through 445 Processing helix chain 'S1' and resid 463 through 479 Processing helix chain 'S1' and resid 497 through 505 Processing helix chain 'S1' and resid 511 through 516 removed outlier: 4.068A 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 596 through 606 Processing helix chain 'S1' and resid 616 through 626 Processing helix chain 'S1' and resid 628 through 630 No H-bonds generated for 'chain 'S1' and resid 628 through 630' Processing helix chain 'S1' and resid 642 through 648 Processing helix chain 'S1' and resid 668 through 672 Processing helix chain 'S1' and resid 676 through 680 Processing helix chain 'S1' and resid 683 through 692 Processing helix chain 'S2' and resid 8 through 13 Processing helix chain 'S2' and resid 87 through 93 Processing helix chain 'S2' and resid 97 through 105 Proline residue: S2 101 - end of helix Processing helix chain 'S2' and resid 113 through 126 Processing helix chain 'S2' and resid 132 through 161 Processing helix chain 'S2' and resid 164 through 184 removed outlier: 4.003A 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 405 removed outlier: 3.714A pdb=" N GLYS2 401 " --> pdb=" O ALAS2 397 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEUS2 402 " --> pdb=" O HISS2 398 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ASPS2 403 " --> pdb=" O LEUS2 399 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N LYSS2 404 " --> pdb=" O ALAS2 400 " (cutoff:3.500A) Processing helix chain 'S2' and resid 411 through 420 Processing helix chain 'S3' and resid 16 through 32 Processing helix chain 'S3' and resid 57 through 64 Processing helix chain 'S3' and resid 120 through 122 No H-bonds generated for 'chain 'S3' and resid 120 through 122' Processing helix chain 'S3' and resid 125 through 138 removed outlier: 4.016A pdb=" N ASNS3 128 " --> pdb=" O LYSS3 125 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N TRPS3 129 " --> pdb=" O ALAS3 126 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYRS3 130 " --> pdb=" O ALAS3 127 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARGS3 132 " --> pdb=" O TRPS3 129 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRPS3 135 " --> pdb=" O ARGS3 132 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N METS3 137 " --> pdb=" O ILES3 134 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHES3 138 " --> pdb=" O TRPS3 135 " (cutoff:3.500A) Processing helix chain 'S3' and resid 207 through 209 No H-bonds generated for 'chain 'S3' and resid 207 through 209' Processing helix chain 'S7' and resid 25 through 43 Processing helix chain 'S7' and resid 54 through 62 Processing helix chain 'S7' and resid 94 through 105 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 169 Processing helix chain 'S7' and resid 172 through 177 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 160 Processing helix chain 'S8' and resid 163 through 171 Processing helix chain 'V3' and resid 43 through 45 No H-bonds generated for 'chain 'V3' and resid 43 through 45' Processing helix chain 'V3' and resid 50 through 57 Processing helix chain 'S6' and resid 24 through 27 No H-bonds generated for 'chain 'S6' and resid 24 through 27' Processing helix chain 'S6' and resid 41 through 43 No H-bonds generated for 'chain 'S6' and resid 41 through 43' 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 49 through 51 No H-bonds generated for 'chain 'S4' and resid 49 through 51' Processing helix chain 'S4' and resid 90 through 98 Processing helix chain 'S4' and resid 118 through 122 Processing helix chain 'A9' and resid 30 through 41 Processing helix chain 'A9' and resid 53 through 58 Processing helix chain 'A9' and resid 60 through 62 No H-bonds generated for 'chain 'A9' and resid 60 through 62' Processing helix chain 'A9' and resid 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 177 through 183 Processing helix chain 'A9' and resid 207 through 219 Processing helix chain 'A9' and resid 238 through 248 Processing helix chain 'A9' and resid 282 through 289 Processing helix chain 'A9' and resid 310 through 317 Processing helix chain 'A2' and resid 27 through 37 Processing helix chain 'A2' and resid 41 through 46 Processing helix chain 'A2' and resid 83 through 93 Processing helix chain 'A5' and resid 20 through 36 Processing helix chain 'A5' and resid 43 through 59 Processing helix chain 'A5' and resid 65 through 70 Processing helix chain 'A5' and resid 77 through 94 Processing helix chain 'A6' and resid 24 through 48 Proline residue: A6 43 - end of helix Processing helix chain 'A6' and resid 55 through 68 Processing helix chain 'A6' and resid 75 through 93 Processing helix chain 'A6' and resid 99 through 104 Processing helix chain 'A6' and resid 117 through 122 Processing helix chain 'A7' and resid 5 through 13 Processing helix chain 'A7' and resid 59 through 61 No H-bonds generated for 'chain 'A7' and resid 59 through 61' Processing helix chain 'AL' and resid 14 through 17 No H-bonds generated for 'chain 'AL' and resid 14 through 17' Processing helix chain 'AL' and resid 20 through 29 Processing helix chain 'AL' and resid 84 through 90 Processing helix chain 'AA' and resid 8 through 21 Processing helix chain 'AA' and resid 44 through 57 Processing helix chain 'AA' and resid 64 through 68 Processing helix chain 'AA' and resid 73 through 83 Processing sheet with id= A, first strand: chain 'D5' and resid 61 through 67 Processing sheet with id= B, first strand: chain 'D4' and resid 50 through 52 Processing sheet with id= C, first strand: chain 'AJ' and resid 122 through 125 removed outlier: 6.576A pdb=" N VALAJ 168 " --> pdb=" O THRAJ 26 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ASPAJ 28 " --> pdb=" O VALAJ 168 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ILEAJ 170 " --> pdb=" O ASPAJ 28 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLUAJ 219 " --> pdb=" O VALAJ 169 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N TYRAJ 171 " --> pdb=" O GLUAJ 219 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LEUAJ 221 " --> pdb=" O TYRAJ 171 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'a1' and resid 15 through 19 removed outlier: 6.766A pdb=" N METa1 195 " --> pdb=" O ARGa1 24 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ALAa1 26 " --> pdb=" O METa1 195 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEUa1 197 " --> pdb=" O ALAa1 26 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N GLUa1 28 " --> pdb=" O LEUa1 197 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ALAa1 199 " --> pdb=" O GLUa1 28 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'a1' and resid 240 through 244 removed outlier: 6.080A pdb=" N VALa1 422 " --> pdb=" O ILEa1 241 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N HISa1 243 " --> pdb=" O VALa1 422 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLYa1 424 " --> pdb=" O HISa1 243 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'a2' and resid 25 through 29 Processing sheet with id= G, first strand: chain 'a2' and resid 242 through 247 Processing sheet with id= H, first strand: chain 'f1' and resid 74 through 77 Processing sheet with id= I, first strand: chain 'f1' and resid 85 through 88 Processing sheet with id= J, first strand: chain 'a3' and resid 15 through 19 Processing sheet with id= K, first strand: chain 'a3' and resid 240 through 244 removed outlier: 6.165A pdb=" N VALa3 422 " --> pdb=" O ILEa3 241 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N HISa3 243 " --> pdb=" O VALa3 422 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLYa3 424 " --> pdb=" O HISa3 243 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'a4' and