Starting phenix.real_space_refine (version: 1.21rc1) on Sat May 13 03:03:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk1_34841/05_2023/8hk1_34841_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk1_34841/05_2023/8hk1_34841.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk1_34841/05_2023/8hk1_34841_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk1_34841/05_2023/8hk1_34841_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk1_34841/05_2023/8hk1_34841_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk1_34841/05_2023/8hk1_34841.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk1_34841/05_2023/8hk1_34841.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk1_34841/05_2023/8hk1_34841_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk1_34841/05_2023/8hk1_34841_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.116 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 146 5.49 5 S 116 5.16 5 C 17829 2.51 5 N 5676 2.21 5 O 6465 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 GLU 491": "OE1" <-> "OE2" Residue "1 ARG 495": "NH1" <-> "NH2" Residue "1 ASP 521": "OD1" <-> "OD2" Residue "1 GLU 545": "OE1" <-> "OE2" Residue "1 ASP 546": "OD1" <-> "OD2" Residue "1 GLU 548": "OE1" <-> "OE2" Residue "1 ASP 557": "OD1" <-> "OD2" Residue "1 ARG 558": "NH1" <-> "NH2" Residue "1 ASP 564": "OD1" <-> "OD2" Residue "1 ASP 565": "OD1" <-> "OD2" Residue "1 ASP 586": "OD1" <-> "OD2" Residue "1 ARG 590": "NH1" <-> "NH2" Residue "1 ASP 616": "OD1" <-> "OD2" Residue "1 GLU 622": "OE1" <-> "OE2" Residue "1 ARG 684": "NH1" <-> "NH2" Residue "1 GLU 688": "OE1" <-> "OE2" Residue "1 GLU 691": "OE1" <-> "OE2" Residue "1 ARG 736": "NH1" <-> "NH2" Residue "1 ASP 758": "OD1" <-> "OD2" Residue "1 TYR 765": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 768": "OE1" <-> "OE2" Residue "1 ASP 799": "OD1" <-> "OD2" Residue "1 GLU 802": "OE1" <-> "OE2" Residue "1 GLU 809": "OE1" <-> "OE2" Residue "1 ARG 822": "NH1" <-> "NH2" Residue "1 ARG 827": "NH1" <-> "NH2" Residue "1 ARG 831": "NH1" <-> "NH2" Residue "1 GLU 848": "OE1" <-> "OE2" Residue "1 GLU 860": "OE1" <-> "OE2" Residue "1 GLU 873": "OE1" <-> "OE2" Residue "1 ASP 885": "OD1" <-> "OD2" Residue "1 ASP 894": "OD1" <-> "OD2" Residue "1 PHE 900": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 902": "OE1" <-> "OE2" Residue "1 ASP 907": "OD1" <-> "OD2" Residue "1 ARG 939": "NH1" <-> "NH2" Residue "1 ARG 948": "NH1" <-> "NH2" Residue "1 GLU 985": "OE1" <-> "OE2" Residue "1 GLU 988": "OE1" <-> "OE2" Residue "1 ARG 1027": "NH1" <-> "NH2" Residue "1 ASP 1037": "OD1" <-> "OD2" Residue "1 ASP 1044": "OD1" <-> "OD2" Residue "1 ARG 1045": "NH1" <-> "NH2" Residue "1 GLU 1048": "OE1" <-> "OE2" Residue "1 ARG 1053": "NH1" <-> "NH2" Residue "1 GLU 1054": "OE1" <-> "OE2" Residue "1 GLU 1061": "OE1" <-> "OE2" Residue "1 GLU 1064": "OE1" <-> "OE2" Residue "1 ARG 1075": "NH1" <-> "NH2" Residue "1 PHE 1081": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 1092": "OD1" <-> "OD2" Residue "1 GLU 1105": "OE1" <-> "OE2" Residue "1 GLU 1135": "OE1" <-> "OE2" Residue "1 GLU 1140": "OE1" <-> "OE2" Residue "1 PHE 1153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 1160": "OE1" <-> "OE2" Residue "1 GLU 1174": "OE1" <-> "OE2" Residue "1 ASP 1175": "OD1" <-> "OD2" Residue "1 ASP 1179": "OD1" <-> "OD2" Residue "1 ARG 1180": "NH1" <-> "NH2" Residue "1 TYR 1214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 1235": "OE1" <-> "OE2" Residue "1 ARG 1245": "NH1" <-> "NH2" Residue "1 TYR 1249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 1265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 1269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 1273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 459": "NH1" <-> "NH2" Residue "2 ARG 471": "NH1" <-> "NH2" Residue "2 TYR 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 573": "OD1" <-> "OD2" Residue "2 PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 593": "OE1" <-> "OE2" Residue "2 ASP 704": "OD1" <-> "OD2" Residue "2 GLU 712": "OE1" <-> "OE2" Residue "3 GLU 57": "OE1" <-> "OE2" Residue "3 PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 199": "OE1" <-> "OE2" Residue "3 GLU 229": "OE1" <-> "OE2" Residue "3 GLU 230": "OE1" <-> "OE2" Residue "3 ASP 243": "OD1" <-> "OD2" Residue "3 PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 266": "OD1" <-> "OD2" Residue "3 ARG 274": "NH1" <-> "NH2" Residue "3 ARG 275": "NH1" <-> "NH2" Residue "3 ASP 279": "OD1" <-> "OD2" Residue "3 PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 320": "OD1" <-> "OD2" Residue "3 ARG 326": "NH1" <-> "NH2" Residue "3 TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 352": "OE1" <-> "OE2" Residue "3 ASP 366": "OD1" <-> "OD2" Residue "3 GLU 370": "OE1" <-> "OE2" Residue "3 GLU 380": "OE1" <-> "OE2" Residue "3 ASP 399": "OD1" <-> "OD2" Residue "3 ASP 419": "OD1" <-> "OD2" Residue "3 TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 429": "NH1" <-> "NH2" Residue "3 GLU 443": "OE1" <-> "OE2" Residue "3 GLU 446": "OE1" <-> "OE2" Residue "3 ARG 464": "NH1" <-> "NH2" Residue "3 ASP 471": "OD1" <-> "OD2" Residue "3 PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 489": "OE1" <-> "OE2" Residue "3 GLU 493": "OE1" <-> "OE2" Residue "3 ASP 514": "OD1" <-> "OD2" Residue "3 ASP 522": "OD1" <-> "OD2" Residue "3 ARG 528": "NH1" <-> "NH2" Residue "3 TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 567": "OE1" <-> "OE2" Residue "3 GLU 582": "OE1" <-> "OE2" Residue "3 ASP 586": "OD1" <-> "OD2" Residue "3 PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 620": "OD1" <-> "OD2" Residue "3 GLU 638": "OE1" <-> "OE2" Residue "3 GLU 644": "OE1" <-> "OE2" Residue "3 TYR 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 680": "OD1" <-> "OD2" Residue "3 ASP 685": "OD1" <-> "OD2" Residue "3 ASP 688": "OD1" <-> "OD2" Residue "3 ARG 690": "NH1" <-> "NH2" Residue "3 ARG 718": "NH1" <-> "NH2" Residue "3 TYR 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 729": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 737": "OE1" <-> "OE2" Residue "3 PHE 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 809": "OE1" <-> "OE2" Residue "3 ARG 815": "NH1" <-> "NH2" Residue "3 GLU 822": "OE1" <-> "OE2" Residue "3 GLU 825": "OE1" <-> "OE2" Residue "3 GLU 837": "OE1" <-> "OE2" Residue "3 GLU 849": "OE1" <-> "OE2" Residue "3 PHE 852": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 883": "OE1" <-> "OE2" Residue "3 ARG 895": "NH1" <-> "NH2" Residue "3 ASP 902": "OD1" <-> "OD2" Residue "3 TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 928": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 1013": "NH1" <-> "NH2" Residue "3 PHE 1024": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 1050": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 1115": "OE1" <-> "OE2" Residue "3 TYR 1119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 1136": "OE1" <-> "OE2" Residue "3 ASP 1159": "OD1" <-> "OD2" Residue "3 TYR 1166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 1195": "OE1" <-> "OE2" Residue "3 GLU 1196": "OE1" <-> "OE2" Residue "3 ASP 1198": "OD1" <-> "OD2" Residue "3 GLU 1203": "OE1" <-> "OE2" Residue "3 TYR 1215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 81": "OD1" <-> "OD2" Residue "6 ARG 21": "NH1" <-> "NH2" Residue "6 ASP 34": "OD1" <-> "OD2" Residue "6 TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 38": "NH1" <-> "NH2" Residue "6 GLU 48": "OE1" <-> "OE2" Residue "6 ARG 57": "NH1" <-> "NH2" Residue "C TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 428": "OE1" <-> "OE2" Residue "C ARG 436": "NH1" <-> "NH2" Residue "C GLU 453": "OE1" <-> "OE2" Residue "C GLU 469": "OE1" <-> "OE2" Residue "C ASP 474": "OD1" <-> "OD2" Residue "C GLU 477": "OE1" <-> "OE2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "D ASP 130": "OD1" <-> "OD2" Residue "D ARG 131": "NH1" <-> "NH2" Residue "D TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 147": "OD1" <-> "OD2" Residue "D PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "D PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 175": "OD1" <-> "OD2" Residue "D ASP 183": "OD1" <-> "OD2" Residue "D ARG 191": "NH1" <-> "NH2" Residue "D GLU 192": "OE1" <-> "OE2" Residue "D GLU 195": "OE1" <-> "OE2" Residue "D ASP 202": "OD1" <-> "OD2" Residue "D GLU 203": "OE1" <-> "OE2" Residue "D ASP 204": "OD1" <-> "OD2" Residue "D ARG 207": "NH1" <-> "NH2" Residue "D TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 214": "OE1" <-> "OE2" Residue "D PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 252": "OE1" <-> "OE2" Residue "E PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 70": "OD1" <-> "OD2" Residue "E ASP 78": "OD1" <-> "OD2" Residue "E ARG 133": "NH1" <-> "NH2" Residue "E TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 30236 Number of models: 1 Model: "" Number of chains: 24 Chain: "H" Number of atoms: 3142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 3142 Inner-chain residues flagged as termini: ['pdbres=" U H 69 "', 'pdbres=" G H 81 "'] Classifications: {'RNA': 148} Modifications used: {'5*END': 2, 'rna2p_pur': 6, 'rna2p_pyr': 9, 'rna3p_pur': 68, 'rna3p_pyr': 65} Link IDs: {'rna2p': 15, 'rna3p': 132} Chain breaks: 2 Chain: "1" Number of atoms: 6487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 815, 6487 Classifications: {'peptide': 815} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 780} Chain: "2" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1210 Classifications: {'peptide': 182} Incomplete info: {'backbone_only': 61} Link IDs: {'PTRANS': 22, 'TRANS': 159} Chain breaks: 4 Unresolved non-hydrogen bonds: 277 Unresolved non-hydrogen angles: 397 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 80 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 138 Chain: "3" Number of atoms: 9247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1180, 9247 Classifications: {'peptide': 1180} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1119} Chain breaks: 5 Chain: "4" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 664 Classifications: {'peptide': 160} Incomplete info: {'backbone_only': 140} Link IDs: {'PTRANS': 8, 'TRANS': 151} Chain breaks: 1 Unresolved non-hydrogen bonds: 620 Unresolved non-hydrogen angles: 895 Unresolved non-hydrogen dihedrals: 400 Unresolved non-hydrogen chiralities: 181 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 4, 'TYR:plan': 8, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 10, 'GLU:plan': 9, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 324 Chain: "5" Number of atoms: 623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 623 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "6" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 645 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain: "A" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 504 Classifications: {'peptide': 123} Incomplete info: {'backbone_only': 117} Link IDs: {'PTRANS': 4, 'TRANS': 118} Unresolved non-hydrogen bonds: 576 Unresolved non-hydrogen angles: 815 Unresolved non-hydrogen dihedrals: 390 Unresolved non-hydrogen chiralities: 146 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 10, 'GLU:plan': 14, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 327 Chain: "B" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 421 Classifications: {'peptide': 100} Incomplete info: {'backbone_only': 89} Link IDs: {'PTRANS': 7, 'TRANS': 92} Chain breaks: 1 Unresolved non-hydrogen bonds: 459 Unresolved non-hydrogen angles: 647 Unresolved non-hydrogen dihedrals: 325 Unresolved non-hydrogen chiralities: 109 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 1, 'TRP:plan': 3, 'ASP:plan': 4, 'PHE:plan': 7, 'GLU:plan': 11, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 264 Chain: "C" Number of atoms: 2103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 2103 Classifications: {'peptide': 422} Incomplete info: {'backbone_only': 293, 'truncation_to_alanine': 22} Link IDs: {'PTRANS': 12, 'TRANS': 409} Chain breaks: 2 Unresolved non-hydrogen bonds: 1490 Unresolved non-hydrogen angles: 2092 Unresolved non-hydrogen dihedrals: 996 Unresolved non-hydrogen chiralities: 366 Planarities with less than four sites: {'GLN:plan1': 17, 'ASP:plan': 22, 'TYR:plan': 18, 'ASN:plan1': 17, 'TRP:plan': 2, 'HIS:plan': 7, 'PHE:plan': 13, 'GLU:plan': 51, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 844 Chain: "D" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 930 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 579 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain breaks: 1 Chain: "F" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 666 Classifications: {'peptide': 162} Incomplete info: {'backbone_only': 150} Link IDs: {'PTRANS': 6, 'TRANS': 155} Unresolved non-hydrogen bonds: 660 Unresolved non-hydrogen angles: 948 Unresolved non-hydrogen dihedrals: 402 Unresolved non-hydrogen chiralities: 207 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 10, 'ASP:plan': 11, 'PHE:plan': 5, 'GLU:plan': 11, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 305 Chain: "G" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 685 Classifications: {'peptide': 166} Incomplete info: {'backbone_only': 149} Link IDs: {'PTRANS': 7, 'TRANS': 158} Chain breaks: 2 Unresolved non-hydrogen bonds: 678 Unresolved non-hydrogen angles: 960 Unresolved non-hydrogen dihedrals: 446 Unresolved non-hydrogen chiralities: 189 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 3, 'TYR:plan': 6, 'ASN:plan1': 11, 'ASP:plan': 7, 'PHE:plan': 13, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 337 Chain: "a" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 372 Classifications: {'peptide': 90} Incomplete info: {'backbone_only': 83} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain breaks: 1 Unresolved non-hydrogen bonds: 366 Unresolved non-hydrogen angles: 522 Unresolved non-hydrogen dihedrals: 228 Unresolved non-hydrogen chiralities: 111 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 168 Chain: "b" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 308 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 61} Link IDs: {'PTRANS': 4, 'TRANS': 69} Unresolved non-hydrogen bonds: 277 Unresolved non-hydrogen angles: 400 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 125 Chain: "c" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 319 Classifications: {'peptide': 79} Incomplete info: {'backbone_only': 74} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 341 Unresolved non-hydrogen angles: 487 Unresolved non-hydrogen dihedrals: 217 Unresolved non-hydrogen chiralities: 99 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 168 Chain: "d" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 305 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 64} Link IDs: {'PTRANS': 3, 'TRANS': 70} Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 391 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 85 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 117 Chain: "e" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 341 Classifications: {'peptide': 83} Incomplete info: {'backbone_only': 74} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 79} Unresolved non-hydrogen bonds: 317 Unresolved non-hydrogen angles: 456 Unresolved non-hydrogen dihedrals: 193 Unresolved non-hydrogen chiralities: 101 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 140 Chain: "f" Number of atoms: 293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 293 Classifications: {'peptide': 71} Incomplete info: {'backbone_only': 62} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain breaks: 1 Unresolved non-hydrogen bonds: 283 Unresolved non-hydrogen angles: 399 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 130 Chain: "g" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 337 Classifications: {'peptide': 82} Incomplete info: {'backbone_only': 75} Link IDs: {'PTRANS': 3, 'TRANS': 78} Unresolved non-hydrogen bonds: 318 Unresolved non-hydrogen angles: 460 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 110 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 120 Chain: "1" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'9B0': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 21501 SG CYS 6 23 130.582 88.141 156.767 1.00 30.04 S ATOM 21525 SG CYS 6 26 128.343 88.092 153.706 1.00 30.51 S ATOM 21772 SG CYS 6 58 126.649 88.085 157.128 1.00 30.08 S ATOM 21793 SG CYS 6 61 128.566 84.675 156.773 1.00 32.29 S ATOM 21414 SG CYS 6 11 112.719 83.213 160.570 1.00 25.68 S ATOM 21677 SG CYS 6 46 113.130 85.248 163.964 1.00 22.63 S ATOM 21700 SG CYS 6 49 116.234 84.180 162.548 1.00 35.44 S ATOM 21971 SG CYS 6 85 114.738 87.034 160.821 1.00 22.11 S ATOM 21552 SG CYS 6 30 119.231 94.547 149.853 1.00 19.69 S ATOM 21573 SG CYS 6 33 119.054 94.292 146.163 1.00 21.17 S ATOM 21868 SG CYS 6 72 118.082 97.514 147.463 1.00 15.15 S ATOM 21892 SG CYS 6 75 115.423 94.777 147.914 1.00 15.21 S ATOM 24361 SG CYS C 408 82.505 77.256 106.009 1.00 93.55 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ASN 2 624 " occ=0.00 ... (2 atoms not shown) pdb=" O ASN 2 624 " occ=0.00 residue: pdb=" N ALA 2 625 " occ=0.00 ... (2 atoms not shown) pdb=" O ALA 2 625 " occ=0.00 residue: pdb=" N HIS 2 626 " occ=0.00 ... (2 atoms not shown) pdb=" O HIS 2 626 " occ=0.00 residue: pdb=" N LYS 2 627 " occ=0.00 ... (2 atoms not shown) pdb=" O LYS 2 627 " occ=0.00 Time building chain proxies: 16.64, per 1000 atoms: 0.55 Number of scatterers: 30236 At special positions: 0 Unit cell: (184.79, 190.225, 227.183, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 116 16.00 P 146 15.00 O 6465 8.00 N 5676 7.00 C 17829 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.19 Conformation dependent library (CDL) restraints added in 4.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 6 201 " pdb="ZN ZN 6 201 " - pdb=" SG CYS 6 61 " pdb="ZN ZN 6 201 " - pdb=" SG CYS 6 23 " pdb="ZN ZN 6 201 " - pdb=" SG CYS 6 26 " pdb="ZN ZN 6 201 " - pdb=" SG CYS 6 58 " pdb=" ZN 6 202 " pdb="ZN ZN 6 202 " - pdb=" SG CYS 6 11 " pdb="ZN ZN 6 202 " - pdb=" SG CYS 6 46 " pdb="ZN ZN 6 202 " - pdb=" SG CYS 6 85 " pdb="ZN ZN 6 202 " - pdb=" SG CYS 6 49 " pdb=" ZN 6 203 " pdb="ZN ZN 6 203 " - pdb=" SG CYS 6 33 " pdb="ZN ZN 6 203 " - pdb=" SG CYS 6 30 " pdb="ZN ZN 6 203 " - pdb=" SG CYS 6 72 " pdb="ZN ZN 6 203 " - pdb=" SG CYS 6 75 " pdb=" ZN C1000 " pdb="ZN ZN C1000 " - pdb=" NE2 HIS C 425 " pdb="ZN ZN C1000 " - pdb=" ND1 HIS C 431 " pdb="ZN ZN C1000 " - pdb=" SG CYS C 408 " Number of angles added : 18 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4928 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 128 helices and 48 sheets defined 33.0% alpha, 17.8% beta 33 base pairs and 80 stacking pairs defined. Time for finding SS restraints: 11.10 Creating SS restraints... Processing helix chain '1' and resid 492 through 505 removed outlier: 5.210A pdb=" N LEU 1 500 " --> pdb=" O LYS 1 496 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N LEU 1 501 " --> pdb=" O ILE 1 497 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LEU 1 502 " --> pdb=" O MET 1 498 " (cutoff:3.500A) Processing helix chain '1' and resid 509 through 526 removed outlier: 4.761A pdb=" N ARG 1 524 " --> pdb=" O THR 1 520 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N GLU 1 525 " --> pdb=" O ASP 1 521 " (cutoff:3.500A) Processing helix chain '1' and resid 528 through 539 Proline residue: 1 537 - end of helix Processing helix chain '1' and resid 546 through 561 Processing helix chain '1' and resid 568 through 578 removed outlier: 5.382A pdb=" N HIS 1 572 " --> pdb=" O PRO 1 569 " (cutoff:3.500A) Processing helix chain '1' and resid 587 through 603 Processing helix chain '1' and resid 606 through 613 Processing helix chain '1' and resid 615 through 617 No H-bonds generated for 'chain '1' and resid 615 through 617' Processing helix chain '1' and resid 622 through 639 removed outlier: 3.618A pdb=" N ASN 1 626 " --> pdb=" O GLU 1 622 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR 1 627 " --> pdb=" O TYR 1 623 " (cutoff:3.500A) Processing helix chain '1' and resid 642 through 653 Proline residue: 1 646 - end of helix removed outlier: 3.957A pdb=" N LYS 1 653 " --> pdb=" O LYS 1 649 " (cutoff:3.500A) Processing helix chain '1' and resid 658 through 695 removed outlier: 7.428A pdb=" N CYS 1 677 " --> pdb=" O ILE 1 673 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ALA 1 678 " --> pdb=" O LEU 1 674 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ILE 1 679 " --> pdb=" O MET 1 675 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LEU 1 680 " --> pdb=" O GLY 1 676 " (cutoff:3.500A) Proline residue: 1 681 - end of helix removed outlier: 5.217A pdb=" N ARG 1 684 " --> pdb=" O LEU 1 680 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N SER 1 685 " --> pdb=" O PRO 1 681 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N HIS 1 692 " --> pdb=" O GLU 1 688 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLY 1 693 " --> pdb=" O ILE 1 689 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU 1 694 " --> pdb=" O ILE 1 690 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N VAL 1 695 " --> pdb=" O GLU 1 691 " (cutoff:3.500A) Processing helix chain '1' and resid 699 through 716 Processing helix chain '1' and resid 728 through 737 Processing helix chain '1' and resid 741 through 756 Proline residue: 1 755 - end of helix Processing helix chain '1' and resid 759 through 778 removed outlier: 3.652A pdb=" N GLU 1 768 " --> pdb=" O TYR 1 764 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLN 1 778 " --> pdb=" O ILE 1 774 " (cutoff:3.500A) Processing helix chain '1' and resid 782 through 797 removed outlier: 3.515A pdb=" N GLY 1 797 " --> pdb=" O LYS 1 793 " (cutoff:3.500A) Processing helix chain '1' and resid 803 through 809 Processing helix chain '1' and resid 811 through 817 Processing helix chain '1' and resid 821 through 825 Processing helix chain '1' and resid 830 through 844 removed outlier: 3.831A pdb=" N LYS 1 843 " --> pdb=" O GLU 1 839 " (cutoff:3.500A) Processing helix chain '1' and resid 846 through 856 removed outlier: 4.874A pdb=" N ASP 1 856 " --> pdb=" O ARG 1 852 " (cutoff:3.500A) Processing helix chain '1' and resid 862 through 878 Processing helix chain '1' and resid 886 through 901 Processing helix chain '1' and resid 908 through 924 removed outlier: 6.516A pdb=" N LYS 1 923 " --> pdb=" O ASN 1 919 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ARG 1 924 " --> pdb=" O ALA 1 920 " (cutoff:3.500A) Processing helix chain '1' and resid 927 through 941 Processing helix chain '1' and resid 946 through 964 removed outlier: 3.587A pdb=" N GLN 1 950 " --> pdb=" O LYS 1 946 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL 1 960 " --> pdb=" O SER 1 956 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL 1 961 " --> pdb=" O ARG 1 957 " (cutoff:3.500A) Processing helix chain '1' and resid 969 through 982 removed outlier: 3.903A pdb=" N LEU 1 982 " --> pdb=" O LEU 1 978 " (cutoff:3.500A) Processing helix chain '1' and resid 987 through 1003 Processing helix chain '1' and resid 1013 through 1025 Proline residue: 11018 - end of helix Proline residue: 11022 - end of helix removed outlier: 4.706A pdb=" N LYS 11025 " --> pdb=" O THR 11021 " (cutoff:3.500A) Processing helix chain '1' and resid 1029 through 1045 Processing helix chain '1' and resid 1047 through 1049 No H-bonds generated for 'chain '1' and resid 1047 through 1049' Processing helix chain '1' and resid 1052 through 1067 removed outlier: 4.431A pdb=" N GLU 11064 " --> pdb=" O PHE 11060 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU 11065 " --> pdb=" O GLU 11061 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU 11066 " --> pdb=" O LEU 11062 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LYS 11067 " --> pdb=" O LEU 11063 " (cutoff:3.500A) Processing helix chain '1' and resid 1071 through 1088 Processing helix chain '1' and resid 1090 through 1102 Processing helix chain '1' and resid 1106 through 1122 Processing helix chain '1' and resid 1125 through 1135 removed outlier: 4.325A pdb=" N LEU 11129 " --> pdb=" O PHE 11126 " (cutoff:3.500A) Proline residue: 11130 - end of helix removed outlier: 3.520A pdb=" N ASN 11134 " --> pdb=" O ALA 11131 " (cutoff:3.500A) Processing helix chain '1' and resid 1144 through 1164 removed outlier: 7.028A pdb=" N GLU 11160 " --> pdb=" O GLU 11156 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N MET 11161 " --> pdb=" O TYR 11157 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLY 11162 " --> pdb=" O ILE 11158 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LYS 11163 " --> pdb=" O GLY 11159 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ASP 11164 " --> pdb=" O GLU 11160 " (cutoff:3.500A) Processing helix chain '1' and resid 1166 through 1177 Proline residue: 11171 - end of helix Processing helix chain '1' and resid 1182 through 1198 Processing helix chain '1' and resid 1205 through 1220 removed outlier: 3.689A pdb=" N TYR 11214 " --> pdb=" O HIS 11210 " (cutoff:3.500A) Proline residue: 11217 - end of helix removed outlier: 5.400A pdb=" N PHE 11220 " --> pdb=" O TRP 11216 " (cutoff:3.500A) Processing helix chain '1' and resid 1224 through 1240 removed outlier: 3.604A pdb=" N VAL 11239 " --> pdb=" O GLU 11235 " (cutoff:3.500A) Processing helix chain '1' and resid 1243 through 1253 removed outlier: 5.029A pdb=" N GLN 11252 " --> pdb=" O GLN 11248 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N GLY 11253 " --> pdb=" O TYR 11249 " (cutoff:3.500A) Processing helix chain '1' and resid 1259 through 1274 Processing helix chain '1' and resid 1279 through 1282 Processing helix chain '1' and resid 1299 through 1301 No H-bonds generated for 'chain '1' and resid 1299 through 1301' Processing helix chain '2' and resid 462 through 468 removed outlier: 3.613A pdb=" N LEU 2 468 " --> pdb=" O GLU 2 464 " (cutoff:3.500A) Processing helix chain '2' and resid 472 through 474 No H-bonds generated for 'chain '2' and resid 472 through 474' Processing helix chain '2' and resid 477 through 481 removed outlier: 4.026A pdb=" N VAL 2 480 " --> pdb=" O MET 2 477 " (cutoff:3.500A) Processing helix chain '2' and resid 485 through 493 Processing helix chain '2' and resid 526 through 529 No H-bonds generated for 'chain '2' and resid 526 through 529' Processing helix chain '2' and resid 569 through 577 Processing helix chain '2' and resid 611 through 617 Processing helix chain '2' and resid 633 through 639 Processing helix chain '3' and resid 191 through 193 No H-bonds generated for 'chain '3' and resid 191 through 193' Processing helix chain '3' and resid 430 through 432 No H-bonds generated for 'chain '3' and resid 430 through 432' Processing helix chain '3' and resid 809 through 824 Processing helix chain '3' and resid 839 through 842 No H-bonds generated for 'chain '3' and resid 839 through 842' Processing helix chain '3' and resid 849 through 852 No H-bonds generated for 'chain '3' and resid 849 through 852' Processing helix chain '3' and resid 1135 through 1151 removed outlier: 3.722A pdb=" N SER 31150 " --> pdb=" O MET 31146 " (cutoff:3.500A) Processing helix chain '3' and resid 1160 through 1164 Processing helix chain '3' and resid 1176 through 1184 removed outlier: 3.958A pdb=" N GLN 31181 " --> pdb=" O ASP 31177 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE 31182 " --> pdb=" O LEU 31178 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ASN 31183 " --> pdb=" O CYS 31179 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER 31184 " --> pdb=" O GLU 31180 " (cutoff:3.500A) Processing helix chain '3' and resid 1187 through 1194 Processing helix chain '3' and resid 1201 through 1215 removed outlier: 3.642A pdb=" N ILE 31211 " --> pdb=" O LYS 31207 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG 31212 " --> pdb=" O LEU 31208 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR 31215 " --> pdb=" O ILE 31211 " (cutoff:3.500A) Processing helix chain '4' and resid 26 through 32 removed outlier: 3.701A pdb=" N TRP 4 30 " --> pdb=" O GLU 4 26 " (cutoff:3.500A) Processing helix chain '4' and resid 64 through 73 Processing helix chain '4' and resid 113 through 120 Processing helix chain '4' and resid 152 through 160 Processing helix chain '5' and resid 7 through 17 removed outlier: 3.604A pdb=" N SER 5 16 " --> pdb=" O GLU 5 12 " (cutoff:3.500A) Processing helix chain '5' and resid 28 through 45 Processing helix chain '5' and resid 47 through 56 Processing helix chain '5' and resid 61 through 72 Processing helix chain '6' and resid 52 through 54 No H-bonds generated for 'chain '6' and resid 52 through 54' Processing helix chain '6' and resid 73 through 77 Processing helix chain '6' and resid 80 through 82 No H-bonds generated for 'chain '6' and resid 80 through 82' Processing helix chain 'A' and resid 161 through 174 Processing helix chain 'A' and resid 186 through 189 No H-bonds generated for 'chain 'A' and resid 186 through 189' Processing helix chain 'A' and resid 204 through 219 Processing helix chain 'A' and resid 236 through 271 Processing helix chain 'B' and resid 105 through 108 No H-bonds generated for 'chain 'B' and resid 105 through 108' Processing helix chain 'C' and resid 6 through 27 Processing helix chain 'C' and resid 33 through 58 Processing helix chain 'C' and resid 64 through 71 removed outlier: 4.717A pdb=" N LYS C 69 " --> pdb=" O ASP C 65 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLU C 70 " --> pdb=" O GLY C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 87 Processing helix chain 'C' and resid 103 through 108 Processing helix chain 'C' and resid 126 through 128 No H-bonds generated for 'chain 'C' and resid 126 through 128' Processing helix chain 'C' and resid 143 through 153 Processing helix chain 'C' and resid 160 through 167 Processing helix chain 'C' and resid 182 through 200 removed outlier: 3.544A pdb=" N MET C 188 " --> pdb=" O ARG C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 219 Processing helix chain 'C' and resid 221 through 223 No H-bonds generated for 'chain 'C' and resid 221 through 223' Processing helix chain 'C' and resid 294 through 301 Processing helix chain 'C' and resid 304 through 307 No H-bonds generated for 'chain 'C' and resid 304 through 307' Processing helix chain 'C' and resid 318 through 333 Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'C' and resid 394 through 399 removed outlier: 3.584A pdb=" N LYS C 398 " --> pdb=" O TYR C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 427 removed outlier: 3.668A pdb=" N ARG C 424 " --> pdb=" O LYS C 420 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE C 426 " --> pdb=" O PHE C 422 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ALA C 427 " --> pdb=" O GLN C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 438 removed outlier: 4.095A pdb=" N LEU C 438 " --> pdb=" O GLY C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 446 No H-bonds generated for 'chain 'C' and resid 444 through 446' Processing helix chain 'C' and resid 452 through 469 Processing helix chain 'C' and resid 495 through 500 Processing helix chain 'D' and resid 146 through 156 removed outlier: 4.414A pdb=" N PHE D 156 " --> pdb=" O LEU D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 201 removed outlier: 3.535A pdb=" N LYS D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 245 Processing helix chain 'E' and resid 71 through 76 Processing helix chain 'E' and resid 115 through 136 Processing helix chain 'E' and resid 149 through 152 No H-bonds generated for 'chain 'E' and resid 149 through 152' Processing helix chain 'E' and resid 156 through 166 Processing helix chain 'F' and resid 6 through 10 Processing helix chain 'F' and resid 37 through 39 No H-bonds generated for 'chain 'F' and resid 37 through 39' Processing helix chain 'F' and resid 83 through 86 No H-bonds generated for 'chain 'F' and resid 83 through 86' Processing helix chain 'F' and resid 103 through 106 Processing helix chain 'F' and resid 108 through 111 removed outlier: 3.603A pdb=" N SER F 111 " --> pdb=" O PRO F 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 108 through 111' Processing helix chain 'F' and resid 131 through 138 Processing helix chain 'F' and resid 152 through 160 Processing helix chain 'G' and resid 23 through 34 Processing helix chain 'G' and resid 62 through 71 Processing helix chain 'G' and resid 92 through 98 Processing helix chain 'G' and resid 164 through 173 removed outlier: 4.494A pdb=" N GLN G 173 " --> pdb=" O MET G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 206 Processing helix chain 'a' and resid 20 through 26 Processing helix chain 'a' and resid 28 through 37 removed outlier: 3.980A pdb=" N GLN a 34 " --> pdb=" O VAL a 31 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL a 36 " --> pdb=" O THR a 33 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LYS a 37 " --> pdb=" O GLN a 34 " (cutoff:3.500A) Processing helix chain 'b' and resid 7 through 13 Processing helix chain 'c' and resid 17 through 27 Processing helix chain 'e' and resid 5 through 12 Processing helix chain 'f' and resid 74 through 76 No H-bonds generated for 'chain 'f' and resid 74 through 76' Processing helix chain 'g' and resid 3 through 8 Processing helix chain 'g' and resid 76 through 79 No H-bonds generated for 'chain 'g' and resid 76 through 79' Processing sheet with id= A, first strand: chain '3' and resid 1173 through 1175 removed outlier: 6.864A pdb=" N LEU 3 3 " --> pdb=" O ILE 31174 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE 31126 " --> pdb=" O LEU 3 8 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N GLU 31115 " --> pdb=" O PRO 31131 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER 31103 " --> pdb=" O THR 31120 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '3' and resid 16 through 20 removed outlier: 3.667A pdb=" N PHE 3 16 " --> pdb=" O SER 3 33 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU 3 54 " --> pdb=" O LEU 3 40 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ARG 3 42 " --> pdb=" O THR 3 52 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N THR 3 52 " --> pdb=" O ARG 3 42 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '3' and resid 62 through 68 removed outlier: 6.733A pdb=" N GLY 3 81 " --> pdb=" O ARG 3 63 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU 3 65 " --> pdb=" O VAL 3 79 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL 3 79 " --> pdb=" O LEU 3 65 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ALA 3 67 " --> pdb=" O TYR 3 77 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TYR 3 77 " --> pdb=" O ALA 3 67 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N SER 3 82 " --> pdb=" O ARG 3 86 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ARG 3 86 " --> pdb=" O SER 3 82 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLU 3 91 " --> pdb=" O LYS 3 101 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LYS 3 101 " --> pdb=" O GLU 3 91 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLN 3 93 " --> pdb=" O PHE 3 99 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N PHE 3 99 " --> pdb=" O GLN 3 93 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '3' and resid 120 through 123 Processing sheet with id= E, first strand: chain '3' and resid 144 through 146 Processing sheet with id= F, first strand: chain '3' and resid 165 through 173 removed outlier: 6.623A pdb=" N LEU 3 185 " --> pdb=" O TYR 3 168 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL 3 170 " --> pdb=" O ALA 3 183 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA 3 183 " --> pdb=" O VAL 3 170 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLY 3 172 " --> pdb=" O MET 3 181 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N MET 3 181 " --> pdb=" O GLY 3 172 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR 3 224 " --> pdb=" O PHE 3 210 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLU 3 212 " --> pdb=" O ARG 3 222 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ARG 3 222 " --> pdb=" O GLU 3 212 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ASP 3 214 " --> pdb=" O VAL 3 220 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL 3 220 " --> pdb=" O ASP 3 214 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '3' and resid 235 through 237 Processing sheet with id= H, first strand: chain '3' and resid 287 through 294 removed outlier: 6.874A pdb=" N GLN 3 304 " --> pdb=" O VAL 3 288 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER 3 290 " --> pdb=" O LEU 3 302 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU 3 302 " --> pdb=" O SER 3 290 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N THR 3 292 " --> pdb=" O PHE 3 300 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N PHE 3 300 " --> pdb=" O THR 3 292 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N PHE 3 299 " --> pdb=" O LEU 3 315 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LEU 3 315 " --> pdb=" O PHE 3 299 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ASP 3 309 " --> pdb=" O THR 3 305 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LYS 3 312 " --> pdb=" O TYR 3 329 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N TYR 3 329 " --> pdb=" O LYS 3 312 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N THR 3 314 " --> pdb=" O LEU 3 327 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N LEU 3 327 " --> pdb=" O THR 3 314 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLU 3 316 " --> pdb=" O ILE 3 325 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ILE 3 325 " --> pdb=" O GLU 3 316 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '3' and resid 336 through 342 removed outlier: 7.355A pdb=" N ALA 3 350 " --> pdb=" O ALA 3 337 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N MET 3 339 " --> pdb=" O PHE 3 348 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE 3 348 " --> pdb=" O MET 3 339 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N VAL 3 341 " --> pdb=" O PHE 3 346 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N PHE 3 346 " --> pdb=" O VAL 3 341 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLN 3 360 " --> pdb=" O LEU 3 397 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N LEU 3 397 " --> pdb=" O GLN 3 360 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '3' and resid 774 through 780 Processing sheet with id= K, first strand: chain '3' and resid 474 through 477 Processing sheet with id= L, first strand: chain '3' and resid 533 through 537 removed outlier: 3.822A pdb=" N GLN 3 518 " --> pdb=" O ARG 3 525 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '3' and resid 546 through 548 removed outlier: 4.331A pdb=" N LYS 3 546 " --> pdb=" O ALA 3 557 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL 3 564 " --> pdb=" O ILE 3 556 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain '3' and resid 566 through 568 Processing sheet with id= O, first strand: chain '3' and resid 587 through 592 removed outlier: 6.648A pdb=" N GLY 3 608 " --> pdb=" O VAL 3 588 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N MET 3 590 " --> pdb=" O ALA 3 606 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ALA 3 606 " --> pdb=" O MET 3 590 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU 3 609 " --> pdb=" O THR 3 613 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N THR 3 613 " --> pdb=" O LEU 3 609 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER 3 629 " --> pdb=" O ILE 3 616 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain '3' and resid 640 through 643 removed outlier: 3.618A pdb=" N CYS 3 641 " --> pdb=" O ASN 3 666 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain '3' and resid 700 through 706 removed outlier: 3.666A pdb=" N VAL 3 712 " --> pdb=" O SER 3 722 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain '3' and resid 754 through 756 removed outlier: 6.032A pdb=" N ALA 3 766 " --> pdb=" O GLU 3 446 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLU 3 446 " --> pdb=" O ALA 3 766 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain '3' and resid 785 through 790 removed outlier: 7.110A pdb=" N ILE 3 800 " --> pdb=" O ARG 3 786 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N PHE 3 788 " --> pdb=" O ILE 3 798 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE 3 798 " --> pdb=" O PHE 3 788 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain '3' and resid 886 through 894 removed outlier: 6.604A pdb=" N GLY 3 908 " --> pdb=" O PHE 3 889 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL 3 891 " --> pdb=" O LEU 3 906 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU 3 906 " --> pdb=" O VAL 3 891 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL 3 893 " --> pdb=" O TYR 3 904 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N TYR 3 904 " --> pdb=" O VAL 3 893 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N HIS 3 941 " --> pdb=" O THR 3 927 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain '3' and resid 949 through 955 removed outlier: 6.774A pdb=" N GLY 3 962 " --> pdb=" O ALA 3 950 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ILE 3 952 " --> pdb=" O LEU 3 960 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU 3 960 " --> pdb=" O ILE 3 952 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ARG 3 958 " --> pdb=" O PRO 3 954 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N CYS 3 981 " --> pdb=" O VAL 3 969 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ASP 3 971 " --> pdb=" O ARG 3 979 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ARG 3 979 " --> pdb=" O ASP 3 971 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain '3' and resid 990 through 996 removed outlier: 6.540A pdb=" N SER 31003 " --> pdb=" O SER 3 991 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE 3 993 " --> pdb=" O ILE 31001 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE 31001 " --> pdb=" O ILE 3 993 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N THR 3 995 " --> pdb=" O ARG 3 999 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ARG 3 999 " --> pdb=" O THR 3 995 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA 31025 " --> pdb=" O TRP 31011 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ARG 31013 " --> pdb=" O ILE 31023 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ILE 31023 " --> pdb=" O ARG 31013 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N LYS 31015 " --> pdb=" O LEU 31021 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU 31021 " --> pdb=" O LYS 31015 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain '3' and resid 1036 through 1038 removed outlier: 3.528A pdb=" N MET 31093 " --> pdb=" O VAL 31055 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ARG 31057 " --> pdb=" O VAL 31091 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N VAL 31091 " --> pdb=" O ARG 31057 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain '4' and resid 85 through 88 Processing sheet with id= Y, first strand: chain '4' and resid 77 through 79 Processing sheet with id= Z, first strand: chain '4' and resid 144 through 147 Processing sheet with id= AA, first