Starting phenix.real_space_refine on Tue Nov 21 19:07:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc3_4495/11_2023/6qc3_4495_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc3_4495/11_2023/6qc3_4495.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc3_4495/11_2023/6qc3_4495_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/6qc3_4495/11_2023/6qc3_4495_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc3_4495/11_2023/6qc3_4495_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc3_4495/11_2023/6qc3_4495.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc3_4495/11_2023/6qc3_4495.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc3_4495/11_2023/6qc3_4495_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qc3_4495/11_2023/6qc3_4495_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 38 7.16 5 Zn 1 6.06 5 P 14 5.49 5 S 626 5.16 5 C 62295 2.51 5 N 16450 2.21 5 O 17473 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a1 TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a1 PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a2 PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a2 ARG 240": "NH1" <-> "NH2" Residue "a2 PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a2 PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b1 TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c1 TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c1 PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c1 TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b2 TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b2 ARG 313": "NH1" <-> "NH2" Residue "c2 TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c2 ARG 139": "NH1" <-> "NH2" Residue "d2 TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q2 PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h2 PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V1 PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V1 TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V1 ARG 32": "NH1" <-> "NH2" Residue "V1 ARG 237": "NH1" <-> "NH2" Residue "V1 ARG 423": "NH1" <-> "NH2" Residue "V2 ARG 187": "NH1" <-> "NH2" Residue "V2 PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S1 TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S2 TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S2 TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S2 TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S3 PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S3 PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S7 ARG 174": "NH1" <-> "NH2" Residue "S7 ARG 178": "NH1" <-> "NH2" Residue "S8 TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S8 PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V3 PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S4 ARG 64": "NH1" <-> "NH2" Residue "A9 ARG 97": "NH1" <-> "NH2" Residue "A9 PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A9 ARG 186": "NH1" <-> "NH2" Residue "A9 TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A9 ARG 292": "NH1" <-> "NH2" Residue "A2 ARG 33": "NH1" <-> "NH2" Residue "A6 ARG 22": "NH1" <-> "NH2" Residue "AL PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AL ARG 106": "NH1" <-> "NH2" Residue "AA TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D1 PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D1 ARG 195": "NH1" <-> "NH2" Residue "D1 TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D1 PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D1 ARG 274": "NH1" <-> "NH2" Residue "D6 PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D6 TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D6 PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D6 ARG 173": "NH1" <-> "NH2" Residue "D5 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D5 TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D5 TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D5 TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D5 PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D4 PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D4 TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D2 PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AK ARG 19": "NH1" <-> "NH2" Residue "B5 ARG 26": "NH1" <-> "NH2" Residue "AJ PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AJ ARG 95": "NH1" <-> "NH2" Residue "AJ PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AJ TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AJ TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AJ ARG 305": "NH1" <-> "NH2" Residue "A3 ARG 46": "NH1" <-> "NH2" Residue "B3 PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C2 ARG 5": "NH1" <-> "NH2" Residue "C2 ARG 120": "NH1" <-> "NH2" Residue "B4 ARG 41": "NH1" <-> "NH2" Residue "B4 PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AM TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "BK TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A1 ARG 25": "NH1" <-> "NH2" Residue "A1 TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.21s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 96897 Number of models: 1 Model: "" Number of chains: 84 Chain: "a1" Number of atoms: 3409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3409 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 18, 'TRANS': 420} Chain breaks: 1 Chain: "a2" Number of atoms: 3126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3126 Classifications: {'peptide': 414} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 399} Chain breaks: 1 Chain: "b1" Number of atoms: 3019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3019 Classifications: {'peptide': 378} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 353} Chain: "c1" Number of atoms: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1909 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 22, 'TRANS': 216} Chain: "f1" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1520 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "d1" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 886 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "q1" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 618 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 5, 'TRANS': 67} Chain: "h1" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "x1" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 114 Classifications: {'peptide': 23} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 22} Link IDs: {'TRANS': 22} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 23} Unresolved non-hydrogen planarities: 23 Chain: "i1" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 459 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "a3" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3447 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 18, 'TRANS': 425} Chain: "a4" Number of atoms: 3122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3122 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 398} Chain breaks: 1 Chain: "b2" Number of atoms: 3019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3019 Classifications: {'peptide': 378} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 353} Chain: "c2" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1903 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 22, 'TRANS': 215} Chain: "f2" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1514 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "d2" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 888 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "q2" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 631 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 6, 'TRANS': 68} Chain: "h2" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "x2" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 130 Classifications: {'peptide': 26} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'TRANS': 25} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'UNK:plan-1': 26} Unresolved non-hydrogen planarities: 26 Chain: "i2" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 473 Classifications: {'peptide': 57} Link IDs: {'TRANS': 56} Chain: "V1" Number of atoms: 3312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3312 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 21, 'TRANS': 408} Chain: "V2" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1647 Classifications: {'peptide': 212} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 189} Chain: "S1" Number of atoms: 5275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5275 Classifications: {'peptide': 688} Link IDs: {'CIS': 3, 'PTRANS': 32, 'TRANS': 652} Chain: "S2" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3414 Classifications: {'peptide': 424} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 396} 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: 2293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2293 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 14, 'TRANS': 272} Chain breaks: 2 Chain: "A2" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 665 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "A5" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 901 Classifications: {'peptide': 111} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 101} Chain: "A6" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 969 Classifications: {'peptide': 114} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 106} Chain: "A7" Number of atoms: 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: 1201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1201 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 11, 'TRANS': 132} 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: "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: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2415 Classifications: {'peptide': 303} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 19, 'TRANS': 279} Chain breaks: 1 Chain: "D6" Number of atoms: 1308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1308 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 3, 'TRANS': 164} Chain breaks: 1 Chain: "4L" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 748 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 96} Chain: "D5" Number of atoms: 4805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4805 Classifications: {'peptide': 606} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 26, 'TRANS': 578} Chain: "D4" Number of atoms: 3646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3646 Classifications: {'peptide': 459} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 437} Chain: "D2" Number of atoms: 2724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2724 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 326} Chain: "AK" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1025 Classifications: {'peptide': 140} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 4, 'TRANS': 132} Chain: "B5" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1156 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 128} Chain: "AB" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 702 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain: "A8" Number of atoms: 1404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1404 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 12, 'TRANS': 156} Chain: "BJ" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1441 Classifications: {'peptide': 171} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 159} Chain: "AJ" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2583 Classifications: {'peptide': 319} Link IDs: {'CIS': 6, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 298} Chain: "S5" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 822 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "A3" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 582 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 62} Chain: "B3" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 578 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "C2" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 997 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 10, 'TRANS': 106} Chain: "B4" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1059 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 117} Chain: "AM" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1143 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 130} Chain: "B6" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 815 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 12, 'TRANS': 83} 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: "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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'3PE': 1, 'HEC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'3PE:plan-1': 1, '3PE:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "f1" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "b2" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'HEM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "c2" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "f2" Number of atoms: 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 Chain: "D1" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "D5" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 53 Chain: "D4" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "AK" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Chain: "AB" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12558 SG CYSf1 139 141.233 103.387 62.848 1.00148.29 S ATOM 12694 SG CYSf1 158 143.701 100.529 64.480 1.00143.36 S ATOM 28172 SG CYSf2 139 205.441 113.865 53.973 1.00160.26 S ATOM 28308 SG CYSf2 158 203.364 116.204 51.467 1.00166.38 S ATOM 33966 SG CYSV1 365 45.930 160.779 215.077 1.00 49.79 S ATOM 34290 SG CYSV1 405 47.304 162.582 221.197 1.00 42.76 S ATOM 33946 SG CYSV1 362 51.656 161.065 216.775 1.00 56.80 S ATOM 33927 SG CYSV1 359 48.734 166.727 216.273 1.00 36.79 S ATOM 35367 SG CYSV2 103 27.962 170.164 220.943 1.00 75.87 S ATOM 35401 SG CYSV2 108 25.330 168.198 223.684 1.00 62.33 S ATOM 35681 SG CYSV2 144 31.994 168.550 224.005 1.00 68.31 S ATOM 35704 SG CYSV2 148 29.123 167.998 226.795 1.00 80.74 S ATOM 37036 SG CYSS1 114 58.582 154.906 196.911 1.00 44.84 S ATOM 36975 SG CYSS1 105 53.996 152.580 193.217 1.00 42.39 S ATOM 36996 SG CYSS1 108 56.477 158.346 191.991 1.00 26.79 S ATOM 37368 SG CYSS1 156 58.320 163.961 204.599 1.00 44.78 S ATOM 37345 SG CYSS1 153 52.723 166.005 201.644 1.00 37.04 S ATOM 37392 SG CYSS1 159 57.577 170.009 202.244 1.00 26.28 S ATOM 37722 SG CYSS1 203 58.347 164.926 198.364 1.00 34.44 S ATOM 36481 SG CYSS1 41 61.045 162.136 211.492 1.00 22.32 S ATOM 36567 SG CYSS1 52 59.559 158.582 210.342 1.00 16.62 S ATOM 36592 SG CYSS1 55 62.612 157.030 215.191 1.00 24.03 S ATOM 36693 SG CYSS1 69 63.384 160.967 215.188 1.00 20.27 S ATOM 47378 SG CYSS7 119 69.080 130.850 169.650 1.00 15.91 S ATOM 47608 SG CYSS7 149 63.364 130.274 171.714 1.00 16.43 S ATOM 46880 SG CYSS7 55 65.086 127.331 166.011 1.00 32.44 S ATOM 46874 SG CYSS7 54 66.910 124.754 171.279 1.00 24.54 S ATOM 48826 SG CYSS8 119 60.854 136.441 177.379 1.00 42.08 S ATOM 48800 SG CYSS8 116 60.050 138.797 171.546 1.00 30.12 S ATOM 48847 SG CYSS8 122 56.575 141.300 176.372 1.00 13.75 S ATOM 48574 SG CYSS8 87 63.128 142.192 176.018 1.00 46.61 S ATOM 48876 SG CYSS8 126 51.450 146.657 179.909 1.00 41.54 S ATOM 48547 SG CYSS8 83 57.871 147.408 178.059 1.00 22.01 S ATOM 48505 SG CYSS8 77 53.778 152.002 176.672 1.00 18.50 S ATOM 48524 SG CYSS8 80 54.802 150.559 182.992 1.00 29.77 S ATOM 50097 SG CYSS6 59 39.518 156.685 185.121 1.00 52.11 S ATOM 50275 SG CYSS6 84 43.301 158.025 184.962 1.00 34.41 S ATOM 50297 SG CYSS6 87 40.636 156.362 182.979 1.00 29.55 S Time building chain proxies: 37.24, per 1000 atoms: 0.38 Number of scatterers: 96897 At special positions: 0 Unit cell: (249.2, 225.4, 271.6, 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 14 15.00 O 17473 8.00 N 16450 7.00 C 62295 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYSf1 144 " - pdb=" SG CYSf1 160 " distance=2.03 Simple disulfide: pdb=" SG CYSh1 24 " - pdb=" SG CYSh1 68 " distance=2.03 Simple disulfide: pdb=" SG CYSh1 40 " - pdb=" SG CYSh1 54 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYSAK 17 " - pdb=" SG CYSAK 74 " distance=2.03 Simple disulfide: pdb=" SG CYSAK 94 " - pdb=" SG CYSAK 114 " distance=2.04 Simple disulfide: pdb=" SG CYSA8 35 " - pdb=" SG CYSA8 65 " distance=2.04 Simple disulfide: pdb=" SG CYSA8 45 " - pdb=" SG CYSA8 55 " distance=2.03 Simple disulfide: pdb=" SG CYSA8 77 " - pdb=" SG CYSA8 109 " distance=2.03 Simple disulfide: pdb=" SG CYSA8 87 " - pdb=" SG CYSA8 99 " distance=2.03 Simple disulfide: pdb=" SG CYSBJ 76 " - pdb=" SG CYSBJ 83 " distance=2.03 Simple disulfide: pdb=" SG CYSBJ 112 " - pdb=" SG CYSBJ 124 " distance=2.03 Simple disulfide: pdb=" SG CYSS5 32 " - pdb=" SG CYSS5 65 " distance=2.04 Simple disulfide: pdb=" SG CYSS5 42 " - pdb=" SG CYSS5 55 " distance=2.04 Simple disulfide: pdb=" SG CYSB7 58 " - pdb=" SG CYSB7 89 " distance=2.03 Simple disulfide: pdb=" SG CYSB7 68 " - pdb=" SG CYSB7 79 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 29.29 Conformation dependent library (CDL) restraints added in 12.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FESS1 803 " pdb="FE1 FESS1 803 " - pdb=" SG CYSS1 52 " pdb="FE1 FESS1 803 " - pdb=" SG CYSS1 41 " pdb="FE2 FESS1 803 " - pdb=" SG CYSS1 55 " pdb="FE2 FESS1 803 " - pdb=" SG CYSS1 69 " pdb=" FESV2 300 " pdb="FE2 FESV2 300 " - pdb=" SG CYSV2 148 " pdb="FE2 FESV2 300 " - pdb=" SG CYSV2 144 " pdb="FE1 FESV2 300 " - pdb=" SG CYSV2 103 " pdb="FE1 FESV2 300 " - pdb=" SG CYSV2 108 " pdb=" FESf1 501 " pdb="FE1 FESf1 501 " - pdb=" SG CYSf1 139 " pdb="FE1 FESf1 501 " - pdb=" SG CYSf1 158 " pdb="FE2 FESf1 501 " - pdb=" ND1 HISf1 141 " pdb="FE2 FESf1 501 " - pdb=" ND1 HISf1 161 " pdb=" FESf2 202 " pdb="FE1 FESf2 202 " - pdb=" SG CYSf2 139 " pdb="FE1 FESf2 202 " - pdb=" SG CYSf2 158 " pdb="FE2 FESf2 202 " - pdb=" ND1 HISf2 141 " pdb="FE2 FESf2 202 " - pdb=" ND1 HISf2 161 " pdb=" SF4S1 801 " pdb="FE3 SF4S1 801 " - pdb=" NE2 HISS1 101 " pdb="FE4 SF4S1 801 " - pdb=" SG CYSS1 108 " pdb="FE1 SF4S1 801 " - pdb=" SG CYSS1 114 " pdb="FE2 SF4S1 801 " - pdb=" SG CYSS1 105 " pdb=" SF4S1 802 " pdb="FE2 SF4S1 802 " - pdb=" SG CYSS1 153 " pdb="FE3 SF4S1 802 " - pdb=" SG CYSS1 159 " pdb="FE4 SF4S1 802 " - pdb=" SG CYSS1 203 " pdb="FE1 SF4S1 802 " - pdb=" SG CYSS1 156 " 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="FE3 SF4S8 201 " - pdb=" SG CYSS8 122 " pdb="FE1 SF4S8 201 " - pdb=" SG CYSS8 119 " pdb="FE2 SF4S8 201 " - pdb=" SG CYSS8 116 " pdb="FE4 SF4S8 201 " - pdb=" SG CYSS8 87 " pdb=" SF4S8 202 " pdb="FE2 SF4S8 202 " - pdb=" SG CYSS8 83 " 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=" SF4V1 500 " pdb="FE1 SF4V1 500 " - pdb=" SG CYSV1 365 " pdb="FE3 SF4V1 500 " - pdb=" SG CYSV1 362 " pdb="FE2 SF4V1 500 " - pdb=" SG CYSV1 405 " pdb="FE4 SF4V1 500 " - pdb=" SG CYSV1 359 " Number of angles added : 87 Zn2+ tetrahedral coordination pdb=" ZNS6 300 " pdb="ZN ZNS6 300 " - pdb=" NE2 HISS6 68 " pdb="ZN ZNS6 300 " - pdb=" SG CYSS6 87 " pdb="ZN ZNS6 300 " - pdb=" SG CYSS6 84 " pdb="ZN ZNS6 300 " - pdb=" SG CYSS6 59 " Number of angles added : 3 23724 Ramachandran restraints generated. 11862 Oldfield, 0 Emsley, 11862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 22642 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 467 helices and 39 sheets defined 49.1% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 13.71 Creating SS restraints... Processing helix chain 'a1' and resid 4 through 9 Processing helix chain 'a1' and resid 45 through 47 No H-bonds generated for 'chain 'a1' and resid 45 through 47' Processing helix chain 'a1' and resid 55 through 62 Processing helix chain 'a1' and resid 74 through 82 Processing helix chain 'a1' and resid 103 through 118 Proline residue: a1 107 - end of helix removed outlier: 4.129A pdb=" N GLNa1 118 " --> pdb=" O ASPa1 115 " (cutoff:3.500A) Processing helix chain 'a1' and resid 124 through 143 removed outlier: 4.554A pdb=" N THRa1 143 " --> pdb=" O GLNa1 139 " (cutoff:3.500A) 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 174 No H-bonds generated for 'chain 'a1' and resid 171 through 174' Processing helix chain 'a1' and resid 179 through 188 Processing helix chain 'a1' and resid 205 through 215 Processing helix chain 'a1' and resid 265 through 276 removed outlier: 3.630A pdb=" N ASNa1 274 " --> pdb=" O GLNa1 271 " (cutoff:3.500A) Processing helix chain 'a1' and resid 293 through 300 Processing helix chain 'a1' and resid 328 through 347 removed outlier: 4.095A pdb=" N ILEa1 331 " --> pdb=" O HISa1 328 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASPa1 332 " --> pdb=" O METa1 329 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASPa1 333 " --> pdb=" O SERa1 330 " (cutoff:3.500A) Processing helix chain 'a1' and resid 351 through 368 Processing helix chain 'a1' and resid 373 through 385 Processing helix chain 'a1' and resid 392 through 400 Processing helix chain 'a1' and resid 404 through 414 Processing helix chain 'a1' and resid 434 through 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 180 through 182 No H-bonds generated for 'chain 'a2' and resid 180 through 182' Processing helix chain 'a2' and resid 188 through 198 Processing helix chain 'a2' and resid 201 through 203 No H-bonds generated for 'chain 'a2' and resid 201 through 203' Processing helix chain 'a2' and resid 213 through 222 Processing helix chain 'a2' and resid 267 through 279 Processing helix chain 'a2' and resid 294 through 302 Processing helix chain 'a2' and resid 330 through 348 removed outlier: 3.754A pdb=" N ALAa2 333 " --> pdb=" O ALAa2 330 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLYa2 334 " --> pdb=" O ALAa2 331 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASPa2 335 " --> pdb=" O SERa2 332 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYSa2 338 " --> pdb=" O ASPa2 335 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALAa2 340 " --> pdb=" O ILEa2 337 " (cutoff:3.500A) Processing helix chain 'a2' and resid 354 through 370 Processing helix chain 'a2' and resid 376 through 389 Processing helix chain 'a2' and resid 395 through 403 Processing helix chain 'a2' and resid 407 through 419 Processing helix chain 'b1' and resid 4 through 7 No H-bonds generated for 'chain 'b1' and resid 4 through 7' Processing helix chain 'b1' and resid 9 through 15 removed outlier: 4.119A pdb=" N ILEb1 13 " --> pdb=" O PROb1 9 " (cutoff:3.500A) Processing helix chain 'b1' and resid 29 through 54 removed outlier: 4.755A pdb=" N PHEb1 33 " --> pdb=" O TRPb1 30 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLYb1 34 " --> pdb=" O TRPb1 31 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEUb1 36 " --> pdb=" O PHEb1 33 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N CYSb1 40 " --> pdb=" O LEUb1 37 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILEb1 42 " --> pdb=" O ILEb1 39 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THRb1 47 " --> pdb=" O GLNb1 44 " (cutoff:3.500A) removed outlier: 3.525A 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 157 through 165 Processing helix chain 'b1' and resid 172 through 203 Proline residue: b1 186 - end of helix Processing helix chain 'b1' and resid 223 through 245 Processing helix chain 'b1' and resid 247 through 250 No H-bonds generated for 'chain 'b1' and resid 247 through 250' Processing helix chain 'b1' and resid 272 through 283 removed outlier: 5.231A pdb=" N PHEb1 276 " --> pdb=" O TYRb1 273 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ILEb1 280 " --> pdb=" O ALAb1 277 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEUb1 281 " --> pdb=" O TYRb1 278 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SERb1 283 " --> pdb=" O ILEb1 280 " (cutoff:3.500A) Processing helix chain 'b1' and resid 288 through 305 Proline residue: b1 305 - end of helix Processing helix chain 'b1' and resid 319 through 340 Processing helix chain 'b1' and resid 345 through 363 Processing helix chain 'b1' and resid 365 through 376 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 103 Processing helix chain 'c1' and resid 117 through 119 No H-bonds generated for 'chain 'c1' and resid 117 through 119' Processing helix chain 'c1' and resid 125 through 132 Processing helix chain 'c1' and resid 178 through 193 Processing helix chain 'c1' and resid 197 through 226 Proline residue: c1 216 - end of helix removed outlier: 3.559A pdb=" N TYRc1 219 " --> pdb=" O LEUc1 215 " (cutoff:3.500A) Processing helix chain 'c1' and resid 229 through 231 No H-bonds generated for 'chain 'c1' and resid 229 through 231' Processing helix chain 'f1' and resid 29 through 61 Processing helix chain 'f1' and resid 103 through 110 Processing helix chain 'f1' and resid 123 through 125 No H-bonds generated for 'chain 'f1' and resid 123 through 125' Processing helix chain 'd1' and resid 12 through 24 Processing helix chain 'd1' and resid 26 through 29 No H-bonds generated for 'chain 'd1' and resid 26 through 29' Processing helix chain 'd1' and resid 33 through 35 No H-bonds generated for 'chain 'd1' and resid 33 through 35' Processing helix chain 'd1' and resid 41 through 48 Processing helix chain 'd1' and resid 52 through 70 Processing helix chain 'd1' and resid 77 through 79 No H-bonds generated for 'chain 'd1' and resid 77 through 79' Processing helix chain 'd1' and resid 83 through 85 No H-bonds generated for 'chain 'd1' and resid 83 through 85' Processing helix chain 'd1' and resid 91 through 109 Processing helix chain 'q1' and resid 33 through 42 Processing helix chain 'q1' and resid 45 through 70 Proline residue: q1 50 - end of helix Processing helix chain 'h1' and resid 16 through 24 Processing helix chain 'h1' and resid 28 through 46 Processing helix chain 'h1' and resid 56 through 72 Processing helix chain 'i1' and resid 7 through 13 Processing helix chain 'i1' and resid 17 through 46 Processing helix chain 'i1' and resid 52 through 57 Processing helix chain 'a3' and resid 4 through 10 removed outlier: 3.516A pdb=" N SERa3 10 " --> pdb=" O GLNa3 6 " (cutoff:3.500A) Processing helix chain 'a3' and resid 55 through 63 Processing helix chain 'a3' and resid 74 through 81 Processing helix chain 'a3' and resid 106 through 117 Processing helix chain 'a3' and resid 124 through 141 Processing helix chain 'a3' and resid 145 through 157 Processing helix chain 'a3' and resid 162 through 164 No H-bonds generated for 'chain 'a3' and resid 162 through 164' Processing helix chain 'a3' and resid 171 through 174 No H-bonds generated for 'chain 'a3' and resid 171 through 174' Processing helix chain 'a3' and resid 179 through 189 Processing helix chain 'a3' and resid 205 through 215 Processing helix chain 'a3' and resid 265 through 277 removed outlier: 3.521A pdb=" N ASNa3 274 " --> pdb=" O GLNa3 271 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILEa3 277 " --> pdb=" O ASNa3 274 " (cutoff:3.500A) Processing helix chain 'a3' and resid 287 through 289 No H-bonds generated for 'chain 'a3' and resid 287 through 289' Processing helix chain 'a3' and resid 293 through 300 Processing helix chain 'a3' and resid 331 through 347 Processing helix chain 'a3' and resid 352 through 368 Processing helix chain 'a3' and resid 372 through 385 Processing helix chain 'a3' and resid 392 through 400 Processing helix chain 'a3' and resid 404 through 414 Processing