resid 25 through 29 Processing sheet with id= M, first strand: chain 'a4' and resid 242 through 247 Processing sheet with id= N, first strand: chain 'f2' and resid 74 through 77 Processing sheet with id= O, first strand: chain 'f2' and resid 85 through 88 Processing sheet with id= P, first strand: chain 'V1' and resid 220 through 224 removed outlier: 6.780A pdb=" N TYRV1 92 " --> pdb=" O THRV1 221 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ALAV1 223 " --> pdb=" O TYRV1 92 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VALV1 94 " --> pdb=" O ALAV1 223 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ALAV1 133 " --> pdb=" O LEUV1 93 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N VALV1 95 " --> pdb=" O ALAV1 133 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TYRV1 135 " --> pdb=" O VALV1 95 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALAV1 97 " --> pdb=" O TYRV1 135 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N TYRV1 137 " --> pdb=" O ALAV1 97 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASPV1 174 " --> pdb=" O ALAV1 134 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ILEV1 136 " --> pdb=" O ASPV1 174 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N PHEV1 176 " --> pdb=" O ILEV1 136 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ILEV1 138 " --> pdb=" O PHEV1 176 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VALV1 178 " --> pdb=" O ILEV1 138 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'V1' and resid 294 through 298 removed outlier: 6.703A pdb=" N METV1 337 " --> pdb=" O LEUV1 295 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VALV1 297 " --> pdb=" O ILEV1 335 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILEV1 335 " --> pdb=" O VALV1 297 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'V2' and resid 138 through 142 Processing sheet with id= S, first strand: chain 'S1' and resid 16 through 20 removed outlier: 6.310A pdb=" N TRPS1 77 " --> pdb=" O PHES1 12 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'S1' and resid 146 through 148 Processing sheet with id= U, first strand: chain 'S1' and resid 173 through 177 Processing sheet with id= V, first strand: chain 'S1' and resid 223 through 228 Processing sheet with id= W, first strand: chain 'S1' and resid 283 through 286 Processing sheet with id= X, first strand: chain 'S1' and resid 342 through 345 removed outlier: 6.415A pdb=" N METS1 521 " --> pdb=" O ALAS1 316 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ILES1 318 " --> pdb=" O METS1 521 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N PHES1 523 " --> pdb=" O ILES1 318 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VALS1 559 " --> pdb=" O TYRS1 545 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N GLYS1 547 " --> pdb=" O VALS1 559 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LEUS1 561 " --> pdb=" O GLYS1 547 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'S1' and resid 405 through 409 Processing sheet with id= Z, first strand: chain 'S1' and resid 572 through 574 Processing sheet with id= AA, first strand: chain 'S2' and resid 47 through 51 Processing sheet with id= AB, first strand: chain 'S2' and resid 361 through 368 Processing sheet with id= AC, first strand: chain 'S3' and resid 74 through 76 removed outlier: 6.532A pdb=" N LEUS3 48 " --> pdb=" O ARGS3 106 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LYSS3 108 " --> pdb=" O LEUS3 48 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ILES3 50 " --> pdb=" O LYSS3 108 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N TYRS3 110 " --> pdb=" O ILES3 50 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ILES3 52 " --> pdb=" O TYRS3 110 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'S3' and resid 172 through 177 Processing sheet with id= AE, first strand: chain 'S7' and resid 85 through 89 removed outlier: 6.370A pdb=" N TYRS7 112 " --> pdb=" O METS7 86 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VALS7 88 " --> pdb=" O TYRS7 112 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VALS7 114 " --> pdb=" O VALS7 88 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILES7 144 " --> pdb=" O SERS7 115 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'S8' and resid 93 through 95 Processing sheet with id= AG, first strand: chain 'S6' and resid 56 through 59 Processing sheet with id= AH, 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= AI, first strand: chain 'A9' and resid 90 through 92 removed outlier: 6.318A pdb=" N GLNA9 44 " --> pdb=" O ALAA9 21 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VALA9 23 " --> pdb=" O GLNA9 44 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILEA9 46 " --> pdb=" O VALA9 23 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ILEA9 69 " --> pdb=" O VALA9 47 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'A9' and resid 130 through 134 removed outlier: 6.173A pdb=" N THRA9 164 " --> pdb=" O HISA9 131 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N SERA9 133 " --> pdb=" O THRA9 164 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILEA9 166 " --> pdb=" O SERA9 133 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ Processing sheet with id= AK, first strand: chain 'A9' and resid 170 through 172 Processing sheet with id= AL, first strand: chain 'A2' and resid 53 through 56 removed outlier: 6.991A pdb=" N ARGA2 67 " --> pdb=" O ARGA2 16 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ILEA2 18 " --> pdb=" O TRPA2 65 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N TRPA2 65 " --> pdb=" O ILEA2 18 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILEA2 20 " --> pdb=" O LYSA2 63 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LYSA2 63 " --> pdb=" O ILEA2 20 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'AL' and resid 47 through 50 4258 hydrogen bonds defined for protein. 12159 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: 35.38 Time building geometry restraints manager: 34.80 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: 41535 1.42 - 1.64: 56733 1.64 - 1.86: 1004 1.86 - 2.08: 24 2.08 - 2.31: 88 Bond restraints: 99384 Sorted by residual: bond pdb=" C2D HECc2 501 " pdb=" C3D HECc2 501 " ideal model delta sigma weight residual 1.544 1.315 0.229 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C2D HECc1 501 " pdb=" C3D HECc1 501 " ideal model delta sigma weight residual 1.544 1.317 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" CAC HECc2 501 " pdb=" CBC HECc2 501 " ideal model delta sigma weight residual 1.544 1.361 0.183 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 1.362 0.182 2.00e-02 2.50e+03 8.31e+01 bond pdb=" CAB HECc1 501 " pdb=" CBB HECc1 501 " ideal model delta sigma weight residual 1.544 1.398 0.146 2.00e-02 2.50e+03 5.35e+01 ... (remaining 99379 not shown) Histogram of bond angle deviations from ideal: 68.87 - 90.88: 98 90.88 - 112.89: 54811 112.89 - 134.90: 79950 134.90 - 156.91: 14 156.91 - 178.92: 12 Bond angle restraints: 134885 Sorted by residual: angle pdb=" S1 FESf1 501 " pdb=" FE2 FESf1 501 " pdb=" S2 FESf1 501 " ideal model delta sigma weight residual 104.33 90.41 13.92 1.14e+00 7.69e-01 1.49e+02 angle pdb=" PA NDPA9 401 " pdb=" O3 NDPA9 401 " pdb=" PN NDPA9 401 " ideal model delta sigma weight residual 107.74 131.15 -23.41 1.95e+00 2.62e-01 1.44e+02 angle pdb=" S1 FESf2 202 " pdb=" FE2 FESf2 202 " pdb=" S2 FESf2 202 " ideal model delta sigma weight residual 104.33 90.73 13.60 1.14e+00 7.69e-01 1.42e+02 angle pdb=" S1 FESS1 803 " pdb=" FE2 FESS1 803 " pdb=" S2 FESS1 803 " ideal model delta sigma weight residual 104.33 91.04 