strand: chain '6' and resid 39 through 42 removed outlier: 6.228A pdb=" N TYR 6 71 " --> pdb=" O CYS 6 40 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'B' and resid 118 through 121 removed outlier: 4.004A pdb=" N LYS B 118 " --> pdb=" O ASP B 137 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'B' and resid 148 through 153 removed outlier: 4.029A pdb=" N GLN B 167 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 406 through 408 removed outlier: 3.617A pdb=" N TYR C 414 " --> pdb=" O CYS C 408 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 212 through 215 removed outlier: 3.804A pdb=" N LYS D 181 " --> pdb=" O TYR D 173 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N TYR D 173 " --> pdb=" O LYS D 181 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ASP D 183 " --> pdb=" O LYS D 171 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N LYS D 171 " --> pdb=" O ASP D 183 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 13 through 16 removed outlier: 4.136A pdb=" N ALA F 13 " --> pdb=" O ASP F 25 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ALA F 46 " --> pdb=" O LEU F 24 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR F 68 " --> pdb=" O ILE F 47 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLU F 92 " --> pdb=" O LEU F 69 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TYR F 117 " --> pdb=" O LEU F 93 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 83 through 86 Processing sheet with id= AH, first strand: chain 'G' and resid 219 through 222 removed outlier: 3.651A pdb=" N GLU G 179 " --> pdb=" O GLU G 193 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'a' and resid 90 through 96 Processing sheet with id= AJ, first strand: chain 'a' and resid 98 through 101 removed outlier: 6.682A pdb=" N GLU a 68 " --> pdb=" O VAL a 56 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N VAL a 56 " --> pdb=" O GLU a 68 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'b' and resid 57 through 60 removed outlier: 3.800A pdb=" N GLY b 57 " --> pdb=" O GLU b 49 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N THR b 47 " --> pdb=" O LEU b 59 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N MET b 27 " --> pdb=" O LEU b 23 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'b' and resid 62 through 64 removed outlier: 6.575A pdb=" N ALA b 45 " --> pdb=" O LEU b 33 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N LEU b 33 " --> pdb=" O ALA b 45 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'c' and resid 84 through 89 removed outlier: 6.759A pdb=" N TRP c 34 " --> pdb=" O THR c 85 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU c 87 " --> pdb=" O GLN c 32 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLN c 32 " --> pdb=" O LEU c 87 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N SER c 89 " --> pdb=" O ARG c 30 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ARG c 30 " --> pdb=" O SER c 89 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU c 35 " --> pdb=" O MET c 41 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N MET c 41 " --> pdb=" O LEU c 35 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY c 75 " --> pdb=" O ALA c 61 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLU c 63 " --> pdb=" O GLN c 73 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N GLN c 73 " --> pdb=" O GLU c 63 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N HIS c 65 " --> pdb=" O ARG c 71 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ARG c 71 " --> pdb=" O HIS c 65 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'c' and resid 56 through 58 Processing sheet with id= AO, first strand: chain 'd' and resid 54 through 58 removed outlier: 5.858A pdb=" N CYS d 45 " --> pdb=" O ILE d 57 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N HIS d 26 " --> pdb=" O MET d 48 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET d 69 " --> pdb=" O LYS d 20 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'd' and resid 40 through 42 Processing sheet with id= AQ, first strand: chain 'e' and resid 47 through 50 removed outlier: 4.428A pdb=" N GLU e 26 " --> pdb=" O THR e 22 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'e' and resid 60 through 63 removed outlier: 7.057A pdb=" N SER e 44 " --> pdb=" O LEU e 32 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU e 32 " --> pdb=" O SER e 44 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'f' and resid 65 through 68 removed outlier: 3.771A pdb=" N LEU f 67 " --> pdb=" O CYS f 45 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N CYS f 45 " --> pdb=" O LEU f 67 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR f 15 " --> pdb=" O PHE f 31 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER f 79 " --> pdb=" O ILE f 20 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'f' and resid 40 through 42 Processing sheet with id= AU, first strand: chain 'g' and resid 53 through 55 removed outlier: 3.939A pdb=" N GLU g 13 " --> pdb=" O ILE g 29 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'g' and resid 57 through 60 removed outlier: 6.713A pdb=" N LYS g 41 " --> pdb=" O ILE g 29 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ILE g 29 " --> pdb=" O LYS g 41 " (cutoff:3.500A) 1238 hydrogen bonds defined for protein. 3489 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 88 hydrogen bonds 172 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 80 stacking parallelities Total time for adding SS restraints: 16.29 Time building geometry restraints manager: 13.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5578 1.32 - 1.45: 8467 1.45 - 1.57: 16547 1.57 - 1.69: 288 1.69 - 1.81: 179 Bond restraints: 31059 Sorted by residual: bond pdb=" C10 9B0 11500 " pdb=" C9 9B0 11500 " ideal model delta sigma weight residual 1.622 1.298 0.324 2.00e-02 2.50e+03 2.63e+02 bond pdb=" C16 9B0 11500 " pdb=" C17 9B0 11500 " ideal model delta sigma weight residual 1.561 1.322 0.239 2.00e-02 2.50e+03 1.43e+02 bond pdb=" C PRO 5 78 " pdb=" N PRO 5 79 " ideal model delta sigma weight residual 1.334 1.503 -0.169 2.34e-02 1.83e+03 5.22e+01 bond pdb=" C29 9B0 11500 " pdb=" N1 9B0 11500 " ideal model delta sigma weight residual 1.490 1.349 0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" C29 9B0 11500 " pdb=" O5 9B0 11500 " ideal model delta sigma weight residual 1.470 1.341 0.129 2.00e-02 2.50e+03 4.16e+01 ... (remaining 31054 not shown) Histogram of bond angle deviations from ideal: 59.64 - 74.89: 3 74.89 - 90.15: 0 90.15 - 105.40: 1347 105.40 - 120.66: 28883 120.66 - 135.92: 11915 Bond angle restraints: 42148 Sorted by residual: angle pdb=" C11 9B0 11500 " pdb=" C10 9B0 11500 " pdb=" C9 9B0 11500 " ideal model delta sigma weight residual 85.83 127.11 -41.28 3.00e+00 1.11e-01 1.89e+02 angle pdb=" C13 9B0 11500 " pdb=" C14 9B0 11500 " pdb=" C15 9B0 11500 " ideal model delta sigma weight residual 74.55 114.20 -39.65 3.00e+00 1.11e-01 1.75e+02 angle pdb=" C17 9B0 11500 " pdb=" C18 9B0 11500 " pdb=" C19 9B0 11500 " ideal model delta sigma weight residual 85.92 124.97 -39.05 3.00e+00 1.11e-01 1.69e+02 angle pdb=" O2' C H 28 " pdb=" C2' C H 28 " pdb=" C1' C H 28 " ideal model delta sigma weight residual 108.40 90.23 18.17 1.50e+00 4.44e-01 1.47e+02 angle pdb=" C PRO 5 78 " pdb=" N PRO 5 79 " pdb=" CA PRO 5 79 " ideal model delta sigma weight residual 119.84 134.29 -14.45 1.25e+00 6.40e-01 1.34e+02 ... (remaining 42143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.00: 15568 34.00 - 67.99: 637 67.99 - 101.99: 47 101.99 - 135.98: 6 135.98 - 169.98: 4 Dihedral angle restraints: 16262 sinusoidal: 7070 harmonic: 9192 Sorted by residual: dihedral pdb=" O4' U H 47 " pdb=" C1' U H 47 " pdb=" N1 U H 47 " pdb=" C2 U H 47 " ideal model delta sinusoidal sigma weight residual 200.00 45.26 154.74 1 1.50e+01 4.44e-03 8.13e+01 dihedral pdb=" CA GLU 3 136 " pdb=" C GLU 3 136 " pdb=" N LYS 3 137 " pdb=" CA LYS 3 137 " ideal model delta harmonic sigma weight residual 180.00 -152.47 -27.53 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA ILE 3 996 " pdb=" C ILE 3 996 " pdb=" N GLY 3 997 " pdb=" CA GLY 3 997 " ideal model delta harmonic sigma weight residual 180.00 -153.13 -26.87 0 5.00e+00 4.00e-02 2.89e+01 ... (remaining 16259 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.070: 3943 1.070 - 2.140: 0 2.140 - 3.210: 0 3.210 - 4.280: 0 4.280 - 5.350: 2 Chirality restraints: 3945 Sorted by residual: chirality pdb=" C6 9B0 11500 " pdb=" C5 9B0 11500 " pdb=" C7 9B0 11500 " pdb=" C8 9B0 11500 " both_signs ideal model delta sigma weight residual False -2.77 2.58 -5.35 2.00e-01 2.50e+01 7.16e+02 chirality pdb=" C34 9B0 11500 " pdb=" C35 9B0 11500 " pdb=" C40 9B0 11500 " pdb=" N2 9B0 11500 " both_signs ideal model delta sigma weight residual False -2.61 2.30 -4.91 2.00e-01 2.50e+01 6.03e+02 chirality pdb=" C3' G H 42 " pdb=" C4' G H 42 " pdb=" O3' G H 42 " pdb=" C2' G H 42 " both_signs ideal model delta sigma weight residual False -2.48 -1.80 -0.68 2.00e-01 2.50e+01 1.16e+01 ... (remaining 3942 not shown) Planarity restraints: 5471 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C16 9B0 11500 " 0.190 2.00e-02 2.50e+03 1.73e-01 2.99e+02 pdb=" C17 9B0 11500 " -0.204 2.00e-02 2.50e+03 pdb=" C18 9B0 11500 " -0.137 2.00e-02 2.50e+03 pdb=" C19 9B0 11500 " 0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U H 43 " -0.025 2.00e-02 2.50e+03 9.03e-02 1.84e+02 pdb=" N1 U H 43 " 0.067 2.00e-02 2.50e+03 pdb=" C2 U H 43 " -0.002 2.00e-02 2.50e+03 pdb=" O2 U H 43 " -0.046 2.00e-02 2.50e+03 pdb=" N3 U H 43 " -0.000 2.00e-02 2.50e+03 pdb=" C4 U H 43 " 0.055 2.00e-02 2.50e+03 pdb=" O4 U H 43 " 0.039 2.00e-02 2.50e+03 pdb=" C5 U H 43 " -0.214 2.00e-02 2.50e+03 pdb=" C6 U H 43 " 0.126 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 9B0 11500 " 0.099 2.00e-02 2.50e+03 9.30e-02 8.66e+01 pdb=" C11 9B0 11500 " -0.094 2.00e-02 2.50e+03 pdb=" C8 9B0 11500 " -0.092 2.00e-02 2.50e+03 pdb=" C9 9B0 11500 " 0.087 2.00e-02 2.50e+03 ... (remaining 5468 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 5 1.99 - 2.72: 1430 2.72 - 3.44: 39060 3.44 - 4.17: 69572 4.17 - 4.90: 115226 Nonbonded interactions: 225293 Sorted by model distance: nonbonded pdb=" OE2 GLU 1 622 " pdb=" OE2 GLU E 77 " model vdw 1.262 3.040 nonbonded pdb=" NH1 ARG 1 828 " pdb=" OE1 GLU E 71 " model vdw 1.325 2.520 nonbonded pdb=" NZ LYS 1 741 " pdb=" O PHE E 76 " model vdw 1.465 2.520 nonbonded pdb=" OE2 GLU 1 622 " pdb=" CD GLU E 77 " model vdw 1.832 3.270 nonbonded pdb=" NH2 ARG 1 828 " pdb=" CB GLU E 71 " model vdw 1.873 3.520 ... (remaining 225288 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 10.000 Check model and map are aligned: 0.470 Set scattering table: 0.280 Process input model: 96.420 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.120 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: 0.010 Load rotamer database and sin/cos tables:12.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5809 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 : 0.005 0.324 31059 Z= 0.355 Angle : 0.889 41.283 42148 Z= 0.514 Chirality : 0.127 5.350 3945 Planarity : 0.006 0.173 5471 Dihedral : 16.221 169.976 11334 Min Nonbonded Distance : 1.262 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.59 % Favored : 96.32 % Rotamer Outliers : 5.96 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.81 (0.11), residues: 4127 helix: -1.69 (0.11), residues: 1429 sheet: -1.00 (0.17), residues: 901 loop : -2.40 (0.12), residues: 1797 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 483 time to evaluate : 3.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 135 outliers final: 25 residues processed: 590 average time/residue: 1.3760 time to fit residues: 955.3231 Evaluate side-chains 332 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 307 time to evaluate : 3.579 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 23 residues processed: 3 average time/residue: 0.6695 time to fit residues: 7.5002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 361 optimal weight: 9.9990 chunk 324 optimal weight: 20.0000 chunk 180 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 chunk 218 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 335 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 203 optimal weight: 0.8980 chunk 249 optimal weight: 0.6980 chunk 388 optimal weight: 50.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 518 GLN 1 599 ASN 1 901 GLN 11002 ASN 11007 HIS 11099 ASN 11144 GLN 11194 HIS 11252 GLN 11256 HIS 11293 ASN 2 490 HIS 3 46 ASN 3 194 ASN 3 264 GLN 3 363 HIS 3 480 ASN 3 594 ASN 3 612 ASN 3 776 GLN 3 817 GLN 3 844 ASN 3 916 ASN 3 983 ASN 31052 ASN ** 31147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 13 HIS C 405 ASN C 445 HIS C 472 GLN D 134 ASN D 179 ASN D 243 GLN E 68 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6020 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 31059 Z= 0.359 Angle : 0.766 27.160 42148 Z= 0.368 Chirality : 0.056 1.793 3945 Planarity : 0.005 0.062 5471 Dihedral : 9.268 176.701 6174 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.02 % Favored : 95.93 % Rotamer Outliers : 7.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.12), residues: 4127 helix: -0.20 (0.13), residues: 1432 sheet: -0.60 (0.17), residues: 912 loop : -1.89 (0.13), residues: 1783 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8254 Ramachandran restraints generated. 4127 Oldfield, 0 Emsley, 4127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 336 time to evaluate : 3.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 181 outliers final: 66 residues processed: 472 average time/residue: 1.3141 time to fit residues: 739.3971 Evaluate side-chains 361 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 295 time to evaluate : 3.107 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 56 residues processed: 10 average time/residue: 0.6562 time to fit residues: 12.9940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 216 optimal weight: 4.9990 chunk 120 optimal weight: 0.6980 chunk 323 optimal weight: 3.9990 chunk 264 optimal weight: 50.0000 chunk 107 optimal weight: 2.9990 chunk 389 optimal weight: 40.0000 chunk 420 optimal weight: 0.0870 chunk 346 optimal weight: 50.0000 chunk 386 optimal weight: 50.0000 chunk 132 optimal weight: 1.9990 chunk 312 optimal weight: 10.0000 overall best weight: 1.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: