Starting phenix.real_space_refine on Wed Feb 21 09:58:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk1_34841/02_2024/8hk1_34841_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk1_34841/02_2024/8hk1_34841.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk1_34841/02_2024/8hk1_34841.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk1_34841/02_2024/8hk1_34841.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk1_34841/02_2024/8hk1_34841_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hk1_34841/02_2024/8hk1_34841_updated.pdb" } resolution = 2.7 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= 0.004 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 16.36, per 1000 atoms: 0.54 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: 11.76 Conformation dependent library (CDL) restraints added in 6.0 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: 13.02 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: 15.93 Time building geometry restraints manager: 12.63 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=" 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=" C16 9B0 11500 " pdb=" C17 9B0 11500 " ideal model delta sigma weight residual 1.450 1.322 0.128 2.00e-02 2.50e+03 4.12e+01 bond pdb=" O3' C H 45 " pdb=" P U H 46 " ideal model delta sigma weight residual 1.607 1.522 0.085 1.50e-02 4.44e+03 3.23e+01 bond pdb=" N GLU D 252 " pdb=" CA GLU D 252 " ideal model delta sigma weight residual 1.457 1.488 -0.031 6.40e-03 2.44e+04 2.38e+01 bond pdb=" P U H 55 " pdb=" OP2 U H 55 " ideal model delta sigma weight residual 1.485 1.580 -0.095 2.00e-02 2.50e+03 2.27e+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=" 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 angle pdb=" C4' G H 42 " pdb=" C3' G H 42 " pdb=" O3' G H 42 " ideal model delta sigma weight residual 113.00 127.68 -14.68 1.50e+00 4.44e-01 9.57e+01 angle pdb=" C2' C H 28 " pdb=" C1' C H 28 " pdb=" N1 C H 28 " ideal model delta sigma weight residual 112.00 98.96 13.04 1.50e+00 4.44e-01 7.55e+01 angle pdb=" C3' U H 27 " pdb=" C2' U H 27 " pdb=" C1' U H 27 " ideal model delta sigma weight residual 101.30 107.14 -5.84 1.00e+00 1.00e+00 3.41e+01 ... (remaining 42143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.95: 15675 30.95 - 61.90: 991 61.90 - 92.84: 181 92.84 - 123.79: 12 123.79 - 154.74: 7 Dihedral angle restraints: 16866 sinusoidal: 7674 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 16863 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 3882 0.136 - 0.273: 58 0.273 - 0.409: 4 0.409 - 0.545: 0 0.545 - 0.681: 1 Chirality restraints: 3945 Sorted by residual: 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 chirality pdb=" C3' U H 43 " pdb=" C4' U H 43 " pdb=" O3' U H 43 " pdb=" C2' U H 43 " both_signs ideal model delta sigma weight residual False -2.48 -2.11 -0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" CA TYR C 394 " pdb=" N TYR C 394 " pdb=" C TYR C 394 " pdb=" CB TYR C 394 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 2.99e+00 ... (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: 2.460 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: 0.020 Extract box with map and model: 8.760 Check model and map are aligned: 0.440 Set scattering table: 0.260 Process input model: 94.840 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.130 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:11.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.730 ------------------------------------------------------------------------------- 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 : 0.004 0.169 31059 Z= 0.292 Angle : 0.794 18.167 42148 Z= 0.496 Chirality : 0.051 0.681 3945 Planarity : 0.006 0.173 5471 Dihedral : 18.694 154.741 11938 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 % Allowed : 21.55 % Favored : 72.48 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 395 HIS 0.012 0.001 HIS C 425 PHE 0.018 0.002 PHE D 168 TYR 0.018 0.001 TYR C 394 ARG 0.006 0.000 ARG 3 728 *********************** 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 : 3.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 505 LYS cc_start: 0.6145 (ttpp) cc_final: 0.5904 (ttmt) REVERT: 1 572 HIS cc_start: 0.7572 (t70) cc_final: 0.7333 (t70) REVERT: 1 584 ASP cc_start: 0.6448 (t70) cc_final: 0.6235 (t0) REVERT: 1 768 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7358 (mt-10) REVERT: 1 770 MET cc_start: 0.6482 (tpp) cc_final: 0.6274 (tpp) REVERT: 1 789 LEU cc_start: 0.8036 (mt) cc_final: 0.7478 (mt) REVERT: 1 838 VAL cc_start: 0.8060 (t) cc_final: 0.7822 (m) REVERT: 1 908 SER cc_start: 0.6402 (OUTLIER) cc_final: 0.5929 (m) REVERT: 1 947 VAL cc_start: 0.7912 (t) cc_final: 0.7558 (t) REVERT: 1 1056 MET cc_start: 0.8020 (mmm) cc_final: 0.7765 (tpt) REVERT: 2 483 GLN cc_start: 0.6713 (mt0) cc_final: 0.5569 (mp10) REVERT: 2 509 LYS cc_start: 0.6407 (mttm) cc_final: 0.5978 (pttp) REVERT: 3 513 ASP cc_start: 0.2730 (OUTLIER) cc_final: 0.2307 (p0) REVERT: 3 629 SER cc_start: 0.1643 (OUTLIER) cc_final: 0.1418 (p) REVERT: 5 38 ASP cc_start: 0.7648 (p0) cc_final: 0.7330 (p0) REVERT: C 409 GLU cc_start: 0.6405 (mt-10) cc_final: 0.6167 (mp0) REVERT: D 147 ASP cc_start: 0.7016 (m-30) cc_final: 0.6412 (t70) REVERT: D 214 GLU cc_start: 0.6934 (pt0) cc_final: 0.6377 (pt0) REVERT: E 145 LYS cc_start: 0.4861 (OUTLIER) cc_final: 0.4442 (tptp) outliers start: 135 outliers final: 25 residues processed: 590 average time/residue: 1.4075 time to fit residues: 976.6801 Evaluate side-chains 341 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 311 time to evaluate : 2.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 557 ASP Chi-restraints excluded: chain 1 residue 560 LEU Chi-restraints excluded: chain 1 residue 618 ASP Chi-restraints excluded: chain 1 residue 768 GLU Chi-restraints excluded: chain 1 residue 798 THR Chi-restraints excluded: chain 1 residue 801 VAL Chi-restraints excluded: chain 1 residue 908 SER Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 3 residue 64 SER Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 484 VAL Chi-restraints excluded: chain 3 residue 513 ASP Chi-restraints excluded: chain 3 residue 546 LYS Chi-restraints excluded: chain 3 residue 590 MET Chi-restraints excluded: chain 3 residue 595 VAL Chi-restraints excluded: chain 3 residue 629 SER Chi-restraints excluded: chain 3 residue 689 THR Chi-restraints excluded: chain 3 residue 712 VAL Chi-restraints excluded: chain 3 residue 755 VAL Chi-restraints excluded: chain 3 residue 864 SER Chi-restraints excluded: chain 3 residue 872 ILE Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain 5 residue 8 HIS Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 398 LYS Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 145 LYS 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: 0.8980 chunk 110 optimal weight: 6.9990 chunk 218 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 335 optimal weight: 0.8980 chunk 129 optimal weight: 4.9990 chunk 203 optimal weight: 0.8980 chunk 249 optimal weight: 1.9990 chunk 388 optimal weight: 50.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 11091 HIS 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 5 13 HIS C 400 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: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5969 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 31059 Z= 0.246 Angle : 0.630 12.766 42148 Z= 0.316 Chirality : 0.044 0.168 3945 Planarity : 0.005 0.060 5471 Dihedral : 15.226 157.555 6836 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.63 % Favored : 96.34 % Rotamer: Outliers : 6.71 % Allowed : 23.23 % Favored : 70.05 % Cbeta Deviations : 0.00 % 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: -1.40 (0.12), residues: 4127 helix: -0.04 (0.13), residues: 1430 sheet: -0.51 (0.17), residues: 904 loop : -1.85 (0.13), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP 31032 HIS 0.008 0.002 HIS C 425 PHE 0.018 0.002 PHE 3 788 TYR 0.017 0.002 TYR 3 926 ARG 0.013 0.001 ARG 11041 *********************** 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 491 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 339 time to evaluate : 3.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 505 LYS cc_start: 0.6211 (ttpp) cc_final: 0.5868 (ttmt) REVERT: 1 546 ASP cc_start: 0.5889 (OUTLIER) cc_final: 0.5547 (OUTLIER) REVERT: 1 572 HIS cc_start: 0.7636 (t70) cc_final: 0.7423 (t70) REVERT: 1 584 ASP cc_start: 0.6702 (t70) cc_final: 0.6473 (t0) REVERT: 1 684 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.7286 (ttm-80) REVERT: 1 807 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7236 (ptpp) REVERT: 1 832 GLN cc_start: 0.7380 (OUTLIER) cc_final: 0.7038 (tm-30) REVERT: 1 838 VAL cc_start: 0.8194 (t) cc_final: 0.7912 (m) REVERT: 1 864 TYR cc_start: 0.7434 (t80) cc_final: 0.7053 (t80) REVERT: 1 949 GLN cc_start: 0.6700 (pt0) cc_final: 0.6446 (pt0) REVERT: 1 1056 MET cc_start: 0.8112 (mmm) cc_final: 0.7776 (tpt) REVERT: 1 1277 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.8064 (tt0) REVERT: 2 502 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7807 (ttm170) REVERT: 2 509 LYS cc_start: 0.6501 (mttm) cc_final: 0.6014 (pttp) REVERT: 3 8 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8583 (mp) REVERT: 3 34 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7031 (mpt-90) REVERT: 3 377 MET cc_start: 0.7164 (mtp) cc_final: 0.6878 (mtm) REVERT: 3 583 MET cc_start: 0.4357 (mpp) cc_final: 0.3915 (mmm) REVERT: 3 629 SER cc_start: 0.1732 (OUTLIER) cc_final: 0.1465 (p) REVERT: 3 731 LEU cc_start: 0.8141 (tp) cc_final: 0.7736 (tt) REVERT: 3 881 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7853 (mt0) REVERT: C 422 PHE cc_start: 0.6815 (t80) cc_final: 0.6437 (t80) REVERT: C 472 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.6695 (mp-120) REVERT: D 214 GLU cc_start: 0.6480 (pt0) cc_final: 0.6254 (tp30) REVERT: D 245 LYS cc_start: 0.6479 (mtpt) cc_final: 0.6238 (pttp) REVERT: E 145 LYS cc_start: 0.5122 (OUTLIER) cc_final: 0.4189 (mmtt) REVERT: E 147 ILE cc_start: 0.7068 (pt) cc_final: 0.6779 (pt) REVERT: E 164 MET cc_start: 0.5676 (OUTLIER) cc_final: 0.3434 (tpt) outliers start: 152 outliers final: 54 residues processed: 451 average time/residue: 1.2616 time to fit residues: 676.9538 Evaluate side-chains 374 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 308 time to evaluate : 3.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 520 THR Chi-restraints excluded: chain 1 residue 546 ASP Chi-restraints excluded: chain 1 residue 560 LEU Chi-restraints excluded: chain 1 residue 684 ARG Chi-restraints excluded: chain 1 residue 798 THR Chi-restraints excluded: chain 1 residue 801 VAL Chi-restraints excluded: chain 1 residue 807 LYS Chi-restraints excluded: chain 1 residue 832 GLN Chi-restraints excluded: chain 1 residue 1003 VAL Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1092 ASP Chi-restraints excluded: chain 1 residue 1123 CYS Chi-restraints excluded: chain 1 residue 1207 SER Chi-restraints excluded: chain 1 residue 1222 THR Chi-restraints excluded: chain 1 residue 1277 GLN Chi-restraints excluded: chain 1 residue 1292 LYS Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 502 ARG Chi-restraints excluded: chain 2 residue 706 THR Chi-restraints excluded: chain 3 residue 8 LEU Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 34 ARG Chi-restraints excluded: chain 3 residue 55 THR Chi-restraints excluded: chain 3 residue 56 VAL Chi-restraints excluded: chain 3 residue 57 GLU Chi-restraints excluded: chain 3 residue 187 MET Chi-restraints excluded: chain 3 residue 221 VAL Chi-restraints excluded: chain 3 residue 246 SER Chi-restraints excluded: chain 3 residue 372 GLU Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 461 THR Chi-restraints excluded: chain 3 residue 468 ASP Chi-restraints excluded: chain 3 residue 484 VAL Chi-restraints excluded: chain 3 residue 490 THR Chi-restraints excluded: chain 3 residue 524 ILE Chi-restraints excluded: chain 3 residue 590 MET Chi-restraints excluded: chain 3 residue 629 SER Chi-restraints excluded: chain 3 residue 755 VAL Chi-restraints excluded: chain 3 residue 864 SER Chi-restraints excluded: chain 3 residue 865 VAL Chi-restraints excluded: chain 3 residue 881 GLN Chi-restraints excluded: chain 3 residue 897 SER Chi-restraints excluded: chain 3 residue 902 ASP Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 1008 SER Chi-restraints excluded: chain 3 residue 1017 ASN Chi-restraints excluded: chain 3 residue 1090 GLU Chi-restraints excluded: chain 3 residue 1103 SER Chi-restraints excluded: chain 3 residue 1121 THR Chi-restraints excluded: chain 3 residue 1170 VAL Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain 5 residue 8 HIS Chi-restraints excluded: chain 6 residue 53 SER Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 398 LYS Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 406 TYR Chi-restraints excluded: chain C residue 417 ARG Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 472 GLN Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain E residue 145 LYS Chi-restraints excluded: chain E residue 164 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 216 optimal weight: 0.0270 chunk 120 optimal weight: 0.7980 chunk 323 optimal weight: 0.5980 chunk 264 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 389 optimal weight: 50.0000 chunk 420 optimal weight: 0.0470 chunk 346 optimal weight: 50.0000 chunk 386 optimal weight: 50.0000 chunk 132 optimal weight: 4.9990 chunk 312 optimal weight: 20.0000 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 46 ASN 3 870 ASN 31061 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5933 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 31059 Z= 0.147 Angle : 0.537 11.781 42148 Z= 0.269 Chirality : 0.040 0.214 3945 Planarity : 0.004 0.059 5471 Dihedral : 14.792 158.032 6810 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.81 % Allowed : 24.78 % Favored : 70.41 % Cbeta Deviations : 0.00 % 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: -0.68 (0.13), residues: 4127 helix: 0.80 (0.14), residues: 1424 sheet: -0.31 (0.17), residues: 918 loop : -1.54 (0.13), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 471 HIS 0.009 0.001 HIS C 425 PHE 0.018 0.001 PHE D 168 TYR 0.022 0.001 TYR 1 979 ARG 0.012 0.000 ARG 3 463 *********************** REFINEMENT MACRO_CYCLE 3 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 443 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 334 time to evaluate : 3.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 540 MET cc_start: 0.6091 (tpp) cc_final: 0.5713 (tpt) REVERT: 1 546 ASP cc_start: 0.5746 (OUTLIER) cc_final: 0.5476 (OUTLIER) REVERT: 1 572 HIS cc_start: 0.7542 (t70) cc_final: 0.7340 (t70) REVERT: 1 587 TYR cc_start: 0.7028 (t80) cc_final: 0.6749 (t80) REVERT: 1 684 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.7257 (tpt170) REVERT: 1 795 CYS cc_start: 0.7516 (OUTLIER) cc_final: 0.7307 (t) REVERT: 1 830 TYR cc_start: 0.7298 (t80) cc_final: 0.7007 (t80) REVERT: 1 832 GLN cc_start: 0.7381 (OUTLIER) cc_final: 0.6682 (tm130) REVERT: 1 838 VAL cc_start: 0.8230 (t) cc_final: 0.7919 (m) REVERT: 1 864 TYR cc_start: 0.7443 (t80) cc_final: 0.7163 (t80) REVERT: 1 867 MET cc_start: 0.7410 (ttp) cc_final: 0.7203 (ttp) REVERT: 1 1056 MET cc_start: 0.7973 (mmm) cc_final: 0.7691 (tpt) REVERT: 1 1075 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.6988 (ttm-80) REVERT: 2 509 LYS cc_start: 0.6511 (mttm) cc_final: 0.6076 (pttp) REVERT: 3 331 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.7958 (m-30) REVERT: 3 531 LYS cc_start: 0.0912 (OUTLIER) cc_final: -0.0278 (mmpt) REVERT: 3 568 MET cc_start: 0.3215 (mmp) cc_final: 0.3008 (mmp) REVERT: 3 715 MET cc_start: 0.6438 (mpt) cc_final: 0.6214 (mpp) REVERT: 3 731 LEU cc_start: 0.8150 (tp) cc_final: 0.7761 (tt) REVERT: 3 749 GLN cc_start: 0.0548 (OUTLIER) cc_final: -0.0067 (tp40) REVERT: C 406 TYR cc_start: 0.6100 (m-80) cc_final: 0.5845 (m-80) REVERT: C 422 PHE cc_start: 0.6907 (t80) cc_final: 0.6669 (t80) REVERT: D 147 ASP cc_start: 0.7144 (m-30) cc_final: 0.6616 (t70) REVERT: D 168 PHE cc_start: 0.6226 (OUTLIER) cc_final: 0.5125 (m-80) REVERT: D 242 MET cc_start: 0.6455 (tpp) cc_final: 0.6069 (tpp) REVERT: D 245 LYS cc_start: 0.6405 (mtpt) cc_final: 0.6173 (pttp) REVERT: D 247 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6485 (mp) REVERT: E 145 LYS cc_start: 0.5219 (OUTLIER) cc_final: 0.4176 (mmtt) REVERT: E 162 ARG cc_start: 0.5995 (OUTLIER) cc_final: 0.5744 (mtp-110) REVERT: E 164 MET cc_start: 0.5701 (OUTLIER) cc_final: 0.3440 (tpt) outliers start: 109 outliers final: 48 residues processed: 421 average time/residue: 1.2745 time to fit residues: 640.3754 Evaluate side-chains 365 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 305 time to evaluate : 3.