13.29 1.14e+00 7.69e-01 1.36e+02 angle pdb=" FE1 FESf1 501 " pdb=" S2 FESf1 501 " pdb=" FE2 FESf1 501 " ideal model delta sigma weight residual 75.66 88.92 -13.26 1.14e+00 7.69e-01 1.35e+02 ... (remaining 134880 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.93: 58419 31.93 - 63.85: 857 63.85 - 95.78: 96 95.78 - 127.70: 2 127.70 - 159.63: 1 Dihedral angle restraints: 59375 sinusoidal: 24257 harmonic: 35118 Sorted by residual: dihedral pdb=" CA PHEB7 30 " pdb=" C PHEB7 30 " pdb=" N PROB7 31 " pdb=" CA PROB7 31 " ideal model delta harmonic sigma weight residual 180.00 -119.95 -60.05 0 5.00e+00 4.00e-02 1.44e+02 dihedral pdb=" CA ALAD5 365 " pdb=" C ALAD5 365 " pdb=" N METD5 366 " pdb=" CA METD5 366 " ideal model delta harmonic sigma weight residual -180.00 -122.56 -57.44 0 5.00e+00 4.00e-02 1.32e+02 dihedral pdb=" CA PHEAJ 278 " pdb=" C PHEAJ 278 " pdb=" N LEUAJ 279 " pdb=" CA LEUAJ 279 " ideal model delta harmonic sigma weight residual 180.00 123.42 56.58 0 5.00e+00 4.00e-02 1.28e+02 ... (remaining 59372 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.212: 14777 4.212 - 8.424: 0 8.424 - 12.635: 0 12.635 - 16.847: 0 16.847 - 21.059: 24 Chirality restraints: 14801 Sorted by residual: 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 -10.50 21.06 2.00e-01 2.50e+01 1.11e+04 chirality pdb=" FE3 SF4S1 801 " pdb=" S1 SF4S1 801 " pdb=" S2 SF4S1 801 " pdb=" S4 SF4S1 801 " both_signs ideal model delta sigma weight residual False -10.55 10.50 -21.05 2.00e-01 2.50e+01 1.11e+04 chirality pdb=" FE1 SF4S8 201 " pdb=" S2 SF4S8 201 " pdb=" S3 SF4S8 201 " pdb=" S4 SF4S8 201 " both_signs ideal model delta sigma weight residual False -10.55 10.49 -21.04 2.00e-01 2.50e+01 1.11e+04 ... (remaining 14798 not shown) Planarity restraints: 17106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMNV1 501 " -0.252 2.00e-02 2.50e+03 1.22e-01 7.12e+02 pdb=" C10 FMNV1 501 " -0.022 2.00e-02 2.50e+03 pdb=" C2 FMNV1 501 " 0.125 2.00e-02 2.50e+03 pdb=" C4 FMNV1 501 " -0.017 2.00e-02 2.50e+03 pdb=" C4A FMNV1 501 " -0.065 2.00e-02 2.50e+03 pdb=" C5A FMNV1 501 " -0.131 2.00e-02 2.50e+03 pdb=" C6 FMNV1 501 " -0.069 2.00e-02 2.50e+03 pdb=" C7 FMNV1 501 " 0.043 2.00e-02 2.50e+03 pdb=" C7M FMNV1 501 " 0.198 2.00e-02 2.50e+03 pdb=" C8 FMNV1 501 " 0.054 2.00e-02 2.50e+03 pdb=" C8M FMNV1 501 " 0.173 2.00e-02 2.50e+03 pdb=" C9 FMNV1 501 " -0.035 2.00e-02 2.50e+03 pdb=" C9A FMNV1 501 " -0.109 2.00e-02 2.50e+03 pdb=" N1 FMNV1 501 " 0.062 2.00e-02 2.50e+03 pdb=" N10 FMNV1 501 " -0.081 2.00e-02 2.50e+03 pdb=" N3 FMNV1 501 " 0.080 2.00e-02 2.50e+03 pdb=" N5 FMNV1 501 " -0.129 2.00e-02 2.50e+03 pdb=" O2 FMNV1 501 " 0.234 2.00e-02 2.50e+03 pdb=" O4 FMNV1 501 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VALA7 68 " -0.021 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" C VALA7 68 " 0.073 2.00e-02 2.50e+03 pdb=" O VALA7 68 " -0.027 2.00e-02 2.50e+03 pdb=" N META7 69 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARGc1 237 " -0.021 2.00e-02 2.50e+03 4.21e-02 1.77e+01 pdb=" C ARGc1 237 " 0.073 2.00e-02 2.50e+03 pdb=" O ARGc1 237 " -0.027 2.00e-02 2.50e+03 pdb=" N PROc1 238 " -0.024 2.00e-02 2.50e+03 ... (remaining 17103 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 648 2.53 - 3.13: 73697 3.13 - 3.72: 154039 3.72 - 4.31: 206404 4.31 - 4.90: 334196 Nonbonded interactions: 768984 Sorted by model distance: nonbonded pdb=" NE2 HISb1 97 " pdb="FE HEMb1 402 " model vdw 1.942 3.080 nonbonded pdb=" SD METc2 159 " pdb="FE HECc2 501 " model vdw 1.953 3.360 nonbonded pdb=" NE2 HISb2 83 " pdb="FE HEMb2 402 " model vdw 1.967 3.080 nonbonded pdb=" NE2 HISc1 41 " pdb="FE HECc1 501 " model vdw 1.978 3.080 nonbonded pdb=" NE2 HISb1 182 " pdb="FE HEMb1 401 " model vdw 1.982 3.080 ... (remaining 768979 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' and (resid 2 through 379 or resid 402)) selection = (chain 'b2' and (resid 2 through 379 or resid 402)) } ncs_group { reference = (chain 'c1' and (resid 2 through 239 or resid 501)) selection = (chain 'c2' and (resid 2 through 239 or resid 501)) } ncs_group { reference = (chain 'd1' and resid 11 through 109) selection = (chain 'd2' and resid 11 through 109) } ncs_group { reference = (chain 'f1' and resid 2 through 196) selection = (chain 'f2' and resid 2 through 196) } ncs_group { reference = chain 'h1' selection = chain 'h2' } ncs_group { reference = chain 'i1' selection = (chain 'i2' and resid 5 through 59) } ncs_group { reference = (chain 'q1' and resid 2 through 73) selection = (chain 'q2' and resid 2 through 73) } ncs_group { reference = (chain 'x1' and resid 8 through 38) selection = (chain 'x2' and (resid 1 or (resid 2 and (name N or name CA or name C or name O \ )) or resid 3 through 48)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 38 7.16 5 Zn 1 6.06 5 P 18 5.49 5 S 626 5.16 5 C 62307 2.51 5 N 16441 2.21 5 O 17507 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.980 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: 0.110 Extract box with map and model: 34.080 Check model and map are aligned: 1.130 Convert atoms to be neutral: 0.650 Process input model: 228.730 Find NCS groups from input model: 4.600 Set up NCS constraints: 0.670 Set refine NCS operators: 0.000 Set scattering table: 0.040 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 278.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 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 : 0.009 0.229 99384 Z= 0.570 Angle : 1.243 23.413 134885 Z= 0.656 Chirality : 0.847 21.059 14801 Planarity : 0.009 0.122 17106 Dihedral : 11.747 159.629 36671 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.40 % Favored : 88.51 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.22 % Twisted Proline : 1.49 % Twisted General : 0.47 % 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: -3.91 (0.06), residues: 11848 helix: -1.93 (0.05), residues: 6111 sheet: -1.89 (0.19), residues: 689 loop : -3.53 (0.07), residues: 5048 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23696 Ramachandran restraints generated. 11848 Oldfield, 0 Emsley, 11848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23696 Ramachandran restraints generated. 11848 Oldfield, 0 Emsley, 11848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3934 residues out of total 10392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 3875 time to evaluate : 9.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 8 residues processed: 3918 average time/residue: 0.8979 time to fit residues: 5956.6149 Evaluate side-chains 2101 residues out of total 10392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 2093 time to evaluate : 9.121 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.6850 time to fit residues: 22.5977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1174 random chunks: chunk 991 optimal weight: 0.9990 chunk 889 optimal weight: 10.0000 chunk 493 optimal weight: 10.0000 chunk 303 optimal weight: 3.9990 chunk 600 optimal weight: 0.0980 chunk 475 optimal weight: 10.0000 chunk 920 optimal weight: 2.9990 chunk 356 optimal weight: 0.8980 chunk 559 optimal weight: 5.9990 chunk 684 optimal weight: 10.0000 chunk 1066 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D3 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 5 ASN ** D1 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 194 ASN D1 247 HIS ** D1 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 287 HIS D5 59 GLN D5 72 GLN ** D5 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 200 GLN D5 226 GLN ** D5 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 332 HIS D5 546 GLN ** D5 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 