helix chain 'a3' and resid 434 through 441 Processing helix chain 'a4' and resid 55 through 57 No H-bonds generated for 'chain 'a4' and resid 55 through 57' Processing helix chain 'a4' and resid 65 through 71 Processing helix chain 'a4' and resid 82 through 92 Processing helix chain 'a4' and resid 116 through 128 Processing helix chain 'a4' and resid 134 through 153 Processing helix chain 'a4' and resid 155 through 165 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 189 through 198 Processing helix chain 'a4' and resid 201 through 203 No H-bonds generated for 'chain 'a4' and resid 201 through 203' Processing helix chain 'a4' and resid 213 through 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 333 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 15 Processing helix chain 'b2' and resid 29 through 54 removed outlier: 3.704A pdb=" N PHEb2 33 " --> pdb=" O TRPb2 30 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLYb2 34 " --> pdb=" O TRPb2 31 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLYb2 48 " --> pdb=" O ILEb2 45 " (cutoff:3.500A) Processing helix chain 'b2' and resid 62 through 71 Processing helix chain 'b2' and resid 76 through 103 Processing helix chain 'b2' and resid 106 through 108 No H-bonds generated for 'chain 'b2' and resid 106 through 108' Processing helix chain 'b2' and resid 110 through 132 Processing helix chain 'b2' and resid 137 through 152 Processing helix chain 'b2' and resid 157 through 165 Processing helix chain 'b2' and resid 172 through 203 Proline residue: b2 186 - end of helix Processing helix chain 'b2' and resid 224 through 245 Processing helix chain 'b2' and resid 272 through 281 removed outlier: 4.478A pdb=" N PHEb2 276 " --> pdb=" O TYRb2 273 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N TYRb2 278 " --> pdb=" O LEUb2 275 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ALAb2 279 " --> pdb=" O PHEb2 276 " (cutoff:3.500A) Processing helix chain 'b2' and resid 287 through 302 Processing helix chain 'b2' and resid 305 through 307 No H-bonds generated for 'chain 'b2' and resid 305 through 307' Processing helix chain 'b2' and resid 319 through 339 Processing helix chain 'b2' and resid 345 through 363 Processing helix chain 'b2' and resid 365 through 376 Processing helix chain 'c2' and resid 23 through 35 Processing helix chain 'c2' and resid 48 through 51 Processing helix chain 'c2' and resid 58 through 66 Processing helix chain 'c2' and resid 98 through 104 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 227 Proline residue: c2 216 - end of helix Processing helix chain 'f2' and resid 29 through 61 Processing helix chain 'f2' and resid 103 through 109 Processing helix chain 'f2' and resid 123 through 126 No H-bonds generated for 'chain 'f2' and resid 123 through 126' Processing helix chain 'd2' and resid 10 through 24 removed outlier: 3.524A pdb=" N GLUd2 14 " --> pdb=" O SERd2 10 " (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 90 through 108 Processing helix chain 'q2' and resid 29 through 42 removed outlier: 5.624A pdb=" N ILEq2 34 " --> pdb=" O PHEq2 30 " (cutoff:3.500A) Proline residue: q2 35 - end of helix Processing helix chain 'q2' and resid 45 through 47 No H-bonds generated for 'chain 'q2' and resid 45 through 47' Processing helix chain 'q2' and resid 49 through 70 removed outlier: 3.894A pdb=" N VALq2 54 " --> pdb=" O PROq2 50 " (cutoff:3.500A) Processing helix chain 'h2' and resid 16 through 24 Processing helix chain 'h2' and resid 29 through 45 Processing helix chain 'h2' and resid 56 through 72 removed outlier: 4.101A pdb=" N LYSh2 72 " --> pdb=" O CYSh2 68 " (cutoff:3.500A) Processing helix chain 'i2' and resid 4 through 13 Processing helix chain 'i2' and resid 17 through 45 Processing helix chain 'i2' and resid 52 through 57 Processing helix chain 'V1' and resid 33 through 39 Processing helix chain 'V1' and resid 45 through 51 removed outlier: 3.969A pdb=" N LYSV1 51 " --> pdb=" O GLUV1 47 " (cutoff:3.500A) Processing helix chain 'V1' and resid 53 through 63 Processing helix chain 'V1' and resid 75 through 81 Processing helix chain 'V1' and resid 108 through 113 Processing helix chain 'V1' and resid 115 through 128 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 225 through 236 Proline residue: V1 232 - end of helix Processing helix chain 'V1' and resid 242 through 244 No H-bonds generated for 'chain 'V1' and resid 242 through 244' Processing helix chain 'V1' and resid 276 through 281 Processing helix chain 'V1' and resid 309 through 312 No H-bonds generated for 'chain 'V1' and resid 309 through 312' Processing helix chain 'V1' and resid 319 through 324 Processing helix chain 'V1' and resid 343 through 356 Processing helix chain 'V1' and resid 363 through 380 Processing helix chain 'V1' and resid 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 45 No H-bonds generated for 'chain 'V2' and resid 43 through 45' Processing helix chain 'V2' and resid 47 through 57 Processing helix chain 'V2' and resid 63 through 72 Processing helix chain 'V2' and resid 77 through 86 Processing helix chain 'V2' and resid 107 through 110 No H-bonds generated for 'chain 'V2' and resid 107 through 110' Processing helix chain 'V2' and resid 113 through 124 Processing helix chain 'V2' and resid 166 through 178 Processing helix chain 'S1' and resid 26 through 32 Processing helix chain 'S1' and resid 85 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: 3.507A 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 271 through 274 No H-bonds generated for 'chain 'S1' and resid 271 through 274' Processing helix chain 'S1' and resid 296 through 308 Processing helix chain 'S1' and resid 325 through 338 Processing helix chain 'S1' and resid 359 through 362 removed outlier: 4.379A pdb=" N TYRS1 362 " --> pdb=" O ARGS1 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'S1' and resid 359 through 362' 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 434 Processing helix chain 'S1' and resid 438 through 444 removed outlier: 3.634A pdb=" N VALS1 442 " --> pdb=" O PROS1 438 " (cutoff:3.500A) Processing helix chain 'S1' and resid 455 through 457 No H-bonds generated for 'chain 'S1' and resid 455 through 457' Processing helix chain 'S1' and resid 463 through 479 Processing helix chain 'S1' and resid 497 through 504 Processing helix chain 'S1' and resid 511 through 516 removed outlier: 3.552A pdb=" N LYSS1 516 " --> pdb=" O ALAS1 513 " (cutoff:3.500A) 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 650 removed outlier: 4.053A pdb=" N LYSS1 650 " --> pdb=" O SERS1 646 " (cutoff:3.500A) 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 691 Processing helix chain 'S2' and resid 8 through 13 Processing helix chain 'S2' and resid 87 through 92 Processing helix chain 'S2' and resid 96 through 105 Proline residue: S2 101 - end of helix Processing helix chain 'S2' and resid 113 through 126 Processing helix chain 'S2' and resid 132 through 161 Processing helix chain 'S2' and resid 164 through 184 removed outlier: 4.270A 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 257 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 339 Processing helix chain 'S2' and resid 343 through 353 Processing helix chain 'S2' and resid 394 through 405 removed outlier: 4.268A pdb=" N GLYS2 401 " --> pdb=" O ALAS2 397 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N LEUS2 402 " --> pdb=" O HISS2 398 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ASPS2 403 " --> pdb=" O LEUS2 399 " (cutoff:3.500A) removed outlier: 6.618A 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 137 removed outlier: 4.074A pdb=" N ASNS3 128 " --> pdb=" O LYSS3 125 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N TRPS3 129 " --> pdb=" O ALAS3 126 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N METS3 137 " --> pdb=" O ILES3 134 " (cutoff:3.500A) Processing helix chain 'S7' and resid 25 through 44 removed outlier: 4.393A pdb=" N SERS7 44 " --> pdb=" O ALAS7 40 " (cutoff:3.500A) Processing helix chain 'S7' and resid 55 through 62 Processing helix chain 'S7' and resid 94 through 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 168 Processing helix chain 'S7' and resid 172 through 177 Processing helix chain 'S8' and resid 14 through 26 Processing helix chain 'S8' and resid 29 through 41 Processing helix chain 'S8' and resid 82 through 86 Processing helix chain 'S8' and resid 121 through 125 Processing helix chain 'S8' and resid 144 through 147 removed outlier: 3.533A pdb=" N LEUS8 147 " --> pdb=" O HISS8 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'S8' and resid 144 through 147' Processing helix chain 'S8' and resid 151 through 160 Processing helix chain 'S8' and resid 163 through 172 Processing helix chain 'V3' and resid 50 through 57 Processing helix chain 'S6' and resid 24 through 28 Processing helix chain 'S6' and resid 41 through 45 removed outlier: 3.741A pdb=" N ALAS6 45 " --> pdb=" O ASPS6 42 " (cutoff:3.500A) 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 78 through 81 removed outlier: 4.377A pdb=" N ASNS4 81 " --> pdb=" O PROS4 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'S4' and resid 78 through 81' Processing helix chain 'S4' and resid 89 through 99 Processing helix chain 'S4' and resid 120 through 122 No H-bonds generated for 'chain 'S4' and resid 120 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 78 through 84 Processing helix chain 'A9' and resid 112 through 122 Processing helix chain 'A9' and resid 144 through 158 Processing helix chain 'A9' and resid 178 through 183 Processing helix chain 'A9' and resid 207 through 219 Processing helix chain 'A9' and resid 238 through 248 Processing helix chain 'A9' and resid 282 through 288 Processing helix chain 'A9' and resid 300 through 302 No H-bonds generated for 'chain 'A9' and resid 300 through 302' Processing helix chain 'A9' and resid 310 through 317 Processing helix chain 'A2' and resid 27 through 38 Processing helix chain 'A2' and resid 41 through 46 Processing helix chain 'A2' and resid 83 through 93 Processing helix chain 'A5' and resid 19 through 36 Processing helix chain 'A5' and resid 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 105 Processing helix chain 'A6' and resid 117 through 122 Processing helix chain 'A7' and resid 5 through 14 Processing helix chain 'AL' and resid 4 through 10 removed outlier: 3.618A pdb=" N ARGAL 9 " --> pdb=" O GLNAL 5 " (cutoff:3.500A) Processing helix chain 'AL' and resid 20 through 29 removed outlier: 3.824A pdb=" N VALAL 26 " --> pdb=" O GLYAL 22 " (cutoff:3.500A) Processing helix chain 'AL' and resid 84 through 89 Processing helix chain 'AA' and resid 8 through 21 Processing helix chain 'AA' and resid 44 through 58 Processing helix chain 'AA' and resid 64 through 68 Processing helix chain 'AA' and resid 73 through 83 Processing helix chain 'D3' and resid 2 through 24 removed outlier: 3.793A pdb=" N LEUD3 24 " --> pdb=" O ILED3 20 " (cutoff:3.500A) Processing helix chain 'D3' and resid 54 through 78 removed outlier: 4.283A pdb=" N VALD3 58 " --> pdb=" O LYSD3 54 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALAD3 59 " --> pdb=" O PHED3 55 " (cutoff:3.500A) Proline residue: D3 74 - end of helix removed outlier: 5.258A 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 84 Proline residue: D1 75 - end of helix Processing helix chain 'D1' and resid 102 through 123 Processing helix chain 'D1' and resid 126 through 156 removed outlier: 4.631A pdb=" N TYRD1 142 " --> pdb=" O GLND1 138 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLUD1 143 " --> pdb=" O THRD1 139 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N VALD1 144 " --> pdb=" O ILED1 140 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N THRD1 145 " --> pdb=" O SERD1 141 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N METD1 156 " --> pdb=" O SERD1 152 " (cutoff:3.500A) Processing helix chain 'D1' and resid 163 through 168 Processing helix chain 'D1' and resid 174 through 177 No H-bonds generated for 'chain 'D1' and resid 174 through 177' Processing helix chain 'D1' and resid 180 through 192 Processing helix chain 'D1' and resid 220 through 241 Processing helix chain 'D1' and resid 252 through 276 removed outlier: 4.272A 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 3 through 21 removed outlier: 4.351A pdb=" N VALD6 6 " --> pdb=" O THRD6 3 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHED6 20 " --> pdb=" O PHED6 17 " (cutoff:3.500A) Processing helix chain 'D6' and resid 26 through 47 Processing helix chain 'D6' and resid 52 through 63 removed outlier: 3.872A pdb=" N PHED6 57 " --> pdb=" O GLYD6 53 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEUD6 58 " --> pdb=" O LEUD6 54 " (cutoff:3.500A) Processing helix chain 'D6' and resid 65 through 74 Processing helix chain 'D6' and resid 87 through 108 Processing helix chain 'D6' and resid 139 through 143 Processing helix chain 'D6' and resid 152 through 171 Processing helix chain '4L' and resid 3 through 20 removed outlier: 3.508A pdb=" N THR4L 17 " --> pdb=" O VAL4L 14 " (cutoff:3.500A) Processing helix chain '4L' and resid 26 through 50 Processing helix chain '4L' and resid 59 through 84 Processing helix chain 'D5' and resid 2 through 15 removed outlier: 4.482A pdb=" N LEUD5 15 " --> pdb=" O THRD5 11 " (cutoff:3.500A) Processing helix chain 'D5' and resid 17 through 24 Processing helix chain 'D5' and resid 32 through 56 removed outlier: 4.033A pdb=" N ILED5 49 " --> pdb=" O ILED5 45 " (cutoff:3.500A) Proline residue: D5 50 - end of helix Processing helix chain 'D5' and resid 84 through 88 Processing helix chain 'D5' and resid 90 through 107 Processing helix chain 'D5' and resid 112 through 133 removed outlier: 4.549A pdb=" N ASND5 115 " --> pdb=" O PROD5 112 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLND5 116 " --> pdb=" O ASND5 113 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THRD5 133 " --> pdb=" O ILED5 130 " (cutoff:3.500A) 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 232 through 238 Processing helix chain 'D5' and resid 241 through 247 Processing helix chain 'D5' and resid 255 through 262 removed outlier: 3.569A pdb=" N LEUD5 259 " --> pdb=" O ALAD5 255 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEUD5 260 " --> pdb=" O GLYD5 256 " (cutoff:3.500A) 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 349 Processing helix chain 'D5' and resid 367 through 379 Processing helix chain 'D5' and resid 387 through 400 removed outlier: 4.099A pdb=" N SERD5 391 " --> pdb=" O THRD5 387 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYSD5 392 " --> pdb=" O GLYD5 388 " (cutoff:3.500A) Processing helix chain 'D5' and resid 408 through 430 Processing helix chain 'D5' and resid 448 through 470 removed outlier: 3.882A pdb=" N PHED5 463 " --> pdb=" O ILED5 459 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N GLYD5 465 " --> pdb=" O SERD5 461 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N PHED5 466 " --> pdb=" O LEUD5 462 " (cutoff:3.500A) Processing helix chain 'D5' and resid 489 through 508 Processing helix chain 'D5' and resid 519 through 524 Processing helix chain 'D5' and resid 526 through 546 removed outlier: 3.683A pdb=" N TYRD5 529 " --> pdb=" O LEUD5 526 " (cutoff:3.500A) Proline residue: D5 530 - end of helix removed outlier: 3.633A pdb=" N METD5 533 " --> pdb=" O PROD5 530 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HISD5 534 " --> pdb=" O THRD5 531 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N THRD5 537 " --> pdb=" O HISD5 534 " (cutoff:3.500A) Proline residue: D5 538 - end of helix removed outlier: 3.644A pdb=" N ASND5 541 " --> pdb=" O PROD5 538 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEUD5 542 " --> pdb=" O TYRD5 539 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N METD5 544 " --> pdb=" O ASND5 541 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SERD5 545 " --> pdb=" O LEUD5 542 " (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 16 Proline residue: D4 7 - end of helix removed outlier: 4.068A pdb=" N METD4 12 " --> pdb=" O THRD4 8 " (cutoff:3.500A) Proline residue: D4 13 - end of helix Processing helix chain 'D4' and resid 23 through 41 removed outlier: 4.162A pdb=" N LEUD4 41 " --> pdb=" O THRD4 37 " (cutoff:3.500A) Processing helix chain 'D4' and resid 60 through 79 Proline residue: D4 64 - end of helix Proline residue: D4 74 - end of helix Processing helix chain 'D4' and resid 89 through 110 Processing helix chain 'D4' and resid 115 through 135 Proline residue: D4 128 - end of helix removed outlier: 3.550A pdb=" N ILED4 131 " --> pdb=" O VALD4 127 " (cutoff:3.500A) Processing helix chain 'D4' and resid 142 through 168 Proline residue: D4 159 - end of helix removed outlier: 4.030A 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 216 through 221 Processing helix chain 'D4' and resid 225 through 246 Processing helix chain 'D4' and resid 259 through 277 removed outlier: 3.967A pdb=" N LEUD4 277 " --> pdb=" O SERD4 273 " (cutoff:3.500A) Processing helix chain 'D4' and resid 282 through 302 removed outlier: 3.960A pdb=" N ILED4 286 " --> pdb=" O LEUD4 282 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALAD4 287 " --> pdb=" O LYSD4 283 " (cutoff:3.500A) Processing helix chain 'D4' and resid 306 through 336 Processing helix chain 'D4' and resid 355 through 366 Processing helix chain 'D4' and resid 373 through 388 Processing helix chain 'D4' and resid 392 through 414 removed outlier: 3.568A pdb=" N GLYD4 397 " --> pdb=" O ILED4 394 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILED4 402 " --> pdb=" O ASND4 399 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYRD4 406 " --> pdb=" O THRD4 403 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SERD4 407 " --> pdb=" O ALAD4 404 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEUD4 408 " --> pdb=" O LEUD4 405 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILED4 412 " --> pdb=" O TYRD4 409 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THRD4 413 " --> pdb=" O METD4 410 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N THRD4 414 " --> pdb=" O LEUD4 411 " (cutoff:3.500A) Processing helix chain 'D4' and resid 431 through 441 Processing helix chain 'D4' and resid 443 through 449 Processing helix chain 'D4' and resid 451 through 453 No H-bonds generated for 'chain 'D4' and resid 451 through 453' Processing helix chain 'D2' and resid 3 through 22 Processing helix chain 'D2' and resid 26 through 43 Proline residue: D2 42 - end of helix Processing helix chain 'D2' and resid 50 through 79 Processing helix chain 'D2' and resid 92 through 106 Processing helix chain 'D2' and resid 112 through 120 Proline residue: D2 116 - end of helix removed outlier: 3.827A pdb=" N GLND2 120 " --> pdb=" O GLUD2 117 " (cutoff:3.500A) Processing helix chain 'D2' and resid 124 through 148 Proline residue: D2 138 - end of helix removed outlier: 4.242A 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 195 removed outlier: 4.059A pdb=" N VALD2 193 " --> pdb=" O TRPD2 189 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N LEUD2 194 " --> pdb=" O METD2 190 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LEUD2 195 " --> pdb=" O THRD2 191 " (cutoff:3.500A) Processing helix chain 'D2' and resid 198 through 221 Processing helix chain 'D2' and resid 227 through 236 Processing helix chain 'D2' and resid 239 through 252 Processing helix chain 'D2' and resid 261 through 271 Processing helix chain 'D2' and resid 277 through 300 removed outlier: 4.089A pdb=" N LEUD2 290 " --> pdb=" O ALAD2 286 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N TYRD2 291 " --> pdb=" O LEUD2 287 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N PHED2 292 " --> pdb=" O LEUD2 288 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N TYRD2 293 " --> pdb=" O ASND2 289 " (cutoff:3.500A) Processing helix chain 'D2' and resid 311 through 316 removed outlier: 4.310A pdb=" N GLND2 316 " --> pdb=" O LYSD2 312 " (cutoff:3.500A) Processing helix chain 'D2' and resid 327 through 333 Processing helix chain 'D2' and resid 337 through 342 Proline residue: D2 341 - end of helix Processing helix chain 'AK' and resid 2 through 10 Processing helix chain 'AK' and resid 19 through 41 Processing helix chain 'AK' and resid 48 through 80 Processing helix chain 'AK' and resid 87 through 104 Processing helix chain 'AK' and resid 107 through 130 Processing helix chain 'B5' and resid 16 through 46 removed outlier: 4.818A pdb=" N THRB5 32 " --> pdb=" O TYRB5 28 " (cutoff:3.500A) Proline residue: B5 35 - end of helix Processing helix chain 'B5' and resid 70 through 79 Processing helix chain 'B5' and resid 83 through 117 Processing helix chain 'B5' and resid 130 through 132 No H-bonds generated for 'chain 'B5' and resid 130 through 132' Processing helix chain 'AB' and resid 8 through 21 Processing helix chain 'AB' and resid 44 through 58 Processing helix chain 'AB' and resid 64 through 67 No H-bonds generated for 'chain 'AB' and resid 64 through 67' Processing helix chain 'AB' and resid 73 through 84 Processing helix chain 'A8' and resid 21 through 26 Processing helix chain 'A8' and resid 29 through 33 Processing helix chain 'A8' and resid 40 through 48 Processing helix chain 'A8' and resid 55 through 74 removed outlier: 3.508A pdb=" N ILEA8 73 " --> pdb=" O PHEA8 70 " (cutoff:3.500A) Processing helix chain 'A8' and resid 80 through 89 Processing helix chain 'A8' and resid 100 through 113 Processing helix chain 'BJ' and resid 28 through 56 removed outlier: 4.457A 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: 4.759A pdb=" N GLUBJ 86 " --> pdb=" O LEUBJ 82 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 125 through 142 Processing helix chain 'BJ' and resid 152 through 172 Processing helix chain 'AJ' and resid 5 through 10 Processing helix chain 'AJ' and resid 36 through 46 Processing helix chain 'AJ' and resid 58 through 61 No H-bonds generated for 'chain 'AJ' and resid 58 through 61' Processing helix chain 'AJ' and resid 71 through 74 No H-bonds generated for 'chain 'AJ' and resid 71 through 74' Processing helix chain 'AJ' and resid 79 through 84 Processing helix chain 'AJ' and resid 94 through 116 Processing helix chain 'AJ' and resid 128 through 141 Processing helix chain 'AJ' and resid 146 through 162 removed outlier: 3.612A pdb=" N VALAJ 160 " --> pdb=" O LYSAJ 156 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N CYSAJ 161 " --> pdb=" O LYSAJ 157 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N GLUAJ 162 " --> pdb=" O VALAJ 158 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 176 through 186 Processing helix chain 'AJ' and resid 189 through 192 No H-bonds generated for 'chain 'AJ' and resid 189 through 192' Processing helix chain 'AJ' and resid 196 through 208 Processing helix chain 'AJ' and resid 210 through 214 Processing helix chain 'AJ' and resid 232 through 239 Processing helix chain 'AJ' and resid 247 through 249 No H-bonds generated for 'chain 'AJ' and resid 247 through 249' Processing helix chain 'AJ' and resid 254 through 263 Processing helix chain 'AJ' and resid 266 through 272 removed outlier: 5.239A pdb=" N TYRAJ 272 " --> pdb=" O GLUAJ 268 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 286 through 297 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 11 through 13 No H-bonds generated for 'chain 'A3' and resid 11 through 13' 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 48 through 50 No H-bonds generated for 'chain 'B3' and resid 48 through 50' Processing helix chain 'B3' and resid 62 through 82 removed outlier: 3.650A pdb=" N LEUB3 66 " --> pdb=" O PHEB3 62 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N GLYB3 69 " --> pdb=" O ALAB3 65 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N PHEB3 70 " --> pdb=" O LEUB3 66 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N LYSB3 71 " --> pdb=" O LEUB3 67 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N TRPB3 72 " --> pdb=" O LYSB3 68 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLYB3 73 " --> pdb=" O GLYB3 69 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ALAB3 75 " --> pdb=" O LYSB3 71 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALAB3 76 " --> pdb=" O TRPB3 72 " (cutoff:3.500A) Processing helix chain 'C2' and resid 16 through 18 No H-bonds generated for 'chain 'C2' and resid 16 through 18' Processing helix chain 'C2' and resid 29 through 48 Processing helix chain 'C2' and resid 58 through 96 Processing helix chain 'B4' and resid 20 through 22 No H-bonds generated for 'chain 'B4' and resid 20 through 22' Processing helix chain 'B4' and resid 26 through 48 Processing helix chain 'B4' and resid 62 through 71 Processing helix chain 'B4' and resid 83 through 117 Proline residue: B4 96 - end of helix Processing helix chain 'B4' and resid 122 through 124 No H-bonds generated for 'chain 'B4' and resid 122 through 124' Processing helix chain 'AM' and resid 32 through 96 removed outlier: 3.550A 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 135 Processing helix chain 'AM' and resid 138 through 141 No H-bonds generated for 'chain 'AM' and resid 138 through 141' Processing helix chain 'B6' and resid 5 through 25 Processing helix chain 'B6' and resid 68 through 84 Proline residue: B6 77 - end of helix Processing helix chain 'B6' and resid 87 through 91 Processing helix chain 'B7' and resid 2 through 9 Processing helix chain 'B7' and resid 42 through 47 Processing helix chain 'B7' and resid 59 through 71 Processing helix chain 'B7' and resid 81 through 117 Processing helix chain 'B9' and resid 11 through 29 Processing helix chain 'B9' and resid 34 through 48 Processing helix chain 'B9' and resid 57 through 73 Processing helix chain 'B9' and resid 94 through 96 No H-bonds generated for 'chain 'B9' and resid 94 through 96' Processing helix chain 'B9' and resid 108 through 113 Processing helix chain 'B9' and resid 115 through 131 removed outlier: 3.552A pdb=" N SERB9 131 " --> pdb=" O LEUB9 127 " (cutoff:3.500A) Processing helix chain 'B9' and resid 134 through 143 removed outlier: 4.043A pdb=" N THRB9 143 " --> pdb=" O LEUB9 139 " (cutoff:3.500A) 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 42 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 31 through 33 No H-bonds generated for 'chain 'B8' and resid 31 through 33' 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 63 removed outlier: 3.909A pdb=" N VALBK 55 " --> pdb=" O PROBK 51 " (cutoff:3.500A) Processing helix chain 'BK' and resid 70 through 78 Processing helix chain 'BK' and resid 86 through 102 Processing helix chain 'BK' and resid 115 through 117 No H-bonds generated for 'chain 'BK' and resid 115 through 117' Processing helix chain 'C1' and resid 14 through 45 removed outlier: 3.861A pdb=" N GLYC1 18 " --> pdb=" O TRPC1 14 " (cutoff:3.500A) Processing helix chain 'B1' and resid 15 through 33 Processing helix chain 'A1' and resid 2 through 4 No H-bonds generated for 'chain 'A1' and resid 2 through 4' Processing helix chain 'A1' and resid 6 through 30 Proline residue: A1 19 - end of helix Processing helix chain 'A1' and resid 42 through 54 Processing sheet with id= A, first strand: chain 'a1' and resid 16 through 19 removed outlier: 6.292A pdb=" N METa1 195 " --> pdb=" O ARGa1 24 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ALAa1 26 " --> pdb=" O METa1 195 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LEUa1 197 " --> pdb=" O ALAa1 26 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N GLUa1 28 " --> pdb=" O LEUa1 197 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALAa1 199 " --> pdb=" O GLUa1 28 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'a1' and resid 240 through 244 removed outlier: 6.045A pdb=" N VALa1 422 " --> pdb=" O ILEa1 241 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N HISa1 243 " --> pdb=" O VALa1 422 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLYa1 424 " --> pdb=" O HISa1 243 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'a2' and resid 25 through 29 removed outlier: 6.791A pdb=" N METa2 204 " --> pdb=" O VALa2 34 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ALAa2 36 " --> pdb=" O METa2 204 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEUa2 206 " --> pdb=" O ALAa2 36 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N LEUa2 38 " --> pdb=" O LEUa2 206 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLYa2 208 " --> pdb=" O LEUa2 38 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'a2' and resid 242 through 247 Processing sheet with id= E, first strand: chain 'f1' and resid 74 through 77 Processing sheet with id= F, first strand: chain 'f1' and resid 85 through 91 Processing sheet with id= G, first strand: chain 'a3' and resid 15 through 19 Processing sheet with id= H, first strand: chain 'a3' and resid 240 through 244 removed outlier: 6.353A pdb=" N VALa3 422 " --> pdb=" O ILEa3 241 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N HISa3 243 " --> pdb=" O VALa3 422 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N GLYa3 424 " --> pdb=" O HISa3 243 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'a4' and resid 25 through 29 Processing sheet with id= J, first strand: chain 'a4' and resid 242 through 247 Processing sheet with id= K, first strand: chain 'f2' and resid 74 through 77 Processing sheet with id= L, first strand: chain 'f2' and resid 85 through 91 Processing sheet with id= M, first strand: chain 'V1' and resid 219 through 224 removed outlier: 3.636A pdb=" N TYRV1 92 " --> pdb=" O PROV1 219 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ALAV1 133 " --> pdb=" O LEUV1 93 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N VALV1 95 " --> pdb=" O ALAV1 133 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TYRV1 135 " --> pdb=" O VALV1 95 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ALAV1 97 " --> pdb=" O TYRV1 135 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N TYRV1 137 " --> pdb=" O ALAV1 97 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASPV1 174 " --> pdb=" O ALAV1 134 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILEV1 136 " --> pdb=" O ASPV1 174 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N PHEV1 176 " --> pdb=" O ILEV1 136 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ILEV1 138 " --> pdb=" O PHEV1 176 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VALV1 178 " --> pdb=" O ILEV1 138 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'V1' and resid 254 through 258 Processing sheet with id= O, first strand: chain 'V1' and resid 306 through 308 removed outlier: 6.766A pdb=" N METV1 337 " --> pdb=" O LEUV1 295 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VALV1 297 " --> pdb=" O ILEV1 335 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILEV1 335 " --> pdb=" O VALV1 297 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'V2' and resid 138 through 142 Processing sheet with id= Q, first strand: chain 'S1' and resid 16 through 20 removed outlier: 6.160A pdb=" N TRPS1 77 " --> pdb=" O PHES1 12 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'S1' and resid 146 through 148 Processing sheet with id= S, first strand: chain 'S1' and resid 173 through 177 Processing sheet with id= T, first strand: chain 'S1' and resid 223 through 228 Processing sheet with id= U, first strand: chain 'S1' and resid 283 through 286 Processing sheet with id= V, first strand: chain 'S1' and resid 342 through 344 removed outlier: 6.636A pdb=" N METS1 521 " --> pdb=" O ALAS1 316 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ILES1 318 " --> pdb=" O METS1 521 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N PHES1 523 " --> pdb=" O ILES1 318 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VALS1 559 " --> pdb=" O TYRS1 545 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N GLYS1 547 " --> pdb=" O VALS1 559 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEUS1 561 " --> pdb=" O GLYS1 547 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'S1' and resid 420 through 423 removed outlier: 7.142A pdb=" N VALS1 377 " --> pdb=" O ALAS1 407 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N ILES1 409 " --> pdb=" O VALS1 377 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEUS1 379 " --> pdb=" O ILES1 409 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'S1' and resid 572 through 574 Processing sheet with id= Y, first strand: chain 'S2' and resid 47 through 51 Processing sheet with id= Z, first strand: chain 'S2' and resid 361 through 368 Processing sheet with id= AA, first strand: chain 'S3' and resid 74 through 76 removed outlier: 6.752A pdb=" N LEUS3 48 " --> pdb=" O ARGS3 106 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LYSS3 108 " --> pdb=" O LEUS3 48 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ILES3 50 " --> pdb=" O LYSS3 108 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N TYRS3 110 " --> pdb=" O ILES3 50 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ILES3 52 " --> pdb=" O TYRS3 110 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'S3' and resid 172 through 177 Processing sheet with id= AC, first strand: chain 'S7' and resid 85 through 88 removed outlier: 6.734A pdb=" N TYRS7 112 " --> pdb=" O METS7 86 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N VALS7 88 " --> pdb=" O TYRS7 112 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VALS7 114 " --> pdb=" O VALS7 88 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILES7 144 " --> pdb=" O SERS7 115 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'S8' and resid 92 through 98 Processing sheet with id= AE, first strand: chain 'S6' and resid 50 through 52 Processing sheet with id= AF, first strand: chain 'S6' and resid 56 through 59 Processing sheet with id= AG, first strand: chain 'S4' and resid 102 through 105 Processing sheet with id= AH, first strand: chain 'A9' and resid 90 through 93 removed outlier: 6.778A pdb=" N GLNA9 44 " --> pdb=" O ALAA9 21 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N VALA9 23 " --> pdb=" O GLNA9 44 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILEA9 46 " --> pdb=" O VALA9 23 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILEA9 69 " --> pdb=" O VALA9 47 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N TYRA9 49 " --> pdb=" O ILEA9 69 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N META9 71 " --> pdb=" O TYRA9 49 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'A9' and resid 130 through 134 removed outlier: 6.321A pdb=" N THRA9 164 " --> pdb=" O HISA9 131 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N SERA9 133 " --> pdb=" O THRA9 164 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILEA9 166 " --> pdb=" O SERA9 133 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'A2' and resid 53 through 56 Processing sheet with id= AK, first strand: chain 'AL' and resid 47 through 50 Processing sheet with id= AL, first strand: chain 'D5' and resid 61 through 67 Processing sheet with id= AM, first strand: chain 'AJ' and resid 122 through 125 removed outlier: 6.449A pdb=" N VALAJ 168 " --> pdb=" O THRAJ 26 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ASPAJ 28 " --> pdb=" O VALAJ 168 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ILEAJ 170 " --> pdb=" O ASPAJ 28 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLUAJ 219 " --> pdb=" O VALAJ 169 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N TYRAJ 171 " --> pdb=" O GLUAJ 219 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEUAJ 221 " --> pdb=" O TYRAJ 171 " (cutoff:3.500A) 4310 hydrogen bonds defined for protein. 12144 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: 35.92 Time building geometry restraints manager: 32.26 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: 41550 1.42 - 1.64: 56684 1.64 - 1.86: 1004 1.86 - 2.09: 24 2.09 - 2.31: 88 Bond restraints: 99350 Sorted by residual: bond pdb=" C2D HECc2 501 " pdb=" C3D HECc2 501 " ideal model delta sigma weight residual 1.544 1.310 0.234 2.00e-02 2.50e+03 1.36e+02 bond pdb=" C2D HECc1 501 " pdb=" C3D HECc1 501 " ideal model delta sigma weight residual 1.544 1.325 0.219 2.00e-02 2.50e+03 1.19e+02 bond pdb=" CAC HECc2 501 " pdb=" CBC HECc2 501 " ideal model delta sigma weight residual 1.544 1.365 0.179 2.00e-02 2.50e+03 7.97e+01 bond pdb=" CAC HECc1 501 " pdb=" CBC HECc1 501 " ideal model delta sigma weight residual 1.544 1.366 0.178 2.00e-02 2.50e+03 7.94e+01 bond pdb=" CAB HECc2 501 " pdb=" CBB HECc2 501 " ideal model delta sigma weight residual 1.544 1.397 0.147 2.00e-02 2.50e+03 5.40e+01 ... (remaining 99345 not shown) Histogram of bond angle deviations from ideal: 69.11 - 91.16: 99 91.16 - 113.21: 56642 113.21 - 135.26: 78075 135.26 - 157.31: 12 157.31 - 179.36: 12 Bond angle restraints: 134840 Sorted by residual: angle pdb=" S1 FESf2 202 " pdb="FE2 FESf2 202 " pdb=" S2 FESf2 202 " ideal model delta sigma weight residual 104.33 89.41 14.92 1.14e+00 7.69e-01 1.71e+02 angle pdb="FE1 FESf2 202 " pdb=" S2 FESf2 202 " pdb="FE2 FESf2 202 " ideal model delta sigma weight residual 75.66 90.34 -14.68 1.14e+00 7.69e-01 1.66e+02 angle pdb="FE1 FESf2 202 " pdb=" S1 FESf2 202 " pdb="FE2 FESf2 202 " ideal model delta sigma weight residual 75.66 90.43 -14.77 1.20e+00 6.94e-01 1.51e+02 angle pdb=" S1 FESf1 501 " pdb="FE2 FESf1 501 " pdb=" S2 FESf1 501 " ideal model delta sigma weight residual 104.33 90.31 14.02 1.14e+00 7.69e-01 1.51e+02 angle pdb="FE1 FESf1 501 " pdb=" S2 FESf1 501 " pdb="FE2 FESf1 501 " ideal model delta sigma weight residual 75.66 89.68 -14.02 1.14e+00 7.69e-01 1.51e+02 ... (remaining 134835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.50: 58716 35.50 - 70.99: 646 70.99 - 106.49: 69 106.49 - 141.99: 2 141.99 - 177.49: 1 Dihedral angle restraints: 59434 sinusoidal: 24323 harmonic: 35111 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 -121.20 -58.80 0 5.00e+00 4.00e-02 1.38e+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 -121.80 -58.20 0 5.00e+00 4.00e-02 1.36e+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 180.00 122.15 57.85 0 5.00e+00 4.00e-02 1.34e+02 ... (remaining 59431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.207: 14773 4.207 - 8.414: 0 8.414 - 12.621: 0 12.621 - 16.828: 0 16.828 - 21.035: 24 Chirality restraints: 14797 Sorted by residual: chirality pdb="FE3 SF4S8 202 " pdb=" S1 SF4S8 202 " pdb=" S2 SF4S8 202 " pdb=" S4 SF4S8 202 " both_signs ideal model delta sigma weight residual False -10.55 10.48 -21.04 2.00e-01 2.50e+01 1.11e+04 chirality pdb="FE4 SF4S8 201 " pdb=" S1 SF4S8 201 " pdb=" S2 SF4S8 201 " pdb=" S3 SF4S8 201 " both_signs ideal model delta sigma weight residual False 10.55 -10.47 21.02 2.00e-01 2.50e+01 1.11e+04 chirality pdb="FE1 SF4S1 802 " pdb=" S2 SF4S1 802 " pdb=" S3 SF4S1 802 " pdb=" S4 SF4S1 802 " both_signs ideal model delta sigma weight residual False -10.55 10.47 -21.02 2.00e-01 2.50e+01 1.10e+04 ... (remaining 14794 not shown) Planarity restraints: 17105 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMNV1 501 " 0.015 2.00e-02 2.50e+03 8.12e-02 3.13e+02 pdb=" C10 FMNV1 501 " 0.021 2.00e-02 2.50e+03 pdb=" C2 FMNV1 501 " 0.068 2.00e-02 2.50e+03 pdb=" C4 FMNV1 501 " -0.018 2.00e-02 2.50e+03 pdb=" C4A FMNV1 501 " -0.020 2.00e-02 2.50e+03 pdb=" C5A FMNV1 501 " -0.100 2.00e-02 2.50e+03 pdb=" C6 FMNV1 501 " -0.032 2.00e-02 2.50e+03 pdb=" C7 FMNV1 501 " 0.041 2.00e-02 2.50e+03 pdb=" C7M FMNV1 501 " 0.254 2.00e-02 2.50e+03 pdb=" C8 FMNV1 501 " -0.019 2.00e-02 2.50e+03 pdb=" C8M FMNV1 501 " -0.020 2.00e-02 2.50e+03 pdb=" C9 FMNV1 501 " -0.096 2.00e-02 2.50e+03 pdb=" C9A FMNV1 501 " -0.104 2.00e-02 2.50e+03 pdb=" N1 FMNV1 501 " 0.063 2.00e-02 2.50e+03 pdb=" N10 FMNV1 501 " -0.030 2.00e-02 2.50e+03 pdb=" N3 FMNV1 501 " 0.031 2.00e-02 2.50e+03 pdb=" N5 FMNV1 501 " -0.073 2.00e-02 2.50e+03 pdb=" O2 FMNV1 501 " 0.079 2.00e-02 2.50e+03 pdb=" O4 FMNV1 501 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALAS3 80 " 0.029 2.00e-02 2.50e+03 6.16e-02 3.79e+01 pdb=" C ALAS3 80 " -0.106 2.00e-02 2.50e+03 pdb=" O ALAS3 80 " 0.040 2.00e-02 2.50e+03 pdb=" N VALS3 81 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHED5 84 " -0.028 2.00e-02 2.50e+03 5.54e-02 3.07e+01 pdb=" C PHED5 84 " 0.096 2.00e-02 2.50e+03 pdb=" O PHED5 84 " -0.035 2.00e-02 2.50e+03 pdb=" N PHED5 85 " -0.033 2.00e-02 2.50e+03 ... (remaining 17102 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 494 2.48 - 3.08: 67203 3.08 - 3.69: 152795 3.69 - 4.29: 211206 4.29 - 4.90: 339933 Nonbonded interactions: 771631 Sorted by model distance: nonbonded pdb=" NE2 HISb2 83 " pdb="FE HEMb2 401 " model vdw 1.873 3.080 nonbonded pdb=" NE2 HISb1 83 " pdb="FE HEMb1 401 " model vdw 1.925 3.080 nonbonded pdb=" SD METc1 159 " pdb="FE HECc1 501 " model vdw 1.950 3.360 nonbonded pdb=" NE2 HISb1 97 " pdb="FE HEMb1 402 " model vdw 2.007 3.080 nonbonded pdb=" SD METc2 159 " pdb="FE HECc2 501 " model vdw 2.075 3.360 ... (remaining 771626 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'AA' and (resid 5 through 84 or (resid 101 and (name C10 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C19 or name C2 or name C20 or name C21 or name C3 or name C4 or name C5 \ or name C6 or name C7 or name C8 or name C9 or name N1 or name N2 or name O1 or \ name O2 or name O3 or name O4 or name O5 or name O6 or name O7 or name P1 or nam \ e S1 )))) selection = (chain 'AB' and (resid 5 through 84 or resid 101)) } ncs_group { reference = (chain 'a1' and resid 2 through 445) selection = (chain 'a3' and (resid 2 through 222 or resid 229 through 445)) } ncs_group { reference = (chain 'a2' and (resid 20 through 227 or resid 235 through 439)) selection = chain 'a4' } ncs_group { reference = chain 'b1' selection = chain 'b2' } ncs_group { reference = (chain 'c1' and (resid 2 through 239 or resid 501)) selection = chain 'c2' } ncs_group { reference = (chain 'd1' and resid 11 through 109) selection = (chain 'd2' and resid 11 through 109) } ncs_group { reference = (chain 'f1' and resid 2 through 196) 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' selection = (chain 'x2' and (resid 4 through 7 or (resid 8 and (name N or name CA or name C \ or name O )) or resid 9 through 26)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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: 10.