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 520 THR Chi-restraints excluded: chain 1 residue 546 ASP Chi-restraints excluded: chain 1 residue 560 LEU Chi-restraints excluded: chain 1 residue 651 VAL Chi-restraints excluded: chain 1 residue 684 ARG Chi-restraints excluded: chain 1 residue 695 VAL Chi-restraints excluded: chain 1 residue 795 CYS Chi-restraints excluded: chain 1 residue 798 THR Chi-restraints excluded: chain 1 residue 801 VAL Chi-restraints excluded: chain 1 residue 832 GLN Chi-restraints excluded: chain 1 residue 1003 VAL Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1075 ARG Chi-restraints excluded: chain 1 residue 1092 ASP Chi-restraints excluded: chain 1 residue 1207 SER Chi-restraints excluded: chain 1 residue 1292 LYS Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 586 ILE Chi-restraints excluded: chain 2 residue 706 THR Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 55 THR Chi-restraints excluded: chain 3 residue 79 VAL Chi-restraints excluded: chain 3 residue 151 ARG Chi-restraints excluded: chain 3 residue 187 MET Chi-restraints excluded: chain 3 residue 221 VAL Chi-restraints excluded: chain 3 residue 331 ASP Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 484 VAL Chi-restraints excluded: chain 3 residue 531 LYS Chi-restraints excluded: chain 3 residue 546 LYS Chi-restraints excluded: chain 3 residue 704 VAL Chi-restraints excluded: chain 3 residue 712 VAL Chi-restraints excluded: chain 3 residue 749 GLN Chi-restraints excluded: chain 3 residue 755 VAL Chi-restraints excluded: chain 3 residue 865 VAL Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 1008 SER Chi-restraints excluded: chain 3 residue 1017 ASN Chi-restraints excluded: chain 3 residue 1103 SER Chi-restraints excluded: chain 3 residue 1121 THR Chi-restraints excluded: chain 3 residue 1170 VAL Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain 5 residue 8 HIS Chi-restraints excluded: chain 5 residue 19 ILE Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain 6 residue 53 SER Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 398 LYS Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 145 LYS Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 162 ARG Chi-restraints excluded: chain E residue 164 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 384 optimal weight: 40.0000 chunk 292 optimal weight: 30.0000 chunk 202 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 185 optimal weight: 8.9990 chunk 261 optimal weight: 3.9990 chunk 390 optimal weight: 0.2980 chunk 413 optimal weight: 50.0000 chunk 204 optimal weight: 0.9990 chunk 370 optimal weight: 7.9990 chunk 111 optimal weight: 30.0000 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 11002 ASN 11209 ASN 2 467 GLN 3 46 ASN 3 104 GLN 3 203 ASN 3 518 GLN 3 575 ASN ** 3 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 818 GLN 3 870 ASN C 400 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6008 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 31059 Z= 0.243 Angle : 0.586 10.320 42148 Z= 0.294 Chirality : 0.043 0.173 3945 Planarity : 0.004 0.057 5471 Dihedral : 14.742 157.536 6805 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 5.70 % Allowed : 24.65 % Favored : 69.66 % Cbeta Deviations : 0.00 % 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: -0.34 (0.13), residues: 4127 helix: 1.16 (0.14), residues: 1417 sheet: -0.19 (0.17), residues: 924 loop : -1.36 (0.13), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP 31032 HIS 0.010 0.001 HIS C 425 PHE 0.016 0.002 PHE 11155 TYR 0.018 0.002 TYR 1 979 ARG 0.005 0.001 ARG 31016 *********************** REFINEMENT MACRO_CYCLE 4 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 448 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 319 time to evaluate : 3.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 540 MET cc_start: 0.6034 (tpp) cc_final: 0.5769 (tpt) REVERT: 1 546 ASP cc_start: 0.5934 (OUTLIER) cc_final: 0.5699 (t70) REVERT: 1 587 TYR cc_start: 0.7207 (t80) cc_final: 0.6873 (t80) REVERT: 1 606 LEU cc_start: 0.7794 (tp) cc_final: 0.7537 (tp) REVERT: 1 684 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.7097 (ttm-80) REVERT: 1 830 TYR cc_start: 0.7438 (t80) cc_final: 0.7150 (t80) REVERT: 1 832 GLN cc_start: 0.7499 (OUTLIER) cc_final: 0.6718 (tm130) REVERT: 1 838 VAL cc_start: 0.8337 (t) cc_final: 0.8011 (m) REVERT: 1 864 TYR cc_start: 0.7672 (t80) cc_final: 0.7399 (t80) REVERT: 1 867 MET cc_start: 0.7334 (ttp) cc_final: 0.7086 (ttp) REVERT: 1 873 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7501 (pp20) REVERT: 1 1056 MET cc_start: 0.8076 (mmm) cc_final: 0.7799 (tpt) REVERT: 2 458 ASN cc_start: 0.5242 (OUTLIER) cc_final: 0.4667 (p0) REVERT: 2 502 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7564 (ptp-170) REVERT: 3 8 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8597 (mp) REVERT: 3 34 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7249 (mpt-90) REVERT: 3 39 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7379 (mt-10) REVERT: 3 86 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8488 (mtt-85) REVERT: 3 331 ASP cc_start: 0.8504 (OUTLIER) cc_final: 0.8132 (m-30) REVERT: 3 377 MET cc_start: 0.7047 (mtp) cc_final: 0.6828 (mtm) REVERT: 3 531 LYS cc_start: 0.0921 (OUTLIER) cc_final: 0.0089 (mmmt) REVERT: 3 568 MET cc_start: 0.2911 (mmp) cc_final: 0.2005 (mpm) REVERT: 3 665 LEU cc_start: 0.6118 (OUTLIER) cc_final: 0.5668 (tp) REVERT: 3 731 LEU cc_start: 0.8231 (tp) cc_final: 0.7867 (tt) REVERT: 6 7 ASP cc_start: 0.6518 (OUTLIER) cc_final: 0.6141 (m-30) REVERT: C 406 TYR cc_start: 0.6196 (m-80) cc_final: 0.5837 (m-80) REVERT: D 136 TYR cc_start: 0.6048 (t80) cc_final: 0.5842 (t80) REVERT: D 147 ASP cc_start: 0.7221 (m-30) cc_final: 0.6639 (t70) REVERT: D 168 PHE cc_start: 0.6517 (OUTLIER) cc_final: 0.5529 (m-80) REVERT: D 242 MET cc_start: 0.6404 (tpp) cc_final: 0.5997 (tpp) REVERT: D 245 LYS cc_start: 0.6454 (mtpt) cc_final: 0.6193 (pttp) REVERT: D 247 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.6824 (mp) REVERT: E 145 LYS cc_start: 0.4979 (OUTLIER) cc_final: 0.3920 (mmmt) REVERT: E 164 MET cc_start: 0.5858 (OUTLIER) cc_final: 0.3671 (tpt) outliers start: 129 outliers final: 63 residues processed: 413 average time/residue: 1.2350 time to fit residues: 611.2224 Evaluate side-chains 375 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 295 time to evaluate : 3.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 520 THR Chi-restraints excluded: chain 1 residue 546 ASP Chi-restraints excluded: chain 1 residue 555 VAL Chi-restraints excluded: chain 1 residue 560 LEU Chi-restraints excluded: chain 1 residue 567 VAL Chi-restraints excluded: chain 1 residue 577 VAL Chi-restraints excluded: chain 1 residue 684 ARG Chi-restraints excluded: chain 1 residue 695 VAL Chi-restraints excluded: chain 1 residue 798 THR Chi-restraints excluded: chain 1 residue 832 GLN Chi-restraints excluded: chain 1 residue 873 GLU Chi-restraints excluded: chain 1 residue 962 MET Chi-restraints excluded: chain 1 residue 1003 VAL Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1123 CYS Chi-restraints excluded: chain 1 residue 1160 GLU Chi-restraints excluded: chain 1 residue 1207 SER Chi-restraints excluded: chain 1 residue 1222 THR Chi-restraints excluded: chain 1 residue 1292 LYS Chi-restraints excluded: chain 2 residue 458 ASN Chi-restraints excluded: chain 2 residue 467 GLN Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 502 ARG Chi-restraints excluded: chain 2 residue 586 ILE Chi-restraints excluded: chain 2 residue 706 THR Chi-restraints excluded: chain 3 residue 8 LEU Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 34 ARG Chi-restraints excluded: chain 3 residue 55 THR Chi-restraints excluded: chain 3 residue 56 VAL Chi-restraints excluded: chain 3 residue 71 THR Chi-restraints excluded: chain 3 residue 79 VAL Chi-restraints excluded: chain 3 residue 86 ARG Chi-restraints excluded: chain 3 residue 136 GLU Chi-restraints excluded: chain 3 residue 187 MET Chi-restraints excluded: chain 3 residue 197 THR Chi-restraints excluded: chain 3 residue 221 VAL Chi-restraints excluded: chain 3 residue 266 ASP Chi-restraints excluded: chain 3 residue 331 ASP Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 484 VAL Chi-restraints excluded: chain 3 residue 531 LYS Chi-restraints excluded: chain 3 residue 546 LYS Chi-restraints excluded: chain 3 residue 595 VAL Chi-restraints excluded: chain 3 residue 665 LEU Chi-restraints excluded: chain 3 residue 689 THR Chi-restraints excluded: chain 3 residue 712 VAL Chi-restraints excluded: chain 3 residue 755 VAL Chi-restraints excluded: chain 3 residue 865 VAL Chi-restraints excluded: chain 3 residue 902 ASP Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 1008 SER Chi-restraints excluded: chain 3 residue 1017 ASN Chi-restraints excluded: chain 3 residue 1090 GLU Chi-restraints excluded: chain 3 residue 1103 SER Chi-restraints excluded: chain 3 residue 1121 THR Chi-restraints excluded: chain 3 residue 1170 VAL Chi-restraints excluded: chain 3 residue 1196 GLU Chi-restraints excluded: chain 3 residue 1198 ASP Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain 5 residue 8 HIS Chi-restraints excluded: chain 5 residue 19 ILE Chi-restraints excluded: chain 6 residue 7 ASP Chi-restraints excluded: chain 6 residue 53 SER Chi-restraints excluded: chain 6 residue 90 ASN Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 398 LYS Chi-restraints excluded: chain C residue 403 ASN Chi-restraints excluded: chain C residue 417 ARG Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 145 LYS Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 164 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 344 optimal weight: 50.0000 chunk 234 optimal weight: 40.0000 chunk 6 optimal weight: 50.0000 chunk 308 optimal weight: 9.9990 chunk 170 optimal weight: 20.0000 chunk 353 optimal weight: 6.9990 chunk 285 optimal weight: 50.0000 chunk 0 optimal weight: 20.0000 chunk 211 optimal weight: 1.9990 chunk 371 optimal weight: 30.0000 chunk 104 optimal weight: 7.9990 overall best weight: 9.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 506 ASN 11099 ASN 11184 HIS 11209 ASN 2 458 ASN 2 587 HIS 3 46 ASN 3 203 ASN ** 3 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 636 GLN 3 709 GLN 3 817 GLN 3 818 GLN C 433 HIS D 244 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6177 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.189 31059 Z= 1.103 Angle : 1.093 16.355 42148 Z= 0.566 Chirality : 0.076 0.463 3945 Planarity : 0.008 0.085 5471 Dihedral : 15.485 157.104 6804 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.79 % Favored : 94.11 % Rotamer: Outliers : 8.08 % Allowed : 22.53 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.12), residues: 4127 helix: 0.17 (0.14), residues: 1401 sheet: -0.59 (0.17), residues: 900 loop : -1.73 (0.13), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.006 TRP 2 504 HIS 0.027 0.004 HIS 11256 PHE 0.040 0.006 PHE 11255 TYR 0.035 0.005 TYR 3 189 ARG 0.019 0.002 ARG 3 275 *********************** REFINEMENT MACRO_CYCLE 5 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 483 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 300 time to evaluate : 2.831 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: 1 540 MET cc_start: 0.6116 (tpp) cc_final: 0.5848 (tpt) REVERT: 1 546 ASP cc_start: 0.6286 (OUTLIER) cc_final: 0.5950 (t70) REVERT: 1 573 LYS cc_start: 0.6990 (OUTLIER) cc_final: 0.6504 (ttmt) REVERT: 1 832 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7521 (tm-30) REVERT: 1 937 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7152 (mm) REVERT: 1 962 MET cc_start: 0.6951 (mmt) cc_final: 0.6503 (mmm) REVERT: 1 1063 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8498 (mt) REVERT: 1 1075 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7432 (ttm-80) REVERT: 1 1277 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8169 (tt0) REVERT: 2 502 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.6326 (ttp-170) REVERT: 2 511 LEU cc_start: 0.4260 (mm) cc_final: 0.4006 (mm) REVERT: 3 8 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8426 (mp) REVERT: 3 34 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7762 (mpt-90) REVERT: 3 91 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7979 (tp30) REVERT: 3 128 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.8476 (ptt180) REVERT: 3 178 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7512 (mp0) REVERT: 3 190 GLU cc_start: 0.8196 (tt0) cc_final: 0.7988 (tt0) REVERT: 3 274 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.7716 (mtm180) REVERT: 3 364 LEU cc_start: 0.2037 (OUTLIER) cc_final: 0.1754 (mt) REVERT: 3 377 MET cc_start: 0.7284 (OUTLIER) cc_final: 0.7018 (mtm) REVERT: 3 450 SER cc_start: 0.1476 (OUTLIER) cc_final: 0.1150 (p) REVERT: 3 531 LYS cc_start: 0.1262 (OUTLIER) cc_final: -0.0174 (mmpt) REVERT: 3 568 MET cc_start: 0.3147 (mmp) cc_final: 0.2296 (mpm) REVERT: 3 629 SER cc_start: 0.2666 (OUTLIER) cc_final: 0.2120 (m) REVERT: 3 881 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.8089 (mt0) REVERT: 3 1093 MET cc_start: 0.8052 (tmt) cc_final: 0.6548 (tmt) REVERT: 6 90 ASN cc_start: 0.7866 (OUTLIER) cc_final: 0.7492 (p0) REVERT: C 406 TYR cc_start: 0.6766 (m-80) cc_final: 0.6226 (m-80) REVERT: C 425 HIS cc_start: 0.5751 (OUTLIER) cc_final: 0.5286 (p-80) REVERT: D 245 LYS cc_start: 0.6795 (mtpt) cc_final: 0.6182 (mmtt) REVERT: E 145 LYS cc_start: 0.5342 (OUTLIER) cc_final: 0.4250 (mmmt) REVERT: E 148 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7376 (mtp-110) outliers start: 183 outliers final: 92 residues processed: 444 average time/residue: 1.2650 time to fit residues: 673.8526 Evaluate side-chains 398 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 282 time to evaluate : 2.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 502 LEU Chi-restraints excluded: chain 1 residue 520 THR Chi-restraints excluded: chain 1 residue 546 ASP Chi-restraints excluded: chain 1 residue 555 VAL Chi-restraints excluded: chain 1 residue 560 LEU Chi-restraints excluded: chain 1 residue 567 VAL Chi-restraints excluded: chain 1 residue 573 LYS Chi-restraints excluded: chain 1 residue 602 LYS Chi-restraints excluded: chain 1 residue 684 ARG Chi-restraints excluded: chain 1 residue 798 THR Chi-restraints excluded: chain 1 residue 801 VAL Chi-restraints excluded: chain 1 residue 832 GLN Chi-restraints excluded: chain 1 residue 873 GLU Chi-restraints excluded: chain 1 residue 937 LEU Chi-restraints excluded: chain 1 residue 947 VAL Chi-restraints excluded: chain 1 residue 949 GLN Chi-restraints excluded: chain 1 residue 958 THR Chi-restraints excluded: chain 1 residue 960 VAL Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1063 LEU Chi-restraints excluded: chain 1 residue 1075 ARG Chi-restraints excluded: chain 1 residue 1123 CYS Chi-restraints excluded: chain 1 residue 1160 GLU Chi-restraints excluded: chain 1 residue 1207 SER Chi-restraints excluded: chain 1 residue 1222 THR Chi-restraints excluded: chain 1 residue 1241 ILE Chi-restraints excluded: chain 1 residue 1277 GLN Chi-restraints excluded: chain 1 residue 1292 LYS Chi-restraints excluded: chain 2 residue 467 GLN Chi-restraints excluded: chain 2 residue 486 LYS Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 502 ARG Chi-restraints excluded: chain 2 residue 586 ILE Chi-restraints excluded: chain 2 residue 706 THR Chi-restraints excluded: chain 3 residue 7 THR Chi-restraints excluded: chain 3 residue 8 LEU Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 34 ARG Chi-restraints excluded: chain 3 residue 55 THR Chi-restraints excluded: chain 3 residue 56 VAL Chi-restraints excluded: chain 3 residue 71 THR Chi-restraints excluded: chain 3 residue 79 VAL Chi-restraints excluded: chain 3 residue 91 GLU Chi-restraints excluded: chain 3 residue 128 ARG Chi-restraints excluded: chain 3 residue 178 GLU Chi-restraints excluded: chain 3 residue 187 MET Chi-restraints excluded: chain 3 residue 197 THR Chi-restraints excluded: chain 3 residue 221 VAL Chi-restraints excluded: chain 3 residue 246 SER Chi-restraints excluded: chain 3 residue 248 VAL Chi-restraints excluded: chain 3 residue 257 THR Chi-restraints excluded: chain 3 residue 266 ASP Chi-restraints excluded: chain 3 residue 274 ARG Chi-restraints excluded: chain 3 residue 278 LEU Chi-restraints excluded: chain 3 residue 327 LEU Chi-restraints excluded: chain 3 residue 364 LEU Chi-restraints excluded: chain 3 residue 377 MET Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 450 SER Chi-restraints excluded: chain 3 residue 484 VAL Chi-restraints excluded: chain 3 residue 492 GLU Chi-restraints excluded: chain 3 residue 531 LYS Chi-restraints excluded: chain 3 residue 546 LYS Chi-restraints excluded: chain 3 residue 558 LEU Chi-restraints excluded: chain 3 residue 595 VAL Chi-restraints excluded: chain 3 residue 629 SER Chi-restraints excluded: chain 3 residue 677 THR Chi-restraints excluded: chain 3 residue 678 VAL Chi-restraints excluded: chain 3 residue 689 THR Chi-restraints excluded: chain 3 residue 704 VAL Chi-restraints excluded: chain 3 residue 712 VAL Chi-restraints excluded: chain 3 residue 755 VAL Chi-restraints excluded: chain 3 residue 773 VAL Chi-restraints excluded: chain 3 residue 850 SER Chi-restraints excluded: chain 3 residue 865 VAL Chi-restraints excluded: chain 3 residue 881 GLN Chi-restraints excluded: chain 3 residue 897 SER Chi-restraints excluded: chain 3 residue 902 ASP Chi-restraints excluded: chain 3 residue 919 SER Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 1008 SER Chi-restraints excluded: chain 3 residue 1017 ASN Chi-restraints excluded: chain 3 residue 1103 SER Chi-restraints excluded: chain 3 residue 1107 THR Chi-restraints excluded: chain 3 residue 1116 SER Chi-restraints excluded: chain 3 residue 1121 THR Chi-restraints excluded: chain 3 residue 1133 THR Chi-restraints excluded: chain 3 residue 1170 VAL Chi-restraints excluded: chain 3 residue 1188 ASN Chi-restraints excluded: chain 3 residue 1196 GLU Chi-restraints excluded: chain 3 residue 1198 ASP Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain 5 residue 8 HIS Chi-restraints excluded: chain 5 residue 19 ILE Chi-restraints excluded: chain 6 residue 7 ASP Chi-restraints excluded: chain 6 residue 53 SER Chi-restraints excluded: chain 6 residue 90 ASN Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 398 LYS Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 403 ASN Chi-restraints excluded: chain C residue 417 ARG Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 131 MET Chi-restraints excluded: chain E residue 145 LYS Chi-restraints excluded: chain E residue 148 ARG Chi-restraints excluded: chain E residue 154 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 139 optimal weight: 0.6980 chunk 372 optimal weight: 30.0000 chunk 81 optimal weight: 1.9990 chunk 242 optimal weight: 0.0030 chunk 102 optimal weight: 10.0000 chunk 414 optimal weight: 0.8980 chunk 343 optimal weight: 40.0000 chunk 191 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 chunk 136 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 518 GLN 11283 HIS 2 458 ASN 2 467 GLN 3 27 GLN 3 46 ASN 3 666 ASN 3 805 ASN 31142 GLN 31192 ASN D 244 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6045 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31059 Z= 0.206 Angle : 0.592 9.833 42148 Z= 0.301 Chirality : 0.042 0.173 3945 Planarity : 0.004 0.075 5471 Dihedral : 14.883 153.894 6804 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.86 % Allowed : 25.88 % Favored : 69.26 % Cbeta Deviations : 0.00 % 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: -0.53 (0.13), residues: 4127 helix: 1.00 (0.14), residues: 1410 sheet: -0.30 (0.17), residues: 881 loop : -1.45 (0.13), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 2 708 HIS 0.012 0.001 HIS C 425 PHE 0.016 0.002 PHE D 168 TYR 0.021 0.002 TYR 1 979 ARG 0.008 0.001 ARG 31016 *********************** REFINEMENT MACRO_CYCLE 6 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 412 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 302 time to evaluate : 2.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 501 LEU cc_start: 0.7037 (pp) cc_final: 0.6790 (pt) REVERT: 1 832 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7339 (tm-30) REVERT: 1 838 VAL cc_start: 0.8429 (t) cc_final: 0.8194 (m) REVERT: 1 867 MET cc_start: 0.7510 (ttp) cc_final: 0.7270 (ttp) REVERT: 1 876 MET cc_start: 0.6754 (mmt) cc_final: 0.6187 (tpt) REVERT: 1 962 MET cc_start: 0.6913 (OUTLIER) cc_final: 0.6515 (mmm) REVERT: 1 1003 VAL cc_start: 0.7359 (OUTLIER) cc_final: 0.7010 (t) REVERT: 1 1053 ARG cc_start: 0.7552 (mtp-110) cc_final: 0.7314 (mtp85) REVERT: 1 1209 ASN cc_start: 0.8756 (OUTLIER) cc_final: 0.8530 (t0) REVERT: 1 1277 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7791 (tt0) REVERT: 2 502 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7713 (ptp-170) REVERT: 2 511 LEU cc_start: 0.3596 (mm) cc_final: 0.3257 (mm) REVERT: 3 34 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7124 (mpt-90) REVERT: 3 39 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7402 (mt-10) REVERT: 3 190 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7898 (tt0) REVERT: 3 331 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.8186 (m-30) REVERT: 3 447 MET cc_start: 0.2062 (ttm) cc_final: 0.0843 (tpp) REVERT: 3 531 LYS cc_start: 0.1050 (OUTLIER) cc_final: -0.0103 (mmpt) REVERT: 3 568 MET cc_start: 0.3137 (mmp) cc_final: 0.2394 (mpm) REVERT: 3 731 LEU cc_start: 0.8282 (tp) cc_final: 0.7935 (tt) REVERT: 3 817 GLN cc_start: 0.7608 (tp-100) cc_final: 0.7405 (mm-40) REVERT: 5 8 HIS cc_start: 0.4825 (OUTLIER) cc_final: 0.4390 (t-90) REVERT: 6 90 ASN cc_start: 0.7772 (OUTLIER) cc_final: 0.7457 (p0) REVERT: C 406 TYR cc_start: 0.6683 (m-80) cc_final: 0.6073 (m-80) REVERT: C 425 HIS cc_start: 0.5745 (OUTLIER) cc_final: 0.5307 (p-80) REVERT: D 136 TYR cc_start: 0.6043 (t80) cc_final: 0.5776 (t80) REVERT: D 147 ASP cc_start: 0.7223 (m-30) cc_final: 0.6580 (t70) REVERT: D 169 LYS cc_start: 0.7387 (OUTLIER) cc_final: 0.7118 (mttt) REVERT: D 245 LYS cc_start: 0.6773 (mtpt) cc_final: 0.6048 (mmtt) REVERT: D 247 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7466 (mp) outliers start: 110 outliers final: 54 residues processed: 389 average time/residue: 1.2839 time to fit residues: 595.6782 Evaluate side-chains 358 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 289 time to evaluate : 2.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 560 LEU Chi-restraints excluded: chain 1 residue 684 ARG Chi-restraints excluded: chain 1 residue 695 VAL Chi-restraints excluded: chain 1 residue 798 THR Chi-restraints excluded: chain 1 residue 801 VAL Chi-restraints excluded: chain 1 residue 832 GLN Chi-restraints excluded: chain 1 residue 949 GLN Chi-restraints excluded: chain 1 residue 962 MET Chi-restraints excluded: chain 1 residue 1003 VAL Chi-restraints excluded: chain 1 residue 1014 LYS Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1059 CYS Chi-restraints excluded: chain 1 residue 1123 CYS Chi-restraints excluded: chain 1 residue 1207 SER Chi-restraints excluded: chain 1 residue 1209 ASN Chi-restraints excluded: chain 1 residue 1222 THR Chi-restraints excluded: chain 1 residue 1277 GLN Chi-restraints excluded: chain 1 residue 1292 LYS Chi-restraints excluded: chain 2 residue 458 ASN Chi-restraints excluded: chain 2 residue 467 GLN Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 502 ARG Chi-restraints excluded: chain 2 residue 586 ILE Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 34 ARG Chi-restraints excluded: chain 3 residue 55 THR Chi-restraints excluded: chain 3 residue 79 VAL Chi-restraints excluded: chain 3 residue 190 GLU Chi-restraints excluded: chain 3 residue 197 THR Chi-restraints excluded: chain 3 residue 221 VAL Chi-restraints excluded: chain 3 residue 246 SER Chi-restraints excluded: chain 3 residue 266 ASP Chi-restraints excluded: chain 3 residue 331 ASP Chi-restraints excluded: chain 3 residue 398 VAL Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 435 LEU Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 484 VAL Chi-restraints excluded: chain 3 residue 524 ILE Chi-restraints excluded: chain 3 residue 531 LYS Chi-restraints excluded: chain 3 residue 546 LYS Chi-restraints excluded: chain 3 residue 595 VAL Chi-restraints excluded: chain 3 residue 755 VAL Chi-restraints excluded: chain 3 residue 805 ASN Chi-restraints excluded: chain 3 residue 897 SER Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 1008 SER Chi-restraints excluded: chain 3 residue 1017 ASN Chi-restraints excluded: chain 3 residue 1103 SER Chi-restraints excluded: chain 3 residue 1121 THR Chi-restraints excluded: chain 3 residue 1170 VAL Chi-restraints excluded: chain 3 residue 1196 GLU Chi-restraints excluded: chain 3 residue 1198 ASP Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain 5 residue 8 HIS Chi-restraints excluded: chain 5 residue 19 ILE Chi-restraints excluded: chain 6 residue 90 ASN Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 398 LYS Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 403 ASN Chi-restraints excluded: chain C residue 417 ARG Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 169 LYS Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain E residue 154 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 399 optimal weight: 50.0000 chunk 46 optimal weight: 0.4980 chunk 235 optimal weight: 40.0000 chunk 302 optimal weight: 40.0000 chunk 234 optimal weight: 0.9980 chunk 348 optimal weight: 20.0000 chunk 231 optimal weight: 50.0000 chunk 412 optimal weight: 0.6980 chunk 258 optimal weight: 2.9990 chunk 251 optimal weight: 0.5980 chunk 190 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 11194 HIS 2 458 ASN 3 805 ASN 3 998 HIS 31061 ASN 31192 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6025 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31059 Z= 0.171 Angle : 0.558 11.357 42148 Z= 0.281 Chirality : 0.041 0.200 3945 Planarity : 0.004 0.067 5471 Dihedral : 14.658 153.674 6800 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.24 % Allowed : 26.86 % Favored : 68.90 % Cbeta Deviations : 0.00 % 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: -0.14 (0.13), residues: 4127 helix: 1.38 (0.15), residues: 1414 sheet: -0.06 (0.18), residues: 867 loop : -1.28 (0.13), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 2 708 HIS 0.011 0.001 HIS C 425 PHE 0.019 0.001 PHE 2 460 TYR 0.016 0.001 TYR 3 807 ARG 0.013 0.000 ARG 1 495 *********************** REFINEMENT MACRO_CYCLE 7 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 395 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 299 time to evaluate : 3.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 498 MET cc_start: 0.5138 (ppp) cc_final: 0.3763 (ttm) REVERT: 1 684 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.7377 (tpt170) REVERT: 1 832 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.7209 (tm-30) REVERT: 1 867 MET cc_start: 0.7458 (ttp) cc_final: 0.7245 (ttp) REVERT: 1 962 MET cc_start: 0.6864 (OUTLIER) cc_final: 0.6546 (mmm) REVERT: 1 1003 VAL cc_start: 0.7331 (OUTLIER) cc_final: 0.6927 (t) REVERT: 1 1277 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7810 (tt0) REVERT: 2 458 ASN cc_start: 0.5781 (OUTLIER) cc_final: 0.4818 (p0) REVERT: 2 502 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7666 (ptp-170) REVERT: 2 712 GLU cc_start: 0.6197 (mp0) cc_final: 0.5977 (mp0) REVERT: 3 34 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.6888 (mpt-90) REVERT: 3 190 GLU cc_start: 0.8082 (tt0) cc_final: 0.7849 (tt0) REVERT: 3 321 MET cc_start: 0.7360 (mmp) cc_final: 0.6960 (mmp) REVERT: 3 331 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.8076 (m-30) REVERT: 3 447 MET cc_start: 0.2348 (ttm) cc_final: 0.1095 (tpp) REVERT: 3 531 LYS cc_start: 0.1130 (OUTLIER) cc_final: 0.0083 (mmmt) REVERT: 3 568 MET cc_start: 0.2984 (mmp) cc_final: 0.2157 (mpm) REVERT: 3 590 MET cc_start: 0.6474 (pmt) cc_final: 0.6126 (ppp) REVERT: 3 629 SER cc_start: 0.2470 (OUTLIER) cc_final: 0.2163 (p) REVERT: 3 731 LEU cc_start: 0.8211 (tp) cc_final: 0.7895 (tt) REVERT: 3 838 MET cc_start: 0.7121 (mmm) cc_final: 0.6826 (mmp) REVERT: 5 8 HIS cc_start: 0.4660 (OUTLIER) cc_final: 0.4409 (t-90) REVERT: 6 90 ASN cc_start: 0.7766 (OUTLIER) cc_final: 0.7461 (p0) REVERT: C 406 TYR cc_start: 0.6764 (m-80) cc_final: 0.6087 (m-80) REVERT: C 425 HIS cc_start: 0.5680 (OUTLIER) cc_final: 0.5240 (p-80) REVERT: D 147 ASP cc_start: 0.7089 (m-30) cc_final: 0.6571 (t70) REVERT: D 245 LYS cc_start: 0.6759 (mtpt) cc_final: 0.6058 (mmtt) outliers start: 96 outliers final: 55 residues processed: 378 average time/residue: 1.2314 time to fit residues: 559.4126 Evaluate side-chains 357 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 288 time to evaluate : 3.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 560 LEU Chi-restraints excluded: chain 1 residue 684 ARG Chi-restraints excluded: chain 1 residue 695 VAL Chi-restraints excluded: chain 1 residue 798 THR Chi-restraints excluded: chain 1 residue 801 VAL Chi-restraints excluded: chain 1 residue 832 GLN Chi-restraints excluded: chain 1 residue 947 VAL Chi-restraints excluded: chain 1 residue 949 GLN Chi-restraints excluded: chain 1 residue 962 MET Chi-restraints excluded: chain 1 residue 1003 VAL Chi-restraints excluded: chain 1 residue 1014 LYS Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1059 CYS Chi-restraints excluded: chain 1 residue 1207 SER Chi-restraints excluded: chain 1 residue 1222 THR Chi-restraints excluded: chain 1 residue 1277 GLN Chi-restraints excluded: chain 1 residue 1292 LYS Chi-restraints excluded: chain 2 residue 458 ASN Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 502 ARG Chi-restraints excluded: chain 2 residue 586 ILE Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 34 ARG Chi-restraints excluded: chain 3 residue 55 THR Chi-restraints excluded: chain 3 residue 79 VAL Chi-restraints excluded: chain 3 residue 136 GLU Chi-restraints excluded: chain 3 residue 197 THR Chi-restraints excluded: chain 3 residue 221 VAL Chi-restraints excluded: chain 3 residue 246 SER Chi-restraints excluded: chain 3 residue 266 ASP Chi-restraints excluded: chain 3 residue 331 ASP Chi-restraints excluded: chain 3 residue 364 LEU Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 484 VAL Chi-restraints excluded: chain 3 residue 524 ILE Chi-restraints excluded: chain 3 residue 531 LYS Chi-restraints excluded: chain 3 residue 546 LYS Chi-restraints excluded: chain 3 residue 595 VAL Chi-restraints excluded: chain 3 residue 629 SER Chi-restraints excluded: chain 3 residue 755 VAL Chi-restraints excluded: chain 3 residue 824 VAL Chi-restraints excluded: chain 3 residue 897 SER Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 1008 SER Chi-restraints excluded: chain 3 residue 1017 ASN Chi-restraints excluded: chain 3 residue 1103 SER Chi-restraints excluded: chain 3 residue 1121 THR Chi-restraints excluded: chain 3 residue 1146 MET Chi-restraints excluded: chain 3 residue 1170 VAL Chi-restraints excluded: chain 3 residue 1198 ASP Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain 5 residue 8 HIS Chi-restraints excluded: chain 5 residue 19 ILE Chi-restraints excluded: chain 6 residue 90 ASN Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 398 LYS Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 403 ASN Chi-restraints excluded: chain C residue 417 ARG Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 154 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 255 optimal weight: 2.9990 chunk 164 optimal weight: 30.0000 chunk 246 optimal weight: 50.0000 chunk 124 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 262 optimal weight: 0.0570 chunk 281 optimal weight: 30.0000 chunk 203 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 324 optimal weight: 4.9990 overall best weight: 1.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 458 ASN 3 805 ASN 3 881 GLN 31192 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6066 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 31059 Z= 0.279 Angle : 0.620 11.082 42148 Z= 0.312 Chirality : 0.045 0.336 3945 Planarity : 0.004 0.070 5471 Dihedral : 14.671 154.231 6800 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.39 % Favored : 95.59 % Rotamer: Outliers : 4.68 % Allowed : 26.59 % Favored : 68.73 % Cbeta Deviations : 0.00 % 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: -0.12 (0.13), residues: 4127 helix: 1.33 (0.14), residues: 1417 sheet: -0.05 (0.18), residues: 866 loop : -1.21 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP 2 708 HIS 0.010 0.001 HIS C 425 PHE 0.018 0.002 PHE 11155 TYR 0.020 0.002 TYR 1 805 ARG 0.010 0.001 ARG 1 495 *********************** REFINEMENT MACRO_CYCLE 8 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 403 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 297 time to evaluate : 3.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 684 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.7329 (tpt170) REVERT: 1 832 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.7246 (tm-30) REVERT: 1 867 MET cc_start: 0.7461 (ttp) cc_final: 0.7204 (ttp) REVERT: 1 873 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7286 (pp20) REVERT: 1 876 MET cc_start: 0.6762 (mmt) cc_final: 0.6253 (tpp) REVERT: 1 962 MET cc_start: 0.6910 (OUTLIER) cc_final: 0.6612 (mmm) REVERT: 1 1003 VAL cc_start: 0.7323 (OUTLIER) cc_final: 0.6910 (t) REVERT: 1 1207 SER cc_start: 0.8679 (OUTLIER) cc_final: 0.8467 (m) REVERT: 1 1277 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7874 (tt0) REVERT: 2 502 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7733 (ptp-170) REVERT: 2 511 LEU cc_start: 0.3870 (mm) cc_final: 0.3471 (mm) REVERT: 2 712 GLU cc_start: 0.6155 (mp0) cc_final: 0.5929 (mp0) REVERT: 3 34 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7153 (mpt-90) REVERT: 3 178 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7644 (mp0) REVERT: 3 190 GLU cc_start: 0.8105 (tt0) cc_final: 0.7867 (tt0) REVERT: 3 274 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.7318 (mtm180) REVERT: 3 331 ASP cc_start: 0.8555 (OUTLIER) cc_final: 0.8197 (m-30) REVERT: 3 447 MET cc_start: 0.2430 (ttm) cc_final: 0.1120 (tpp) REVERT: 3 531 LYS cc_start: 0.1073 (OUTLIER) cc_final: -0.0010 (mmmt) REVERT: 3 568 MET cc_start: 0.3167 (mmp) cc_final: 0.2503 (mpm) REVERT: 3 590 MET cc_start: 0.6498 (pmt) cc_final: 0.6157 (ppp) REVERT: 3 629 SER cc_start: 0.2499 (OUTLIER) cc_final: 0.2191 (p) REVERT: 3 680 ASP cc_start: 0.3233 (OUTLIER) cc_final: 0.3017 (t0) REVERT: 3 731 LEU cc_start: 0.8238 (tp) cc_final: 0.7887 (tt) REVERT: 3 838 MET cc_start: 0.7191 (mmm) cc_final: 0.6913 (mmp) REVERT: 5 8 HIS cc_start: 0.4748 (OUTLIER) cc_final: 0.4447 (t-90) REVERT: 6 90 ASN cc_start: 0.7776 (OUTLIER) cc_final: 0.7478 (p0) REVERT: C 406 TYR cc_start: 0.6795 (m-80) cc_final: 0.6184 (m-80) REVERT: C 425 HIS cc_start: 0.5666 (OUTLIER) cc_final: 0.5227 (p-80) REVERT: D 136 TYR cc_start: 0.6041 (t80) cc_final: 0.5736 (t80) REVERT: D 147 ASP cc_start: 0.7113 (m-30) cc_final: 0.6565 (t70) REVERT: D 245 LYS cc_start: 0.6693 (mtpt) cc_final: 0.5999 (mmtt) outliers start: 106 outliers final: 64 residues processed: 379 average time/residue: 1.2292 time to fit residues: 560.4003 Evaluate side-chains 364 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 282 time to evaluate : 2.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 551 LEU Chi-restraints excluded: chain 1 residue 555 VAL Chi-restraints excluded: chain 1 residue 560 LEU Chi-restraints excluded: chain 1 residue 684 ARG Chi-restraints excluded: chain 1 residue 695 VAL Chi-restraints excluded: chain 1 residue 798 THR Chi-restraints excluded: chain 1 residue 801 VAL Chi-restraints excluded: chain 1 residue 832 GLN Chi-restraints excluded: chain 1 residue 873 GLU Chi-restraints excluded: chain 1 residue 949 GLN Chi-restraints excluded: chain 1 residue 962 MET Chi-restraints excluded: chain 1 residue 1003 VAL Chi-restraints excluded: chain 1 residue 1014 LYS Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1059 CYS Chi-restraints excluded: chain 1 residue 1123 CYS Chi-restraints excluded: chain 1 residue 1126 PHE Chi-restraints excluded: chain 1 residue 1207 SER Chi-restraints excluded: chain 1 residue 1222 THR Chi-restraints excluded: chain 1 residue 1277 GLN Chi-restraints excluded: chain 1 residue 1292 LYS Chi-restraints excluded: chain 2 residue 467 GLN Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 502 ARG Chi-restraints excluded: chain 2 residue 572 HIS Chi-restraints excluded: chain 2 residue 586 ILE Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 34 ARG Chi-restraints excluded: chain 3 residue 55 THR Chi-restraints excluded: chain 3 residue 56 VAL Chi-restraints excluded: chain 3 residue 57 GLU Chi-restraints excluded: chain 3 residue 79 VAL Chi-restraints excluded: chain 3 residue 136 GLU Chi-restraints excluded: chain 3 residue 178 GLU Chi-restraints excluded: chain 3 residue 187 MET Chi-restraints excluded: chain 3 residue 197 THR Chi-restraints excluded: chain 3 residue 221 VAL Chi-restraints excluded: chain 3 residue 246 SER Chi-restraints excluded: chain 3 residue 257 THR Chi-restraints excluded: chain 3 residue 266 ASP Chi-restraints excluded: chain 3 residue 274 ARG Chi-restraints excluded: chain 3 residue 331 ASP Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 484 VAL Chi-restraints excluded: chain 3 residue 524 ILE Chi-restraints excluded: chain 3 residue 531 LYS Chi-restraints excluded: chain 3 residue 546 LYS Chi-restraints excluded: chain 3 residue 595 VAL Chi-restraints excluded: chain 3 residue 629 SER Chi-restraints excluded: chain 3 residue 680 ASP Chi-restraints excluded: chain 3 residue 755 VAL Chi-restraints excluded: chain 3 residue 805 ASN Chi-restraints excluded: chain 3 residue 824 VAL Chi-restraints excluded: chain 3 residue 850 SER Chi-restraints excluded: chain 3 residue 897 SER Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 1008 SER Chi-restraints excluded: chain 3 residue 1017 ASN Chi-restraints excluded: chain 3 residue 1103 SER Chi-restraints excluded: chain 3 residue 1107 THR Chi-restraints excluded: chain 3 residue 1121 THR Chi-restraints excluded: chain 3 residue 1146 MET Chi-restraints excluded: chain 3 residue 1170 VAL Chi-restraints excluded: chain 3 residue 1198 ASP Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain 5 residue 8 HIS Chi-restraints excluded: chain 5 residue 19 ILE Chi-restraints excluded: chain 6 residue 90 ASN Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 398 LYS Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 403 ASN Chi-restraints excluded: chain C residue 417 ARG Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 154 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 375 optimal weight: 1.9990 chunk 395 optimal weight: 50.0000 chunk 360 optimal weight: 30.0000 chunk 384 optimal weight: 10.0000 chunk 231 optimal weight: 50.0000 chunk 167 optimal weight: 4.9990 chunk 301 optimal weight: 0.0370 chunk 117 optimal weight: 0.0470 chunk 347 optimal weight: 8.9990 chunk 363 optimal weight: 50.0000 chunk 383 optimal weight: 40.0000 overall best weight: 3.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 11209 ASN 2 467 GLN 3 518 GLN 3 670 GLN 3 805 ASN 31061 ASN 31192 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6102 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 31059 Z= 0.413 Angle : 0.694 11.380 42148 Z= 0.354 Chirality : 0.049 0.419 3945 Planarity : 0.005 0.070 5471 Dihedral : 14.789 154.932 6800 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.11 % Favored : 94.84 % Rotamer: Outliers : 4.95 % Allowed : 26.68 % Favored : 68.37 % 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: -0.30 (0.13), residues: 4127 helix: 1.15 (0.14), residues: 1415 sheet: -0.15 (0.17), residues: 885 loop : -1.29 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP 2 504 HIS 0.012 0.002 HIS C 425 PHE 0.024 0.003 PHE 11155 TYR 0.024 0.003 TYR 3 189 ARG 0.011 0.001 ARG 1 495 *********************** REFINEMENT MACRO_CYCLE 9 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 400 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 288 time to evaluate : 3.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 684 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7322 (tpt170) REVERT: 1 832 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.7255 (tm-30) REVERT: 1 867 MET cc_start: 0.7534 (ttp) cc_final: 0.7317 (ttp) REVERT: 1 873 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7355 (pp20) REVERT: 1 876 MET cc_start: 0.6847 (mmt) cc_final: 0.6315 (tpp) REVERT: 1 879 LEU cc_start: 0.7160 (OUTLIER) cc_final: 0.6870 (mp) REVERT: 1 962 MET cc_start: 0.6955 (OUTLIER) cc_final: 0.6575 (mmm) REVERT: 1 1003 VAL cc_start: 0.7460 (OUTLIER) cc_final: 0.7057 (t) REVERT: 2 502 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7624 (ptp-170) REVERT: 3 34 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7381 (mpt-90) REVERT: 3 96 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8253 (mtmm) REVERT: 3 178 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7655 (mp0) REVERT: 3 190 GLU cc_start: 0.8142 (tt0) cc_final: 0.7924 (tt0) REVERT: 3 274 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.7525 (mtm180) REVERT: 3 331 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8249 (m-30) REVERT: 3 447 MET cc_start: 0.2365 (ttm) cc_final: 0.1180 (tpp) REVERT: 3 531 LYS cc_start: 0.1175 (OUTLIER) cc_final: 0.0026 (mmmt) REVERT: 3 568 MET cc_start: 0.3243 (mmp) cc_final: 0.2539 (mpm) REVERT: 3 590 MET cc_start: 0.6544 (pmt) cc_final: 0.6192 (ppp) REVERT: 3 629 SER cc_start: 0.2645 (OUTLIER) cc_final: 0.1974 (m) REVERT: 3 822 GLU cc_start: 0.7344 (tm-30) cc_final: 0.6986 (tp30) REVERT: 5 8 HIS cc_start: 0.5139 (OUTLIER) cc_final: 0.4492 (t-90) REVERT: 6 90 ASN cc_start: 0.7789 (OUTLIER) cc_final: 0.7504 (p0) REVERT: C 406 TYR cc_start: 0.6881 (m-80) cc_final: 0.6338 (m-80) REVERT: C 425 HIS cc_start: 0.5711 (OUTLIER) cc_final: 0.5212 (p-80) REVERT: D 147 ASP cc_start: 0.7115 (m-30) cc_final: 0.6563 (t70) REVERT: D 245 LYS cc_start: 0.6744 (mtpt) cc_final: 0.6172 (mmtt) outliers start: 112 outliers final: 71 residues processed: 377 average time/residue: 1.2109 time to fit residues: 551.6069 Evaluate side-chains 371 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 283 time to evaluate : 2.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 555 VAL Chi-restraints excluded: chain 1 residue 560 LEU Chi-restraints excluded: chain 1 residue 684 ARG Chi-restraints excluded: chain 1 residue 695 VAL Chi-restraints excluded: chain 1 residue 792 VAL Chi-restraints excluded: chain 1 residue 795 CYS Chi-restraints excluded: chain 1 residue 798 THR Chi-restraints excluded: chain 1 residue 801 VAL Chi-restraints excluded: chain 1 residue 832 GLN Chi-restraints excluded: chain 1 residue 873 GLU Chi-restraints excluded: chain 1 residue 879 LEU Chi-restraints excluded: chain 1 residue 962 MET Chi-restraints excluded: chain 1 residue 1003 VAL Chi-restraints excluded: chain 1 residue 1014 LYS Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1059 CYS Chi-restraints excluded: chain 1 residue 1092 ASP Chi-restraints excluded: chain 1 residue 1123 CYS Chi-restraints excluded: chain 1 residue 1126 PHE Chi-restraints excluded: chain 1 residue 1160 GLU Chi-restraints excluded: chain 1 residue 1207 SER Chi-restraints excluded: chain 1 residue 1222 THR Chi-restraints excluded: chain 1 residue 1241 ILE Chi-restraints excluded: chain 1 residue 1292 LYS Chi-restraints excluded: chain 2 residue 458 ASN Chi-restraints excluded: chain 2 residue 467 GLN Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 502 ARG Chi-restraints excluded: chain 2 residue 572 HIS Chi-restraints excluded: chain 2 residue 586 ILE Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 34 ARG Chi-restraints excluded: chain 3 residue 36 LYS Chi-restraints excluded: chain 3 residue 55 THR Chi-restraints excluded: chain 3 residue 56 VAL Chi-restraints excluded: chain 3 residue 79 VAL Chi-restraints excluded: chain 3 residue 96 LYS Chi-restraints excluded: chain 3 residue 136 GLU Chi-restraints excluded: chain 3 residue 178 GLU Chi-restraints excluded: chain 3 residue 187 MET Chi-restraints excluded: chain 3 residue 197 THR Chi-restraints excluded: chain 3 residue 221 VAL Chi-restraints excluded: chain 3 residue 246 SER Chi-restraints excluded: chain 3 residue 257 THR Chi-restraints excluded: chain 3 residue 266 ASP Chi-restraints excluded: chain 3 residue 274 ARG Chi-restraints excluded: chain 3 residue 297 SER Chi-restraints excluded: chain 3 residue 331 ASP Chi-restraints excluded: chain 3 residue 398 VAL Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 484 VAL Chi-restraints excluded: chain 3 residue 531 LYS Chi-restraints excluded: chain 3 residue 546 LYS Chi-restraints excluded: chain 3 residue 595 VAL Chi-restraints excluded: chain 3 residue 629 SER Chi-restraints excluded: chain 3 residue 755 VAL Chi-restraints excluded: chain 3 residue 824 VAL Chi-restraints excluded: chain 3 residue 850 SER Chi-restraints excluded: chain 3 residue 897 SER Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 1008 SER Chi-restraints excluded: chain 3 residue 1017 ASN Chi-restraints excluded: chain 3 residue 1090 GLU Chi-restraints excluded: chain 3 residue 1103 SER Chi-restraints excluded: chain 3 residue 1107 THR Chi-restraints excluded: chain 3 residue 1116 SER Chi-restraints excluded: chain 3 residue 1121 THR Chi-restraints excluded: chain 3 residue 1146 MET Chi-restraints excluded: chain 3 residue 1170 VAL Chi-restraints excluded: chain 3 residue 1196 GLU Chi-restraints excluded: chain 3 residue 1198 ASP Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain 5 residue 8 HIS Chi-restraints excluded: chain 5 residue 19 ILE Chi-restraints excluded: chain 6 residue 90 ASN Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 398 LYS Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 403 ASN Chi-restraints excluded: chain C residue 417 ARG Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain E residue 154 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 252 optimal weight: 0.6980 chunk 406 optimal weight: 7.9990 chunk 248 optimal weight: 0.5980 chunk 192 optimal weight: 0.9980 chunk 282 optimal weight: 30.0000 chunk 426 optimal weight: 50.0000 chunk 392 optimal weight: 50.0000 chunk 339 optimal weight: 20.0000 chunk 35 optimal weight: 1.9990 chunk 262 optimal weight: 0.0370 chunk 208 optimal weight: 2.9990 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 518 GLN 2 467 GLN 31061 ASN 31192 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6037 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31059 Z= 0.174 Angle : 0.564 11.759 42148 Z= 0.284 Chirality : 0.041 0.328 3945 Planarity : 0.004 0.072 5471 Dihedral : 14.626 154.266 6800 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.67 % Allowed : 28.36 % Favored : 67.98 % Cbeta Deviations : 0.00 % 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: 0.00 (0.13), residues: 4127 helix: 1.41 (0.14), residues: 1422 sheet: -0.01 (0.18), residues: 882 loop : -1.12 (0.14), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 2 708 HIS 0.011 0.001 HIS C 425 PHE 0.016 0.001 PHE D 168 TYR 0.022 0.001 TYR 1 805 ARG 0.018 0.000 ARG 1 495 ********************** REFINEMENT MACRO_CYCLE 10 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 376 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 293 time to evaluate : 3.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 832 GLN cc_start: 0.7562 (OUTLIER) cc_final: 0.7078 (tm-30) REVERT: 1 876 MET cc_start: 0.6655 (mmt) cc_final: 0.6148 (tpp) REVERT: 1 962 MET cc_start: 0.6995 (OUTLIER) cc_final: 0.6715 (mmm) REVERT: 1 1003 VAL cc_start: 0.7351 (OUTLIER) cc_final: 0.6922 (t) REVERT: 1 1006 MET cc_start: 0.5082 (mmm) cc_final: 0.4574 (mmt) REVERT: 2 502 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7650 (ptp-170) REVERT: 3 331 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8161 (m-30) REVERT: 3 447 MET cc_start: 0.2137 (ttm) cc_final: 0.1486 (tpp) REVERT: 3 531 LYS cc_start: 0.0998 (OUTLIER) cc_final: -0.0120 (mmmt) REVERT: 3 568 MET cc_start: 0.3143 (mmp) cc_final: 0.2471 (mpm) REVERT: 3 590 MET cc_start: 0.6426 (pmt) cc_final: 0.6087 (ppp) REVERT: 3 629 SER cc_start: 0.2508 (OUTLIER) cc_final: 0.1789 (m) REVERT: 3 822 GLU cc_start: 0.7323 (tm-30) cc_final: 0.7097 (tp30) REVERT: 5 8 HIS cc_start: 0.4718 (OUTLIER) cc_final: 0.4359 (t-90) REVERT: 6 90 ASN cc_start: 0.7754 (OUTLIER) cc_final: 0.7462 (p0) REVERT: C 406 TYR cc_start: 0.6763 (m-80) cc_final: 0.6184 (m-80) REVERT: C 425 HIS cc_start: 0.5662 (OUTLIER) cc_final: 0.5158 (p-80) REVERT: D 147 ASP cc_start: 0.7088 (m-30) cc_final: 0.6565 (t70) REVERT: D 245 LYS cc_start: 0.6709 (mtpt) cc_final: 0.6124 (mmtt) outliers start: 83 outliers final: 57 residues processed: 360 average time/residue: 1.2312 time to fit residues: 531.5109 Evaluate side-chains 349 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 282 time to evaluate : 3.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 560 LEU Chi-restraints excluded: chain 1 residue 695 VAL Chi-restraints excluded: chain 1 residue 795 CYS Chi-restraints excluded: chain 1 residue 798 THR Chi-restraints excluded: chain 1 residue 801 VAL Chi-restraints excluded: chain 1 residue 832 GLN Chi-restraints excluded: chain 1 residue 962 MET Chi-restraints excluded: chain 1 residue 1003 VAL Chi-restraints excluded: chain 1 residue 1014 LYS Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1059 CYS Chi-restraints excluded: chain 1 residue 1092 ASP Chi-restraints excluded: chain 1 residue 1207 SER Chi-restraints excluded: chain 1 residue 1222 THR Chi-restraints excluded: chain 1 residue 1292 LYS Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 502 ARG Chi-restraints excluded: chain 2 residue 572 HIS Chi-restraints excluded: chain 2 residue 586 ILE Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 55 THR Chi-restraints excluded: chain 3 residue 79 VAL Chi-restraints excluded: chain 3 residue 136 GLU Chi-restraints excluded: chain 3 residue 187 MET Chi-restraints excluded: chain 3 residue 197 THR Chi-restraints excluded: chain 3 residue 221 VAL Chi-restraints excluded: chain 3 residue 246 SER Chi-restraints excluded: chain 3 residue 257 THR Chi-restraints excluded: chain 3 residue 266 ASP Chi-restraints excluded: chain 3 residue 331 ASP Chi-restraints excluded: chain 3 residue 398 VAL Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 484 VAL Chi-restraints excluded: chain 3 residue 531 LYS Chi-restraints excluded: chain 3 residue 546 LYS Chi-restraints excluded: chain 3 residue 595 VAL Chi-restraints excluded: chain 3 residue 629 SER Chi-restraints excluded: chain 3 residue 755 VAL Chi-restraints excluded: chain 3 residue 824 VAL Chi-restraints excluded: chain 3 residue 890 SER Chi-restraints excluded: chain 3 residue 897 SER Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 1008 SER Chi-restraints excluded: chain 3 residue 1017 ASN Chi-restraints excluded: chain 3 residue 1103 SER Chi-restraints excluded: chain 3 residue 1116 SER Chi-restraints excluded: chain 3 residue 1121 THR Chi-restraints excluded: chain 3 residue 1170 VAL Chi-restraints excluded: chain 3 residue 1196 GLU Chi-restraints excluded: chain 3 residue 1198 ASP Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain 5 residue 8 HIS Chi-restraints excluded: chain 5 residue 19 ILE Chi-restraints excluded: chain 6 residue 90 ASN Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 398 LYS Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 403 ASN Chi-restraints excluded: chain C residue 417 ARG Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 154 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 269 optimal weight: 5.9990 chunk 361 optimal weight: 10.0000 chunk 104 optimal weight: 0.0050 chunk 313 optimal weight: 20.0000 chunk 50 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 340 optimal weight: 8.9990 chunk 142 optimal weight: 7.9990 chunk 349 optimal weight: 40.0000 chunk 43 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 overall best weight: 3.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 31061 ASN 31192 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.252748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.187880 restraints weight = 35212.436| |-----------------------------------------------------------------------------| r_work (start): 0.4128 rms_B_bonded: 2.38 r_work: 0.3458 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 31059 Z= 0.376 Angle : 0.666 11.228 42148 Z= 0.338 Chirality : 0.047 0.356 3945 Planarity : 0.005 0.068 5471 Dihedral : 14.715 155.182 6800 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.02 % Favored : 94.94 % Rotamer: Outliers : 3.93 % Allowed : 28.22 % Favored : 67.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.15 (0.13), residues: 4127 helix: 1.28 (0.14), residues: 1417 sheet: -0.09 (0.18), residues: 882 loop : -1.21 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP 2 504 HIS 0.012 0.002 HIS 11256 PHE 0.020 0.003 PHE 11155 TYR 0.021 0.002 TYR 3 189 ARG 0.009 0.001 ARG 1 495 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11413.41 seconds wall clock time: 203 minutes 18.65 seconds (12198.65 seconds total)