580 GLN D4 26 ASN D4 82 HIS D4 83 HIS D4 88 ASN ** D4 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2 63 GLN ** D2 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 174 GLN ** D2 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 235 ASN D2 316 GLN B5 124 GLN A8 29 HIS ** BJ 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 54 GLN ** BJ 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 99 GLN BJ 103 ASN BJ 106 GLN BJ 130 GLN AJ 114 HIS AJ 151 HIS AJ 154 GLN AJ 222 GLN AJ 251 GLN AJ 287 HIS S5 26 HIS ** A3 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2 59 HIS C2 88 HIS ** B4 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 75 GLN B6 73 HIS B7 75 ASN ** B7 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B9 11 HIS B9 13 GLN B8 104 HIS ** BK 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 45 HIS A1 27 HIS a1 29 GLN a1 141 ASN a1 159 GLN a1 189 HIS a1 252 HIS a1 264 ASN a1 289 HIS a1 301 ASN a1 363 ASN ** a2 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a2 141 GLN a2 174 ASN a2 297 GLN b1 8 HIS b1 148 ASN b1 322 GLN c1 50 HIS f1 2 HIS f1 53 ASN f1 122 HIS ** d1 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q1 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q1 23 GLN q1 64 GLN q1 73 ASN h1 67 HIS a3 21 ASN a3 61 HIS a3 85 HIS a3 154 HIS a3 189 HIS a3 289 HIS a4 22 GLN a4 125 ASN ** a4 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a4 305 GLN ** a4 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 32 ASN b2 44 GLN b2 85 ASN ** b2 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c2 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c2 165 ASN c2 224 HIS ** f2 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f2 164 HIS ** q2 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h2 23 GLN h2 63 HIS V1 293 ASN V1 373 ASN V2 9 HIS V2 37 ASN ** V2 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V2 150 ASN ** S1 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 43 HIS S1 51 ASN ** S1 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1 665 GLN S2 50 ASN S2 79 HIS S2 84 HIS S2 135 GLN ** S2 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 316 ASN S2 347 HIS ** S2 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S7 38 ASN S7 82 GLN ** S8 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V3 40 ASN ** V3 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S6 16 GLN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S6 94 GLN S4 29 HIS S4 50 ASN S4 67 ASN ** A9 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A9 87 HIS A9 243 GLN A2 80 ASN A5 36 HIS ** A5 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A7 20 GLN ** AL 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.267 99384 Z= 0.477 Angle : 1.462 51.980 134885 Z= 0.906 Chirality : 0.257 6.488 14801 Planarity : 0.006 0.097 17106 Dihedral : 8.402 161.312 13421 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.05 % Favored : 90.93 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.23 % Twisted Proline : 1.04 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.07), residues: 11848 helix: -0.54 (0.06), residues: 6168 sheet: -1.51 (0.19), residues: 698 loop : -3.23 (0.08), residues: 4982 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23696 Ramachandran restraints generated. 11848 Oldfield, 0 Emsley, 11848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23696 Ramachandran restraints generated. 11848 Oldfield, 0 Emsley, 11848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2885 residues out of total 10392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 2865 time to evaluate : 9.392 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 outliers start: 20 outliers final: 5 residues processed: 2879 average time/residue: 0.8830 time to fit residues: 4381.8179 Evaluate side-chains 2023 residues out of total 10392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 2018 time to evaluate : 9.206 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.6618 time to fit residues: 18.4051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1174 random chunks: chunk 592 optimal weight: 0.9990 chunk 330 optimal weight: 10.0000 chunk 887 optimal weight: 8.9990 chunk 725 optimal weight: 0.0980 chunk 294 optimal weight: 4.9990 chunk 1068 optimal weight: 0.6980 chunk 1153 optimal weight: 10.0000 chunk 951 optimal weight: 7.9990 chunk 1059 optimal weight: 5.9990 chunk 364 optimal weight: 10.0000 chunk 856 optimal weight: 9.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D3 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 32 GLN ** D1 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 59 GLN ** D5 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 226 GLN ** D5 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 541 ASN D5 570 GLN ** D4 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2 63 GLN ** D2 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 235 ASN B5 143 ASN ** BJ 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 130 GLN AJ 287 HIS S5 26 HIS S5 33 HIS ** S5 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3 32 GLN C2 12 GLN B4 47 GLN ** B4 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 36 ASN a1 159 GLN a1 264 ASN ** a1 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a2 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a2 141 GLN b1 8 HIS b1 352 GLN f1 122 HIS q1 23 GLN ** a3 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a3 418 GLN ** a4 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 148 ASN b2 345 HIS ** b2 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c2 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c2 155 GLN c2 165 ASN f2 86 ASN f2 164 HIS q2 6 HIS ** q2 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h2 23 GLN ** V1 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S2 34 ASN S2 135 GLN S2 231 ASN ** S2 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 347 HIS ** S2 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 38 GLN ** S3 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 38 ASN S7 82 GLN ** S7 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S8 123 GLN ** S8 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S6 16 GLN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S4 50 ASN ** A9 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A9 119 GLN A9 243 GLN A5 36 HIS ** A5 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 110 GLN A6 57 GLN ** AL 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.277 99384 Z= 0.484 Angle : 1.445 51.306 134885 Z= 0.900 Chirality : 0.257 6.365 14801 Planarity : 0.006 0.097 17106 Dihedral : 7.918 156.422 13421 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.94 % Favored : 90.04 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.24 % Twisted Proline : 0.89 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.07), residues: 11848 helix: 0.01 (0.06), residues: 6157 sheet: -1.39 (0.18), residues: 714 loop : -3.08 (0.08), residues: 4977 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23696 Ramachandran restraints generated. 11848 Oldfield, 0 Emsley, 11848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23696 Ramachandran restraints generated. 11848 Oldfield, 0 Emsley, 11848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2636 residues out of total 10392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 2618 time to evaluate : 9.177 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 outliers start: 18 outliers final: 4 residues processed: 2626 average time/residue: 0.8765 time to fit residues: 4000.8907 Evaluate side-chains 1951 residues out of total 10392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1947 time to evaluate : 9.159 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.6598 time to fit residues: 17.1152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1174 random chunks: chunk 1055 optimal weight: 6.9990 chunk 802 optimal weight: 8.9990 chunk 554 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 509 optimal weight: 20.0000 chunk 717 optimal weight: 7.9990 chunk 1071 optimal weight: 5.9990 chunk 1134 optimal weight: 0.2980 chunk 560 optimal weight: 5.9990 chunk 1015 optimal weight: 6.9990 chunk 305 optimal weight: 1.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D3 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 138 GLN ** D1 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 115 ASN ** D5 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 175 ASN D5 194 ASN ** D5 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D5 354 GLN D5 541 ASN ** D4 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2 63 GLN ** D2 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 186 HIS ** D2 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 235 ASN ** BJ 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 130 GLN BJ 148 HIS ** AJ 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 287 HIS S5 26 HIS ** B4 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B9 32 HIS ** B2 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B8 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 36 ASN a1 264 ASN ** a1 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a2 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a2 305 GLN ** a2 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b1 8 HIS f1 122 HIS q1 12 HIS q1 23 GLN ** a3 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a3 339 GLN ** a4 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b2 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 308 HIS b2 322 GLN ** b2 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c2 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c2 199 HIS c2 224 HIS ** f2 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q2 12 HIS ** V1 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V2 99 HIS V2 101 GLN ** V2 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 36 GLN ** S1 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1 293 HIS ** S1 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1 653 ASN S2 34 ASN ** S2 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 38 ASN S7 82 GLN ** S7 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V3 65 GLN V3 75 HIS S6 16 GLN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S4 50 ASN ** A9 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A9 119 GLN A9 234 ASN A5 36 HIS ** A5 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 57 GLN ** AL 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.266 99384 Z= 0.494 Angle : 1.449 51.194 134885 Z= 0.901 Chirality : 0.257 6.439 14801 Planarity : 0.005 0.096 17106 Dihedral : 7.758 155.745 13421 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.05 % Favored : 89.93 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.24 % Twisted Proline : 0.74 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.08), residues: 11848 helix: 0.24 (0.06), residues: 6159 sheet: -1.36 (0.18), residues: 721 loop : -2.96 (0.08), residues: 4968 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23696 Ramachandran restraints generated. 11848 Oldfield, 0 Emsley, 11848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23696 Ramachandran restraints generated. 11848 Oldfield, 0 Emsley, 11848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2501 residues out of total 10392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 2485 time to evaluate : 9.597 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 outliers start: 16 outliers final: 4 residues processed: 2496 average time/residue: 0.8512 time to fit residues: 3700.6732 Evaluate side-chains 1925 residues out of total 10392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1921 time to evaluate : 9.183 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.7133 time to fit residues: 17.2690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1174 random chunks: chunk 945 optimal weight: 0.1980 chunk 644 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 844 optimal weight: 7.9990 chunk 468 optimal weight: 9.9990 chunk 968 optimal weight: 0.0170 chunk 784 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 579 optimal weight: 0.6980 chunk 1018 optimal weight: 7.9990 chunk 286 optimal weight: 0.8980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D3 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 124 ASN ** D1 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 317 GLN ** D5 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 65 ASN ** D5 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D5 309 GLN D5 323 HIS D5 479 GLN D5 541 ASN ** D4 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2 48 HIS D2 63 GLN ** D2 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 235 ASN ** BJ 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 77 HIS ** BJ 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 130 GLN BJ 148 HIS AJ 97 GLN AJ 147 GLN ** AJ 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 287 HIS B4 47 GLN ** B4 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B7 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B8 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 36 ASN ** a1 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a2 125 ASN a2 141 GLN a2 174 ASN ** a2 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b1 8 HIS ** b1 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c1 199 HIS f1 122 HIS q1 23 GLN h1 23 GLN ** a3 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a3 339 GLN a4 125 ASN a4 276 GLN ** a4 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b2 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 312 GLN b2 322 GLN ** b2 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c2 165 ASN f2 57 GLN ** f2 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f2 164 HIS q2 6 HIS ** V1 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V2 101 GLN ** V2 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 255 HIS ** S1 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S2 34 ASN ** S2 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 95 ASN S3 211 GLN S7 38 ASN ** S7 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S6 16 GLN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 50 ASN ** A9 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A9 119 GLN A9 288 HIS A5 36 HIS ** A5 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 57 GLN AL 17 HIS ** AL 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.275 99384 Z= 0.451 Angle : 1.418 51.036 134885 Z= 0.886 Chirality : 0.258 6.696 14801 Planarity : 0.005 0.093 17106 Dihedral : 7.423 148.795 13421 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.01 % Allowed : 8.81 % Favored : 91.18 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.24 % Twisted Proline : 0.59 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.08), residues: 11848 helix: 0.45 (0.07), residues: 6156 sheet: -1.21 (0.19), residues: 712 loop : -2.86 (0.08), residues: 4980 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23696 Ramachandran restraints generated. 11848 Oldfield, 0 Emsley, 11848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23696 Ramachandran restraints generated. 11848 Oldfield, 0 Emsley, 11848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2641 residues out of total 10392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 2630 time to evaluate : 9.567 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: 11 outliers final: 3 residues processed: 2638 average time/residue: 0.8571 time to fit residues: 3934.1971 Evaluate side-chains 1977 residues out of total 10392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1974 time to evaluate : 9.232 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.8105 time to fit residues: 16.5089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1174 random chunks: chunk 381 optimal weight: 7.9990 chunk 1021 optimal weight: 8.9990 chunk 224 optimal weight: 0.9990 chunk 666 optimal weight: 4.9990 chunk 280 optimal weight: 0.9990 chunk 1135 optimal weight: 5.9990 chunk 942 optimal weight: 0.9990 chunk 525 optimal weight: 0.9980 chunk 94 optimal weight: 7.9990 chunk 375 optimal weight: 8.9990 chunk 596 optimal weight: 0.7980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D3 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 284 GLN ** D5 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 65 ASN D5 175 ASN D5 200 GLN ** D5 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D5 541 ASN D5 570 GLN ** D4 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2 48 HIS D2 63 GLN ** D2 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 235 ASN ** BJ 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 148 HIS AJ 147 GLN ** AJ 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 287 HIS A3 68 HIS B4 47 GLN B7 49 GLN ** B7 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B8 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B8 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 36 ASN A1 68 ASN ** a1 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a2 141 GLN ** a2 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b1 345 HIS ** c1 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f1 122 HIS q1 23 GLN a3 328 HIS a4 276 GLN ** a4 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b2 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 312 GLN ** b2 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c2 165 ASN q2 6 HIS ** V1 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V2 74 GLN ** V2 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S2 34 ASN ** S2 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 409 HIS S7 38 ASN ** S8 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V3 65 GLN S6 16 GLN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 43 ASN S4 50 ASN ** A9 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 36 HIS A5 85 ASN A6 57 GLN ** AL 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 116 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.265 99384 Z= 0.456 Angle : 1.423 50.945 134885 Z= 0.889 Chirality : 0.257 6.532 14801 Planarity : 0.005 0.093 17106 Dihedral : 7.273 145.577 13421 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.01 % Allowed : 8.91 % Favored : 91.08 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.24 % Twisted Proline : 0.59 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.08), residues: 11848 helix: 0.51 (0.07), residues: 6146 sheet: -1.07 (0.19), residues: 715 loop : -2.79 (0.08), residues: 4987 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23696 Ramachandran restraints generated. 11848 Oldfield, 0 Emsley, 11848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23696 Ramachandran restraints generated. 11848 Oldfield, 0 Emsley, 11848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2522 residues out of total 10392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 2515 time to evaluate : 9.388 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 outliers start: 7 outliers final: 2 residues processed: 2521 average time/residue: 0.8613 time to fit residues: 3797.4913 Evaluate side-chains 1950 residues out of total 10392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1948 time to evaluate : 9.190 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.6895 time to fit residues: 14.6741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1174 random chunks: chunk 1095 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 647 optimal weight: 7.9990 chunk 829 optimal weight: 0.7980 chunk 642 optimal weight: 5.9990 chunk 956 optimal weight: 5.9990 chunk 634 optimal weight: 10.0000 chunk 1131 optimal weight: 10.0000 chunk 708 optimal weight: 20.0000 chunk 689 optimal weight: 2.9990 chunk 522 optimal weight: 8.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D3 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3 83 ASN ** D1 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 284 GLN ** D5 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 541 ASN ** D5 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2 63 GLN D2 144 GLN ** D2 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 235 ASN ** A8 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 103 ASN ** BJ 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 147 GLN ** S5 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3 68 HIS B4 49 GLN B7 46 ASN B7 75 ASN ** B7 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B8 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B8 104 HIS ** B8 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 86 GLN A1 68 ASN ** a1 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a1 328 HIS a2 141 GLN ** a2 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b1 8 HIS ** b1 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c1 71 GLN ** f1 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f1 122 HIS q1 23 GLN a3 52 ASN a3 252 HIS ** a4 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a4 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b2 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 312 GLN b2 322 GLN ** b2 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c2 165 ASN ** f2 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f2 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q2 6 HIS ** V1 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 51 ASN ** S1 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S2 34 ASN ** S2 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 38 ASN ** S7 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V3 65 GLN S6 16 GLN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S4 29 HIS S4 50 ASN ** A9 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 36 HIS A5 85 ASN A6 57 GLN ** A7 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.251 99384 Z= 0.536 Angle : 1.481 50.998 134885 Z= 0.914 Chirality : 0.257 6.449 14801 Planarity : 0.006 0.102 17106 Dihedral : 7.454 149.891 13421 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.52 % Favored : 89.46 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.24 % Twisted Proline : 0.74 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.08), residues: 11848 helix: 0.36 (0.06), residues: 6174 sheet: -1.16 (0.19), residues: 719 loop : -2.84 (0.09), residues: 4955 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23696 Ramachandran restraints generated. 11848 Oldfield, 0 Emsley, 11848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23696 Ramachandran restraints generated. 11848 Oldfield, 0 Emsley, 11848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2301 residues out of total 10392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 2297 time to evaluate : 9.341 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: 4 outliers final: 1 residues processed: 2301 average time/residue: 0.8875 time to fit residues: 3581.9093 Evaluate side-chains 1812 residues out of total 10392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1811 time to evaluate : 9.175 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.6787 time to fit residues: 13.3577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1174 random chunks: chunk 700 optimal weight: 0.8980 chunk 451 optimal weight: 4.9990 chunk 675 optimal weight: 10.0000 chunk 340 optimal weight: 0.8980 chunk 222 optimal weight: 0.7980 chunk 219 optimal weight: 4.9990 chunk 719 optimal weight: 0.5980 chunk 770 optimal weight: 0.9990 chunk 559 optimal weight: 0.1980 chunk 105 optimal weight: 0.6980 chunk 889 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D3 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 124 ASN ** D1 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 284 GLN ** D5 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 175 ASN D5 541 ASN ** D5 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 26 ASN ** D4 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2 144 GLN ** D2 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 235 ASN A8 29 HIS A8 34 GLN ** A8 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 147 GLN AJ 180 GLN AJ 287 HIS ** B4 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B7 46 ASN ** B7 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B8 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B8 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BK 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1 31 ASN A1 68 ASN ** a1 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a2 141 GLN ** a2 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c1 71 GLN ** f1 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f1 122 HIS q1 23 GLN ** a3 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a3 328 HIS a4 276 GLN ** a4 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b2 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 312 GLN b2 322 GLN ** b2 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c2 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c2 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c2 165 ASN c2 224 HIS ** f2 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f2 100 HIS q2 6 HIS ** V1 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V1 293 ASN ** V1 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S2 201 GLN ** S2 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 38 ASN ** S7 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V3 65 GLN S6 16 GLN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 50 ASN ** A9 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 36 HIS A6 57 GLN A6 101 HIS ** A7 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A7 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.5179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.273 99384 Z= 0.461 Angle : 1.439 51.176 134885 Z= 0.894 Chirality : 0.257 6.621 14801 Planarity : 0.005 0.102 17106 Dihedral : 7.206 144.984 13421 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.65 % Favored : 91.33 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.24 % Twisted Proline : 0.45 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.08), residues: 11848 helix: 0.56 (0.07), residues: 6145 sheet: -1.00 (0.19), residues: 712 loop : -2.72 (0.09), residues: 4991 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23696 Ramachandran restraints generated. 11848 Oldfield, 0 Emsley, 11848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23696 Ramachandran restraints generated. 11848 Oldfield, 0 Emsley, 11848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2433 residues out of total 10392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 2431 time to evaluate : 9.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 2433 average time/residue: 0.8733 time to fit residues: 3728.9353 Evaluate side-chains 1900 residues out of total 10392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1900 time to evaluate : 9.100 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 11.9215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1174 random chunks: chunk 1029 optimal weight: 0.9980 chunk 1084 optimal weight: 1.9990 chunk 989 optimal weight: 0.9980 chunk 1054 optimal weight: 2.9990 chunk 1083 optimal weight: 9.9990 chunk 634 optimal weight: 2.9990 chunk 459 optimal weight: 0.9980 chunk 828 optimal weight: 20.0000 chunk 323 optimal weight: 7.9990 chunk 952 optimal weight: 10.0000 chunk 997 optimal weight: 9.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D3 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 284 GLN D6 46 ASN ** D5 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D5 541 ASN ** D5 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 26 ASN D4 103 GLN ** D4 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2 204 ASN ** D2 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 235 ASN ** BJ 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 147 GLN ** B4 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B7 46 ASN ** B8 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B8 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B8 136 ASN ** BK 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a2 141 GLN a2 164 HIS ** a2 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b1 8 HIS ** b1 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c1 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c1 105 ASN ** f1 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q1 23 GLN ** a4 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a4 385 GLN ** b2 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 312 GLN b2 322 GLN ** b2 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c2 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c2 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c2 165 ASN c2 224 HIS ** f2 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d2 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q2 6 HIS i2 47 ASN ** V1 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V1 293 ASN ** V1 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 38 ASN ** S7 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V3 65 GLN S6 16 GLN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S6 74 ASN S4 50 ASN ** A9 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 36 HIS A6 57 GLN ** A7 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A7 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 35 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.5325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.268 99384 Z= 0.463 Angle : 1.440 51.059 134885 Z= 0.895 Chirality : 0.257 6.578 14801 Planarity : 0.005 0.095 17106 Dihedral : 7.138 143.640 13421 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.40 % Favored : 90.58 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.24 % Twisted Proline : 0.45 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.08), residues: 11848 helix: 0.54 (0.07), residues: 6168 sheet: -1.00 (0.19), residues: 732 loop : -2.73 (0.09), residues: 4948 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23696 Ramachandran restraints generated. 11848 Oldfield, 0 Emsley, 11848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23696 Ramachandran restraints generated. 11848 Oldfield, 0 Emsley, 11848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2352 residues out of total 10392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 2349 time to evaluate : 9.342 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 outliers start: 3 outliers final: 0 residues processed: 2352 average time/residue: 0.8503 time to fit residues: 3511.4835 Evaluate side-chains 1897 residues out of total 10392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1897 time to evaluate : 9.205 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 11.9798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1174 random chunks: chunk 1050 optimal weight: 7.9990 chunk 692 optimal weight: 2.9990 chunk 1115 optimal weight: 7.9990 chunk 680 optimal weight: 0.5980 chunk 528 optimal weight: 10.0000 chunk 775 optimal weight: 10.0000 chunk 1169 optimal weight: 9.9990 chunk 1076 optimal weight: 8.9990 chunk 931 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 719 optimal weight: 6.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D3 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 284 GLN D6 46 ASN ** D5 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 175 ASN ** D5 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D5 332 HIS D5 541 ASN ** D5 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 26 ASN ** D4 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 293 HIS ** D4 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2 63 GLN ** D2 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 235 ASN ** BJ 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 64 HIS ** BJ 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 147 GLN ** B4 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B8 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B8 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B8 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BK 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a2 141 GLN a2 158 HIS ** a2 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b1 8 HIS ** b1 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c1 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c1 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f1 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f1 164 HIS q1 23 GLN ** a3 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a4 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b2 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 312 GLN b2 322 GLN ** b2 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c2 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c2 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c2 165 ASN c2 224 HIS f2 86 ASN q2 6 HIS ** V1 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V1 293 ASN ** V1 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 546 GLN ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 71 GLN S7 38 ASN ** S7 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S8 123 GLN V3 65 GLN S6 16 GLN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S6 74 ASN S4 50 ASN ** A9 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 36 HIS ** A5 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 57 GLN A6 125 HIS ** A7 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.5395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.255 99384 Z= 0.499 Angle : 1.467 51.114 134885 Z= 0.906 Chirality : 0.258 6.514 14801 Planarity : 0.005 0.098 17106 Dihedral : 7.222 146.508 13421 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.01 % Allowed : 10.09 % Favored : 89.91 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.24 % Twisted Proline : 0.45 % Twisted General : 0.10 % 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: 11848 helix: 0.44 (0.07), residues: 6157 sheet: -1.00 (0.19), residues: 726 loop : -2.76 (0.09), residues: 4965 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23696 Ramachandran restraints generated. 11848 Oldfield, 0 Emsley, 11848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23696 Ramachandran restraints generated. 11848 Oldfield, 0 Emsley, 11848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2243 residues out of total 10392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 2239 time to evaluate : 9.366 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 outliers start: 4 outliers final: 0 residues processed: 2243 average time/residue: 0.8507 time to fit residues: 3362.5252 Evaluate side-chains 1817 residues out of total 10392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1817 time to evaluate : 9.255 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 12.0382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1174 random chunks: chunk 571 optimal weight: 8.9990 chunk 739 optimal weight: 0.3980 chunk 992 optimal weight: 3.9990 chunk 285 optimal weight: 0.9990 chunk 858 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 258 optimal weight: 5.9990 chunk 932 optimal weight: 6.9990 chunk 390 optimal weight: 0.9990 chunk 957 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D3 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 284 GLN D6 46 ASN ** D5 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D5 541 ASN ** D5 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 26 ASN ** D4 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2 63 GLN ** D2 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 235 ASN ** A8 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 147 GLN B7 46 ASN ** B8 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B8 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B8 136 ASN ** a1 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a2 141 GLN ** a2 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c1 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c1 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f1 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f1 164 HIS q1 23 GLN ** a3 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a4 276 GLN ** b2 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 312 GLN b2 322 GLN ** b2 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c2 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c2 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c2 165 ASN c2 224 HIS q2 6 HIS i2 45 HIS ** V1 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V1 293 ASN ** V1 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 38 ASN ** S7 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S7 162 GLN S8 123 GLN V3 65 GLN S6 16 GLN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 50 ASN ** A9 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 36 HIS ** A5 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 57 GLN ** A6 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A7 20 GLN ** A7 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 116 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.095371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.083918 restraints weight = 341733.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.085404 restraints weight = 193018.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.086295 restraints weight = 122310.332| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.5520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.262 99384 Z= 0.462 Angle : 1.447 51.067 134885 Z= 0.897 Chirality : 0.257 6.535 14801 Planarity : 0.005 0.094 17106 Dihedral : 7.105 144.764 13421 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.35 % Favored : 90.62 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.24 % Twisted Proline : 0.45 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.08), residues: 11848 helix: 0.53 (0.07), residues: 6150 sheet: -0.95 (0.19), residues: 735 loop : -2.69 (0.09), residues: 4963 =============================================================================== Job complete usr+sys time: 46487.76 seconds wall clock time: 803 minutes 11.61 seconds (48191.61 seconds total)