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 30.230 Check model and map are aligned: 1.090 Set scattering table: 0.660 Process input model: 223.250 Find NCS groups from input model: 4.390 Set up NCS constraints: 0.650 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 273.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 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 : 0.010 0.234 99350 Z= 0.659 Angle : 1.321 20.576 134840 Z= 0.699 Chirality : 0.846 21.035 14797 Planarity : 0.009 0.116 17105 Dihedral : 12.093 177.487 36738 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.73 % Favored : 88.14 % Rotamer: Outliers : 0.75 % Allowed : 5.69 % Favored : 93.56 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.24 % Twisted Proline : 1.63 % Twisted General : 0.61 % 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: -3.94 (0.06), residues: 11862 helix: -2.01 (0.05), residues: 6166 sheet: -1.50 (0.18), residues: 740 loop : -3.55 (0.08), residues: 4956 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23724 Ramachandran restraints generated. 11862 Oldfield, 0 Emsley, 11862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23724 Ramachandran restraints generated. 11862 Oldfield, 0 Emsley, 11862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3786 residues out of total 10402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 3708 time to evaluate : 8.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 15 residues processed: 3754 average time/residue: 0.9425 time to fit residues: 6035.3008 Evaluate side-chains 2067 residues out of total 10402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 2052 time to evaluate : 8.578 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.7413 time to fit residues: 33.2511 ------------------------------------------------------------------------------- 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: 0.6980 chunk 889 optimal weight: 3.9990 chunk 493 optimal weight: 9.9990 chunk 303 optimal weight: 6.9990 chunk 600 optimal weight: 3.9990 chunk 475 optimal weight: 5.9990 chunk 920 optimal weight: 8.9990 chunk 356 optimal weight: 7.9990 chunk 559 optimal weight: 4.9990 chunk 684 optimal weight: 7.9990 chunk 1066 optimal weight: 0.9980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a1 29 GLN a1 85 HIS ** a1 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a2 213 HIS a2 290 ASN a2 362 ASN a2 412 ASN b1 85 ASN ** b1 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b1 345 HIS c1 97 ASN c1 149 ASN ** c1 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c1 180 GLN c1 199 HIS ** f1 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f1 53 ASN f1 100 HIS d1 38 HIS q1 12 HIS q1 23 GLN q1 28 HIS h1 63 HIS i1 54 HIS ** a3 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a3 151 ASN a3 189 HIS a3 274 ASN a3 363 ASN a3 368 HIS ** a4 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a4 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a4 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a4 290 ASN a4 305 GLN ** a4 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 68 HIS b2 85 ASN b2 312 GLN c2 35 GLN c2 97 ASN c2 197 HIS c2 224 HIS f2 53 ASN f2 122 HIS f2 164 HIS q2 3 GLN q2 6 HIS q2 23 GLN q2 28 HIS h2 71 HIS i2 45 HIS i2 47 ASN ** i2 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V1 165 ASN V1 293 ASN V2 9 HIS ** V2 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V2 42 HIS V2 74 GLN ** V2 101 GLN ** 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 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1 401 HIS S1 437 HIS S1 472 ASN S1 582 GLN S1 665 GLN S1 682 GLN S2 13 GLN ** S2 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 50 ASN S2 84 HIS S2 98 GLN ** S2 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S2 190 HIS S2 347 HIS S2 421 GLN ** S3 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 41 GLN ** S3 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 38 ASN ** S7 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S7 164 GLN ** S8 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V3 44 HIS S6 13 HIS ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 29 HIS S4 46 GLN S4 50 ASN ** S4 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A9 87 HIS A9 115 GLN A9 131 HIS A9 216 ASN ** A9 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2 80 ASN A2 92 ASN ** A5 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A5 52 ASN A5 75 GLN ** A5 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A7 20 GLN AL 17 HIS AL 72 ASN AL 91 HIS D1 124 ASN ** D1 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D6 175 ASN 4L 25 HIS D5 56 HIS D5 59 GLN D5 113 ASN ** D5 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 194 ASN D5 199 GLN D5 200 GLN D5 205 ASN ** D5 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 320 ASN D5 332 HIS D5 351 ASN D5 400 ASN D5 452 ASN D5 509 HIS D5 580 GLN D5 605 HIS D4 51 ASN ** D4 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4 450 ASN D2 134 GLN B5 69 HIS ** B5 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A8 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 22 GLN ** AJ 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 151 HIS AJ 204 ASN AJ 251 GLN AJ 257 HIS ** S5 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 10 ASN A3 45 ASN A3 68 HIS B4 74 ASN B7 46 ASN ** B7 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B7 75 ASN B9 138 GLN ** B2 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B8 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BK 45 HIS C1 9 HIS Total number of N/Q/H flips: 118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.259 99350 Z= 0.499 Angle : 1.482 51.275 134840 Z= 0.917 Chirality : 0.256 6.473 14797 Planarity : 0.007 0.097 17105 Dihedral : 8.810 177.819 13436 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.80 % Favored : 90.17 % Rotamer: Outliers : 0.29 % Allowed : 4.79 % Favored : 94.92 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.24 % Twisted Proline : 1.19 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.07), residues: 11862 helix: -0.59 (0.06), residues: 6201 sheet: -1.26 (0.18), residues: 719 loop : -3.26 (0.08), residues: 4942 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23724 Ramachandran restraints generated. 11862 Oldfield, 0 Emsley, 11862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23724 Ramachandran restraints generated. 11862 Oldfield, 0 Emsley, 11862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2758 residues out of total 10402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 2728 time to evaluate : 10.362 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 outliers start: 30 outliers final: 9 residues processed: 2747 average time/residue: 0.8992 time to fit residues: 4304.9590 Evaluate side-chains 1964 residues out of total 10402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1955 time to evaluate : 8.408 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.7070 time to fit residues: 23.3092 ------------------------------------------------------------------------------- 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: 0.9980 chunk 330 optimal weight: 8.9990 chunk 887 optimal weight: 4.9990 chunk 725 optimal weight: 10.0000 chunk 294 optimal weight: 6.9990 chunk 1068 optimal weight: 7.9990 chunk 1153 optimal weight: 6.9990 chunk 951 optimal weight: 0.9990 chunk 1059 optimal weight: 9.9990 chunk 364 optimal weight: 0.3980 chunk 856 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a1 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a1 305 GLN ** a1 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a2 196 GLN a2 362 ASN b1 68 HIS b1 263 ASN b1 312 GLN ** c1 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f1 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f1 53 ASN f1 57 GLN d1 38 HIS d1 56 ASN q1 6 HIS q1 23 GLN a3 21 ASN ** a3 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a3 368 HIS ** a4 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a4 104 ASN a4 158 HIS ** a4 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a4 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 32 ASN b2 68 HIS b2 312 GLN c2 35 GLN q2 23 GLN h2 71 HIS ** i2 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V1 37 GLN ** V1 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V2 9 HIS ** V2 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 51 ASN ** S1 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1 336 ASN S1 392 ASN S1 401 HIS S1 437 HIS S1 472 ASN S1 582 GLN ** S2 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 98 GLN ** S2 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S2 201 GLN ** S3 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 38 ASN ** S7 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S7 127 HIS ** S7 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 164 GLN ** S8 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S6 94 GLN S4 50 ASN S4 121 ASN ** A9 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A9 216 ASN ** A9 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2 92 ASN A5 20 HIS ** A5 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A7 20 GLN ** A7 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A7 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 54 GLN AL 72 ASN D1 292 ASN ** D1 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4L 52 HIS 4L 97 GLN D5 59 GLN ** D5 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 199 GLN D5 205 ASN D5 226 GLN D5 400 ASN D4 83 HIS D4 180 GLN D4 279 GLN ** D4 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4 349 GLN D4 434 ASN ** D4 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 144 GLN ** B5 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A8 15 GLN A8 34 GLN ** BJ 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 106 GLN AJ 120 GLN S5 15 HIS A3 10 ASN B4 74 ASN B7 84 HIS B7 91 HIS ** B9 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B9 32 HIS ** B2 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1 27 HIS A1 44 GLN Total number of N/Q/H flips: 71 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.246 99350 Z= 0.455 Angle : 1.444 50.714 134840 Z= 0.898 Chirality : 0.258 6.417 14797 Planarity : 0.006 0.109 17105 Dihedral : 8.170 179.560 13436 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.06 % Favored : 89.93 % Rotamer: Outliers : 0.24 % Allowed : 4.52 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.74 % Twisted General : 0.25 % 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: -1.93 (0.07), residues: 11862 helix: 0.02 (0.06), residues: 6159 sheet: -1.11 (0.18), residues: 747 loop : -3.08 (0.08), residues: 4956 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23724 Ramachandran restraints generated. 11862 Oldfield, 0 Emsley, 11862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23724 Ramachandran restraints generated. 11862 Oldfield, 0 Emsley, 11862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2681 residues out of total 10402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 2656 time to evaluate : 8.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 3 residues processed: 2671 average time/residue: 0.8391 time to fit residues: 3909.6736 Evaluate side-chains 1929 residues out of total 10402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1926 time to evaluate : 7.017 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.7410 time to fit residues: 15.4310 ------------------------------------------------------------------------------- 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: 9.9990 chunk 802 optimal weight: 2.9990 chunk 554 optimal weight: 0.8980 chunk 118 optimal weight: 0.0270 chunk 509 optimal weight: 6.9990 chunk 717 optimal weight: 0.9990 chunk 1071 optimal weight: 5.9990 chunk 1134 optimal weight: 7.9990 chunk 560 optimal weight: 2.9990 chunk 1015 optimal weight: 6.9990 chunk 305 optimal weight: 6.9990 overall best weight: 1.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a1 15 GLN ** a1 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a1 328 HIS ** a1 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a2 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a2 362 ASN b1 68 HIS ** b1 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b1 263 ASN c1 75 ASN ** c1 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c1 180 GLN c1 197 HIS f1 53 ASN ** f1 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f1 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d1 22 ASN q1 23 GLN ** a3 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a3 151 ASN ** a3 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a3 308 GLN a3 323 HIS ** a4 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a4 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a4 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 68 HIS b2 201 HIS c2 224 HIS f2 108 GLN q2 3 GLN q2 23 GLN h2 71 HIS ** i2 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V2 16 ASN ** S1 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1 336 ASN S1 392 ASN S1 472 ASN ** S2 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 98 GLN ** S2 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 160 HIS ** S3 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 38 ASN ** S7 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 50 ASN A9 3 HIS ** A9 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A9 216 ASN A9 288 HIS A2 92 ASN ** A5 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A7 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A7 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 72 ASN ** AA 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 59 GLN D5 113 ASN ** D5 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 194 ASN D5 205 ASN ** D5 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D5 400 ASN D4 83 HIS ** D4 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B5 143 ASN AB 47 GLN AB 74 GLN ** A8 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 120 GLN AJ 153 ASN S5 15 HIS ** S5 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 74 ASN B7 46 ASN ** B9 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B9 50 HIS ** B2 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B8 104 HIS BK 86 GLN A1 27 HIS A1 40 HIS Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.247 99350 Z= 0.452 Angle : 1.430 50.722 134840 Z= 0.892 Chirality : 0.257 6.394 14797 Planarity : 0.005 0.110 17105 Dihedral : 7.840 175.112 13436 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.60 % Favored : 90.38 % Rotamer: Outliers : 0.10 % Allowed : 3.72 % Favored : 96.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: -1.64 (0.08), residues: 11862 helix: 0.29 (0.07), residues: 6116 sheet: -0.93 (0.19), residues: 740 loop : -2.98 (0.08), residues: 5006 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23724 Ramachandran restraints generated. 11862 Oldfield, 0 Emsley, 11862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23724 Ramachandran restraints generated. 11862 Oldfield, 0 Emsley, 11862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2563 residues out of total 10402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 2553 time to evaluate : 8.527 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 outliers start: 10 outliers final: 2 residues processed: 2557 average time/residue: 0.8800 time to fit residues: 3947.0516 Evaluate side-chains 1917 residues out of total 10402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1915 time to evaluate : 8.519 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.7133 time to fit residues: 14.0910 ------------------------------------------------------------------------------- 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: 0.9980 chunk 644 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 844 optimal weight: 4.9990 chunk 468 optimal weight: 2.9990 chunk 968 optimal weight: 20.0000 chunk 784 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 579 optimal weight: 10.0000 chunk 1018 optimal weight: 10.0000 chunk 286 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a1 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a2 104 ASN ** a2 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a2 351 ASN a2 362 ASN b1 8 HIS b1 68 HIS ** b1 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b1 148 ASN ** b1 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f1 53 ASN ** f1 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d1 56 ASN q1 23 GLN ** a3 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a3 308 GLN ** a4 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a4 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a4 342 ASN ** a4 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 68 HIS b2 85 ASN b2 312 GLN c2 35 GLN q2 3 GLN q2 12 HIS q2 23 GLN h2 71 HIS ** i2 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V2 16 ASN S1 51 ASN ** S1 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1 336 ASN S1 392 ASN S1 437 HIS S1 472 ASN S1 582 GLN S2 98 GLN S2 150 HIS ** S3 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 38 ASN ** S7 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S8 168 ASN V3 35 ASN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 50 ASN S4 51 ASN ** A9 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A9 216 ASN A2 92 ASN A5 20 HIS ** A5 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 57 GLN A6 125 HIS ** A7 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A7 24 GLN D1 97 ASN ** D1 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4L 52 HIS D5 59 GLN ** D5 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 83 HIS ** D4 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B5 143 ASN AB 47 GLN A8 15 GLN ** A8 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 57 HIS AJ 120 GLN S5 15 HIS S5 26 HIS A3 45 ASN B4 74 ASN ** B9 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B8 97 ASN A1 40 HIS Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.240 99350 Z= 0.480 Angle : 1.453 50.846 134840 Z= 0.902 Chirality : 0.257 6.353 14797 Planarity : 0.006 0.098 17105 Dihedral : 7.729 176.762 13436 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.50 % Favored : 89.49 % Rotamer: Outliers : 0.10 % Allowed : 3.32 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.44 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.08), residues: 11862 helix: 0.34 (0.07), residues: 6126 sheet: -0.96 (0.18), residues: 764 loop : -2.96 (0.08), residues: 4972 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23724 Ramachandran restraints generated. 11862 Oldfield, 0 Emsley, 11862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23724 Ramachandran restraints generated. 11862 Oldfield, 0 Emsley, 11862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2423 residues out of total 10402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 2413 time to evaluate : 8.465 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 outliers start: 10 outliers final: 1 residues processed: 2420 average time/residue: 0.8838 time to fit residues: 3760.3281 Evaluate side-chains 1857 residues out of total 10402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1856 time to evaluate : 8.391 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.7042 time to fit residues: 12.7063 ------------------------------------------------------------------------------- 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: 10.0000 chunk 1021 optimal weight: 7.9990 chunk 224 optimal weight: 1.9990 chunk 666 optimal weight: 7.9990 chunk 280 optimal weight: 0.3980 chunk 1135 optimal weight: 5.9990 chunk 942 optimal weight: 7.9990 chunk 525 optimal weight: 4.9990 chunk 94 optimal weight: 8.9990 chunk 375 optimal weight: 1.9990 chunk 596 optimal weight: 8.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a1 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a2 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a2 362 ASN b1 68 HIS ** b1 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c1 75 ASN ** c1 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c1 180 GLN f1 53 ASN ** f1 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d1 22 ASN d1 73 GLN q1 23 GLN ** a3 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a3 289 HIS a3 308 GLN ** a4 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a4 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a4 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a4 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 68 HIS b2 201 HIS q2 23 GLN h2 67 HIS h2 71 HIS ** i2 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V2 16 ASN ** S1 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1 336 ASN S1 392 ASN S1 472 ASN ** S3 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 38 ASN ** S7 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S8 170 GLN V3 35 ASN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 50 ASN A2 92 ASN ** A5 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 57 GLN ** A6 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A7 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A7 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 59 HIS ** D1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 59 GLN ** D5 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 194 ASN ** D5 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4 83 HIS ** D4 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2 134 GLN D2 204 ASN ** B5 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B5 143 ASN BJ 114 GLN ** BJ 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 74 ASN B6 73 HIS B7 46 ASN B7 84 HIS ** B9 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1 31 ASN A1 40 HIS Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.4957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.243 99350 Z= 0.475 Angle : 1.446 50.654 134840 Z= 0.899 Chirality : 0.258 6.499 14797 Planarity : 0.005 0.117 17105 Dihedral : 7.637 175.931 13436 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.23 % Favored : 89.75 % Rotamer: Outliers : 0.07 % Allowed : 2.79 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.44 % 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: 11862 helix: 0.43 (0.07), residues: 6114 sheet: -0.88 (0.19), residues: 740 loop : -2.87 (0.08), residues: 5008 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23724 Ramachandran restraints generated. 11862 Oldfield, 0 Emsley, 11862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23724 Ramachandran restraints generated. 11862 Oldfield, 0 Emsley, 11862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2387 residues out of total 10402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 2380 time to evaluate : 8.407 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: 7 outliers final: 1 residues processed: 2385 average time/residue: 0.8883 time to fit residues: 3731.4577 Evaluate side-chains 1839 residues out of total 10402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1838 time to evaluate : 8.546 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.6947 time to fit residues: 12.6625 ------------------------------------------------------------------------------- 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: 6.9990 chunk 128 optimal weight: 2.9990 chunk 647 optimal weight: 0.9980 chunk 829 optimal weight: 2.9990 chunk 642 optimal weight: 9.9990 chunk 956 optimal weight: 7.9990 chunk 634 optimal weight: 8.9990 chunk 1131 optimal weight: 3.9990 chunk 708 optimal weight: 10.0000 chunk 689 optimal weight: 0.7980 chunk 522 optimal weight: 0.3980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a1 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a2 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a2 362 ASN b1 8 HIS b1 68 HIS b1 137 GLN ** b1 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c1 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f1 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d1 56 ASN q1 6 HIS ** q1 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a3 308 GLN ** a4 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a4 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a4 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a4 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 68 HIS c2 35 GLN c2 224 HIS q2 3 GLN q2 23 GLN h2 71 HIS ** i2 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1 336 ASN S1 437 HIS S1 472 ASN S2 157 HIS ** S3 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 38 ASN ** S7 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 50 ASN A2 92 ASN ** A5 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A7 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A7 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AA 47 GLN ** D1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 287 HIS D5 59 GLN ** D5 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B5 143 ASN AB 47 GLN ** BJ 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 45 ASN B4 74 ASN B7 46 ASN B7 84 HIS ** B9 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B9 138 GLN B8 137 ASN BK 86 GLN A1 40 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.247 99350 Z= 0.450 Angle : 1.435 50.626 134840 Z= 0.893 Chirality : 0.257 6.386 14797 Planarity : 0.005 0.128 17105 Dihedral : 7.494 171.751 13436 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.92 % Favored : 90.06 % Rotamer: Outliers : 0.07 % Allowed : 1.83 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: -1.33 (0.08), residues: 11862 helix: 0.55 (0.07), residues: 6101 sheet: -0.80 (0.19), residues: 730 loop : -2.81 (0.08), residues: 5031 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23724 Ramachandran restraints generated. 11862 Oldfield, 0 Emsley, 11862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23724 Ramachandran restraints generated. 11862 Oldfield, 0 Emsley, 11862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2420 residues out of total 10402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 2413 time to evaluate : 8.601 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 outliers start: 7 outliers final: 0 residues processed: 2416 average time/residue: 0.9025 time to fit residues: 3844.4748 Evaluate side-chains 1861 residues out of total 10402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1861 time to evaluate : 8.564 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 12.2927 ------------------------------------------------------------------------------- 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: 0.6980 chunk 451 optimal weight: 9.9990 chunk 675 optimal weight: 0.0370 chunk 340 optimal weight: 7.9990 chunk 222 optimal weight: 10.0000 chunk 219 optimal weight: 5.9990 chunk 719 optimal weight: 6.9990 chunk 770 optimal weight: 2.9990 chunk 559 optimal weight: 20.0000 chunk 105 optimal weight: 8.9990 chunk 889 optimal weight: 0.9980 overall best weight: 2.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a1 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a2 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a2 362 ASN b1 68 HIS ** b1 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c1 165 ASN ** f1 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a3 308 GLN ** a4 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a4 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a4 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a4 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 68 HIS b2 201 HIS f2 53 ASN q2 23 GLN ** i2 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 51 ASN ** S1 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1 336 ASN S1 472 ASN ** S2 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 39 GLN ** S3 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 38 ASN ** S7 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S8 170 GLN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 50 ASN ** A9 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2 92 ASN ** A5 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A7 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A7 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 59 GLN ** D5 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 194 ASN ** D5 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2 186 HIS B5 143 ASN AB 47 GLN ** BJ 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 45 ASN B4 74 ASN B7 46 ASN ** B9 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B8 104 HIS A1 40 HIS A1 44 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.5363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.245 99350 Z= 0.458 Angle : 1.444 50.657 134840 Z= 0.897 Chirality : 0.257 6.335 14797 Planarity : 0.005 0.127 17105 Dihedral : 7.426 169.305 13436 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.97 % Favored : 90.01 % Rotamer: Outliers : 0.07 % Allowed : 1.29 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.30 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.08), residues: 11862 helix: 0.56 (0.07), residues: 6113 sheet: -0.76 (0.19), residues: 730 loop : -2.80 (0.08), residues: 5019 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23724 Ramachandran restraints generated. 11862 Oldfield, 0 Emsley, 11862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23724 Ramachandran restraints generated. 11862 Oldfield, 0 Emsley, 11862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2373 residues out of total 10402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 2366 time to evaluate : 9.066 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 outliers start: 7 outliers final: 0 residues processed: 2371 average time/residue: 0.9026 time to fit residues: 3773.3591 Evaluate side-chains 1828 residues out of total 10402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1828 time to evaluate : 8.541 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 11.5244 ------------------------------------------------------------------------------- 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: 3.9990 chunk 1084 optimal weight: 8.9990 chunk 989 optimal weight: 5.9990 chunk 1054 optimal weight: 9.9990 chunk 1083 optimal weight: 0.9980 chunk 634 optimal weight: 8.9990 chunk 459 optimal weight: 0.9990 chunk 828 optimal weight: 8.9990 chunk 323 optimal weight: 6.9990 chunk 952 optimal weight: 4.9990 chunk 997 optimal weight: 8.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a1 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a2 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a2 362 ASN ** b1 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b1 68 HIS ** b1 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f1 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d1 22 ASN d1 56 ASN q1 6 HIS ** a3 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a3 308 GLN ** a4 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a4 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a4 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a4 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 68 HIS c2 35 GLN q2 23 GLN ** i2 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 51 ASN ** S1 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1 336 ASN ** S1 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 38 ASN ** S7 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S8 170 GLN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 50 ASN ** A9 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 92 ASN ** A5 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A7 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A7 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 59 GLN D5 115 ASN ** D5 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 194 ASN ** D5 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2 186 HIS ** B5 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 47 GLN ** BJ 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 141 GLN A3 45 ASN C2 79 GLN B4 74 ASN B7 54 GLN B7 60 HIS B7 84 HIS ** B9 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B8 104 HIS B8 137 ASN A1 40 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.5507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.243 99350 Z= 0.487 Angle : 1.465 50.778 134840 Z= 0.907 Chirality : 0.257 6.332 14797 Planarity : 0.005 0.114 17105 Dihedral : 7.477 170.087 13436 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.01 % Allowed : 10.63 % Favored : 89.36 % Rotamer: Outliers : 0.08 % Allowed : 0.79 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.30 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.08), residues: 11862 helix: 0.48 (0.07), residues: 6103 sheet: -0.80 (0.19), residues: 735 loop : -2.82 (0.08), residues: 5024 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23724 Ramachandran restraints generated. 11862 Oldfield, 0 Emsley, 11862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23724 Ramachandran restraints generated. 11862 Oldfield, 0 Emsley, 11862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2288 residues out of total 10402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 2280 time to evaluate : 8.566 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 outliers start: 8 outliers final: 2 residues processed: 2286 average time/residue: 0.9310 time to fit residues: 3774.8221 Evaluate side-chains 1785 residues out of total 10402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1783 time to evaluate : 9.383 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.7123 time to fit residues: 14.4183 ------------------------------------------------------------------------------- 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: 9.9990 chunk 692 optimal weight: 0.8980 chunk 1115 optimal weight: 6.9990 chunk 680 optimal weight: 4.9990 chunk 528 optimal weight: 0.9980 chunk 775 optimal weight: 6.9990 chunk 1169 optimal weight: 7.9990 chunk 1076 optimal weight: 3.9990 chunk 931 optimal weight: 0.0970 chunk 96 optimal weight: 1.9990 chunk 719 optimal weight: 2.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a1 215 HIS ** a1 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a2 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a2 362 ASN ** b1 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b1 68 HIS ** b1 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f1 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a3 308 GLN a4 31 ASN ** a4 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a4 225 ASN ** a4 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f2 53 ASN q2 23 GLN ** i2 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V1 116 HIS ** V1 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 51 ASN ** S1 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1 336 ASN ** S1 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 38 ASN ** S7 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S7 94 ASN S7 162 GLN ** S8 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 50 ASN ** A9 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2 92 ASN A5 52 ASN A5 82 GLN ** A5 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A7 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 59 GLN ** D5 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 186 HIS B5 143 ASN AB 47 GLN ** BJ 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 114 GLN ** BJ 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B6 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B7 83 GLN B7 84 HIS ** B9 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BK 86 GLN A1 40 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.5689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.257 99350 Z= 0.450 Angle : 1.449 50.770 134840 Z= 0.898 Chirality : 0.257 6.473 14797 Planarity : 0.005 0.118 17105 Dihedral : 7.321 163.203 13436 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.57 % Favored : 90.41 % Rotamer: Outliers : 0.05 % Allowed : 0.36 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.30 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.08), residues: 11862 helix: 0.57 (0.07), residues: 6115 sheet: -0.73 (0.19), residues: 726 loop : -2.76 (0.08), residues: 5021 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23724 Ramachandran restraints generated. 11862 Oldfield, 0 Emsley, 11862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23724 Ramachandran restraints generated. 11862 Oldfield, 0 Emsley, 11862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2365 residues out of total 10402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 2360 time to evaluate : 8.501 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 outliers start: 5 outliers final: 0 residues processed: 2364 average time/residue: 0.8964 time to fit residues: 3738.8110 Evaluate side-chains 1850 residues out of total 10402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1850 time to evaluate : 8.527 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 11.4120 ------------------------------------------------------------------------------- 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: 9.9990 chunk 739 optimal weight: 2.9990 chunk 992 optimal weight: 6.9990 chunk 285 optimal weight: 9.9990 chunk 858 optimal weight: 0.9980 chunk 137 optimal weight: 20.0000 chunk 258 optimal weight: 0.9990 chunk 932 optimal weight: 1.9990 chunk 390 optimal weight: 9.9990 chunk 957 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a1 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a2 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a2 362 ASN ** b1 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b1 68 HIS ** b1 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f1 53 ASN ** f1 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d1 56 ASN q1 6 HIS ** a3 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a3 308 GLN a3 368 HIS ** a4 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a4 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 68 HIS b2 201 HIS b2 267 HIS c2 35 GLN c2 224 HIS q2 23 GLN ** i2 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1 336 ASN ** S1 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 102 ASN ** S3 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 38 ASN ** S7 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S8 157 ASN S8 170 GLN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S6 90 GLN S4 50 ASN ** A9 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2 92 ASN ** A5 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A7 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AA 47 GLN ** D1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 59 GLN ** D5 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 194 ASN ** D5 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D5 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 186 HIS B5 143 ASN AB 47 GLN ** BJ 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 45 ASN C2 79 GLN ** B4 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B7 84 HIS ** B9 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B9 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B8 137 ASN A1 40 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.093941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.082433 restraints weight = 357201.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.083954 restraints weight = 220089.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.085048 restraints weight = 150591.377| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.5794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.249 99350 Z= 0.473 Angle : 1.460 50.691 134840 Z= 0.904 Chirality : 0.258 6.408 14797 Planarity : 0.005 0.106 17105 Dihedral : 7.360 161.894 13436 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.01 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 0.10 % Allowed : 0.46 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.30 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.08), residues: 11862 helix: 0.53 (0.07), residues: 6116 sheet: -0.75 (0.19), residues: 736 loop : -2.76 (0.08), residues: 5010 Origin is already at (0, 0, 0), no shifts will be applied Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: