Starting phenix.real_space_refine on Wed Feb 21 23:20:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evo_31334/02_2024/7evo_31334_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evo_31334/02_2024/7evo_31334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evo_31334/02_2024/7evo_31334.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evo_31334/02_2024/7evo_31334.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evo_31334/02_2024/7evo_31334_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evo_31334/02_2024/7evo_31334_neut_updated.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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 115 5.16 5 C 18779 2.51 5 N 6144 2.21 5 O 6916 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 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 GLU 890": "OE1" <-> "OE2" 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 GLU 157": "OE1" <-> "OE2" Residue "E ARG 161": "NH1" <-> "NH2" Residue "E ASP 205": "OD1" <-> "OD2" Residue "E ASP 209": "OD1" <-> "OD2" Residue "E TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 234": "OE1" <-> "OE2" Residue "E PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 32104 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: 539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 539 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 3, 'TRANS': 62} 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: 1308 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 200, 1292 Classifications: {'peptide': 200} Incomplete info: {'backbone_only': 75, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 191} Chain breaks: 2 Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 526 Unresolved non-hydrogen dihedrals: 247 Unresolved non-hydrogen chiralities: 96 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 6, 'GLU:plan': 6, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 216 Conformer: "B" Number of residues, atoms: 200, 1292 Classifications: {'peptide': 200} Incomplete info: {'backbone_only': 75, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 191} Chain breaks: 2 Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 526 Unresolved non-hydrogen dihedrals: 247 Unresolved non-hydrogen chiralities: 96 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 6, 'GLU:plan': 6, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 216 bond proxies already assigned to first conformer: 1294 Conformer: "C" Number of residues, atoms: 198, 1284 Classifications: {'peptide': 198} Incomplete info: {'backbone_only': 73, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 189} Chain breaks: 4 Unresolved non-hydrogen bonds: 364 Unresolved non-hydrogen angles: 517 Unresolved non-hydrogen dihedrals: 244 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 6, 'GLU:plan': 6, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 212 bond proxies already assigned to first conformer: 1294 Chain: "E" Number of atoms: 2153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 2153 Classifications: {'peptide': 455} Incomplete info: {'backbone_only': 345} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 437} Chain breaks: 3 Unresolved non-hydrogen bonds: 1473 Unresolved non-hydrogen angles: 2114 Unresolved non-hydrogen dihedrals: 915 Unresolved non-hydrogen chiralities: 464 Planarities with less than four sites: {'GLN:plan1': 15, 'ASP:plan': 20, 'TYR:plan': 12, 'ASN:plan1': 10, 'TRP:plan': 1, 'HIS:plan': 8, 'PHE:plan': 12, 'GLU:plan': 25, 'ARG:plan': 26} Unresolved non-hydrogen planarities: 648 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 21417 SG CYS 6 23 102.176 109.505 166.727 1.00 30.04 S ATOM 21441 SG CYS 6 26 100.914 107.712 163.633 1.00 30.51 S ATOM 21688 SG CYS 6 58 103.665 106.007 165.658 1.00 30.08 S ATOM 21709 SG CYS 6 61 105.211 109.272 164.117 1.00 32.29 S ATOM 21330 SG CYS 6 11 113.591 95.594 160.895 1.00 25.68 S ATOM 21593 SG CYS 6 46 114.254 94.845 164.746 1.00 22.63 S ATOM 21616 SG CYS 6 49 113.117 98.173 164.109 1.00 35.44 S ATOM 21887 SG CYS 6 85 110.475 95.656 163.899 1.00 22.11 S ATOM 21468 SG CYS 6 30 96.744 96.911 161.289 1.00 19.69 S ATOM 21489 SG CYS 6 33 94.580 97.084 158.290 1.00 21.17 S ATOM 21784 SG CYS 6 72 93.485 94.690 160.756 1.00 15.15 S ATOM 21808 SG CYS 6 75 96.502 93.528 158.679 1.00 15.21 S ATOM 24277 SG CYS C 408 91.645 74.557 106.113 1.00 93.55 S Residues with excluded nonbonded symmetry interactions: 7 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 residue: pdb=" N AASN D 285 " occ=0.50 ... (6 atoms not shown) pdb=" O BASN D 285 " occ=0.50 residue: pdb=" N ASER D 296 " occ=0.43 ... (6 atoms not shown) pdb=" O BSER D 296 " occ=0.57 residue: pdb=" N ASER D 318 " occ=0.45 ... (10 atoms not shown) pdb=" O CSER D 318 " occ=0.41 Time building chain proxies: 18.58, per 1000 atoms: 0.58 Number of scatterers: 32104 At special positions: 0 Unit cell: (169.572, 178.268, 239.14, 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 115 16.00 P 146 15.00 O 6916 8.00 N 6144 7.00 C 18779 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.42 Conformation dependent library (CDL) restraints added in 7.2 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 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4936 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 143 helices and 51 sheets defined 33.3% alpha, 17.3% beta 33 base pairs and 80 stacking pairs defined. Time for finding SS restraints: 14.95 Creating SS restraints... Processing helix chain '1' and resid 492 through 505 removed outlier: 5.209A pdb=" N LEU 1 500 " --> pdb=" O LYS 1 496 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N LEU 1 501 " --> pdb=" O ILE 1 497 " (cutoff:3.500A) removed outlier: 4.996A 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 562 removed outlier: 3.544A pdb=" N LYS 1 562 " --> pdb=" O ARG 1 558 " (cutoff:3.500A) Processing helix chain '1' and resid 568 through 578 removed outlier: 5.381A 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: 7.623A 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: 5.085A 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: 5.833A pdb=" N SER 1 685 " --> pdb=" O PRO 1 681 " (cutoff:3.500A) removed outlier: 5.109A 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: 4.709A pdb=" N LEU 1 694 " --> pdb=" O ILE 1 690 " (cutoff:3.500A) removed outlier: 5.074A 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: 3.653A pdb=" N GLU 1 768 " --> pdb=" O TYR 1 764 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLN 1 778 " --> pdb=" O ILE 1 774 " (cutoff:3.500A) Processing helix chain '1' and resid 782 through 797 removed outlier: 3.516A 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: 3.833A pdb=" N LYS 1 843 " --> pdb=" O GLU 1 839 " (cutoff:3.500A) Processing helix chain '1' and resid 846 through 856 removed outlier: 4.872A 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: 6.515A pdb=" N LYS 1 923 " --> pdb=" O ASN 1 919 " (cutoff:3.500A) removed outlier: 6.938A 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: 3.588A pdb=" N GLN 1 950 " --> pdb=" O LYS 1 946 " (cutoff:3.500A) removed outlier: 5.574A 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: 4.707A 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: 4.315A pdb=" N LEU 11065 " --> pdb=" O GLU 11061 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU 11066 " --> pdb=" O LEU 11062 " (cutoff:3.500A) removed outlier: 4.996A 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: 4.324A 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: 4.631A pdb=" N GLY 11162 " --> pdb=" O ILE 11158 " (cutoff:3.500A) removed outlier: 4.819A 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: 3.612A 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: 4.027A 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: 3.723A 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: 3.957A pdb=" N GLN 31181 " --> pdb=" O ASP 31177 " (cutoff:3.500A) removed outlier: 4.243A 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: 3.643A 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: 3.645A pdb=" N TYR 31215 " --> pdb=" O ILE 31211 " (cutoff:3.500A) Processing helix chain '4' and resid 26 through 32 removed outlier: 3.700A 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 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: 3.542A 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 426 removed outlier: 3.667A 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) 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: 4.415A pdb=" N PHE D 156 " --> pdb=" O LEU D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 201 removed outlier: 3.537A 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 'D' and resid 283 through 296 Processing helix chain 'D' and resid 322 through 332 Processing helix chain 'E' and resid 153 through 177 Processing helix chain 'E' and resid 227 through 242 Processing helix chain 'E' and resid 352 through 357 removed outlier: 3.664A pdb=" N GLU E 356 " --> pdb=" O VAL E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 376 No H-bonds generated for 'chain 'E' and resid 374 through 376' Processing helix chain 'E' and resid 381 through 390 Processing helix chain 'E' and resid 397 through 407 Proline residue: E 404 - end of helix Processing helix chain 'E' and resid 422 through 436 Proline residue: E 429 - end of helix Processing helix chain 'E' and resid 455 through 468 Processing helix chain 'E' and resid 485 through 493 Processing helix chain 'E' and resid 503 through 511 Processing helix chain 'E' and resid 531 through 534 No H-bonds generated for 'chain 'E' and resid 531 through 534' Processing helix chain 'E' and resid 540 through 548 Processing helix chain 'E' and resid 565 through 571 Processing helix chain 'E' and resid 604 through 614 Processing helix chain 'E' and resid 629 through 641 Processing helix chain 'E' and resid 655 through 667 Processing helix chain 'E' and resid 700 through 708 Processing helix chain 'E' and resid 731 through 741 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: 4.493A 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: 3.979A 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: 4.227A 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: 6.863A 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: 8.452A pdb=" N GLU 31115 " --> pdb=" O PRO 31131 " (cutoff:3.500A) removed outlier: 3.745A 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: 3.593A pdb=" N LEU 3 54 " --> pdb=" O LEU 3 40 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG 3 42 " --> pdb=" O THR 3 52 " (cutoff:3.500A) removed outlier: 5.755A 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: 6.689A pdb=" N VAL 3 79 " --> pdb=" O LEU 3 65 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA 3 67 " --> pdb=" O TYR 3 77 " (cutoff:3.500A) removed outlier: 6.535A 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: 6.080A 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: 4.819A pdb=" N GLY 3 172 " --> pdb=" O MET 3 181 " (cutoff:3.500A) removed outlier: 7.247A 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: 6.582A pdb=" N GLU 3 212 " --> pdb=" O ARG 3 222 " (cutoff:3.500A) removed outlier: 5.553A 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: 6.130A 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: 4.235A pdb=" N SER 3 290 " --> pdb=" O LEU 3 302 " (cutoff:3.500A) removed outlier: 6.472A 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: 7.152A 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: 5.378A pdb=" N LEU 3 315 " --> pdb=" O PHE 3 299 " (cutoff:3.500A) removed outlier: 4.386A 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: 7.258A pdb=" N THR 3 314 " --> pdb=" O LEU 3 327 " (cutoff:3.500A) removed outlier: 5.604A 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: 4.594A 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: 6.630A 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: 5.749A 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: 4.332A pdb=" N LYS 3 546 " --> pdb=" O ALA 3 557 " (cutoff:3.500A) removed outlier: 3.774A 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: 6.846A pdb=" N ALA 3 606 " --> pdb=" O MET 3 590 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU 3 609 " --> pdb=" O THR 3 613 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N THR 3 613 " --> pdb=" O LEU 3 609 " (cutoff:3.500A) removed outlier: 3.677A 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: 3.667A 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: 6.031A pdb=" N ALA 3 766 " --> pdb=" O GLU 3 446 " (cutoff:3.500A) removed outlier: 5.195A 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: 7.111A 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: 6.605A pdb=" N GLY 3 908 " --> pdb=" O PHE 3 889 " (cutoff:3.500A) removed outlier: 4.110A 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: 4.272A 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: 3.857A 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: 6.775A pdb=" N GLY 3 962 " --> pdb=" O ALA 3 950 " (cutoff:3.500A) removed outlier: 4.325A 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: 6.722A 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: 6.370A 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: 6.539A 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: 4.688A 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: 3.704A pdb=" N ALA 31025 " --> pdb=" O TRP 31011 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ARG 31013 " --> pdb=" O ILE 31023 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ILE 31023 " --> pdb=" O ARG 31013 " (cutoff:3.500A) removed outlier: 7.194A 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: 3.529A 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: 6.227A 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: 4.005A 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: 4.030A 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: 3.619A 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: 8.104A 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: 7.380A pdb=" N LYS D 171 " --> pdb=" O ASP D 183 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'D' and resid 343 through 346 Processing sheet with id= AG, first strand: chain 'E' and resid 579 through 581 Processing sheet with id= AH, first strand: chain 'E' and resid 593 through 599 removed outlier: 6.658A pdb=" N GLY E 717 " --> pdb=" O GLU E 594 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N GLN E 596 " --> pdb=" O GLY E 717 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA E 719 " --> pdb=" O GLN E 596 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ILE E 598 " --> pdb=" O ALA E 719 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR E 721 " --> pdb=" O ILE E 598 " (cutoff:3.500A) Processing sheet with id= AI, 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: 7.288A pdb=" N ALA F 46 " --> pdb=" O LEU F 24 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N THR F 68 " --> pdb=" O ILE F 47 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLU F 92 " --> pdb=" O LEU F 69 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N TYR F 117 " --> pdb=" O LEU F 93 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'G' and resid 83 through 86 Processing sheet with id= AK, 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= AL, first strand: chain 'a' and resid 90 through 96 Processing sheet with id= AM, first strand: chain 'a' and resid 98 through 101 removed outlier: 6.683A 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= AN, first strand: chain 'b' and resid 57 through 60 removed outlier: 3.801A pdb=" N GLY b 57 " --> pdb=" O GLU b 49 " (cutoff:3.500A) removed outlier: 5.884A 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= AO, 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: 5.910A pdb=" N LEU b 33 " --> pdb=" O ALA b 45 " (cutoff:3.500A) Processing sheet with id= AP, 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: 6.604A 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: 4.417A pdb=" N LEU c 35 " --> pdb=" O MET c 41 " (cutoff:3.500A) removed outlier: 7.734A 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: 6.407A pdb=" N GLU c 63 " --> pdb=" O GLN c 73 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N GLN c 73 " --> pdb=" O GLU c 63 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N HIS c 65 " --> pdb=" O ARG c 71 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ARG c 71 " --> pdb=" O HIS c 65 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'c' and resid 56 through 58 Processing sheet with id= AR, first strand: chain 'd' and resid 54 through 58 removed outlier: 5.859A pdb=" N CYS d 45 " --> pdb=" O ILE d 57 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N HIS d 26 " --> pdb=" O MET d 48 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N MET d 69 " --> pdb=" O LYS d 20 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'd' and resid 40 through 42 Processing sheet with id= AT, 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= AU, 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: 6.433A pdb=" N LEU e 32 " --> pdb=" O SER e 44 " (cutoff:3.500A) Processing sheet with id= AV, 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: 6.130A 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= AW, first strand: chain 'f' and resid 40 through 42 Processing sheet with id= AX, first strand: chain 'g' and resid 53 through 55 removed outlier: 3.940A pdb=" N GLU g 13 " --> pdb=" O ILE g 29 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'g' and resid 57 through 60 removed outlier: 6.712A pdb=" N LYS g 41 " --> pdb=" O ILE g 29 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ILE g 29 " --> pdb=" O LYS g 41 " (cutoff:3.500A) 1385 hydrogen bonds defined for protein. 3921 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: 15.84 Time building geometry restraints manager: 14.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6688 1.33 - 1.45: 8396 1.45 - 1.57: 17395 1.57 - 1.69: 288 1.69 - 1.81: 177 Bond restraints: 32944 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 5.21e+01 bond pdb=" C16 9B0 11500 " pdb=" C17 9B0 11500 " ideal model delta sigma weight residual 1.450 1.317 0.133 2.00e-02 2.50e+03 4.39e+01 bond pdb=" O3' C H 45 " pdb=" P U H 46 " ideal model delta sigma weight residual 1.607 1.521 0.086 1.50e-02 4.44e+03 3.26e+01 bond pdb=" N GLU D 252 " pdb=" CA GLU D 252 " ideal model delta sigma weight residual 1.457 1.488 -0.032 6.40e-03 2.44e+04 2.44e+01 bond pdb=" C ALA E 178 " pdb=" O ALA E 178 " ideal model delta sigma weight residual 1.231 1.326 -0.095 2.00e-02 2.50e+03 2.27e+01 ... (remaining 32939 not shown) Histogram of bond angle deviations from ideal: 59.47 - 74.77: 3 74.77 - 90.06: 0 90.06 - 105.36: 1402 105.36 - 120.65: 30179 120.65 - 135.95: 12943 Bond angle restraints: 44527 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 90.20 18.20 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 119.84 134.32 -14.48 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 113.00 127.69 -14.69 1.50e+00 4.44e-01 9.59e+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 98.99 13.01 1.50e+00 4.44e-01 7.52e+01 angle pdb=" C3' U H 27 " pdb=" C2' U H 27 " pdb=" C1' U H 27 " ideal model delta sigma weight residual 101.30 107.12 -5.82 1.00e+00 1.00e+00 3.38e+01 ... (remaining 44522 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.55: 16469 35.55 - 71.09: 819 71.09 - 106.64: 71 106.64 - 142.18: 14 142.18 - 177.73: 5 Dihedral angle restraints: 17378 sinusoidal: 7711 harmonic: 9667 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 45.27 154.73 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 -152.55 -27.45 0 5.00e+00 4.00e-02 3.01e+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 -153.11 -26.89 0 5.00e+00 4.00e-02 2.89e+01 ... (remaining 17375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 3906 0.136 - 0.271: 35 0.271 - 0.407: 4 0.407 - 0.543: 0 0.543 - 0.678: 1 Chirality restraints: 3946 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 1.15e+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 3.44e+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 3.04e+00 ... (remaining 3943 not shown) Planarity restraints: 5945 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U H 43 " -0.025 2.00e-02 2.50e+03 9.03e-02 1.83e+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 " 0.054 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 " 0.127 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 9B0 11500 " -0.109 2.00e-02 2.50e+03 1.06e-01 1.11e+02 pdb=" C11 9B0 11500 " 0.106 2.00e-02 2.50e+03 pdb=" C8 9B0 11500 " 0.105 2.00e-02 2.50e+03 pdb=" C9 9B0 11500 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 393 " -0.045 2.00e-02 2.50e+03 8.99e-02 8.09e+01 pdb=" C PRO C 393 " 0.155 2.00e-02 2.50e+03 pdb=" O PRO C 393 " -0.060 2.00e-02 2.50e+03 pdb=" N TYR C 394 " -0.051 2.00e-02 2.50e+03 ... (remaining 5942 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 223 2.62 - 3.19: 25471 3.19 - 3.76: 46671 3.76 - 4.33: 63463 4.33 - 4.90: 99750 Nonbonded interactions: 235578 Sorted by model distance: nonbonded pdb=" OD1 ASP E 226 " pdb=" CD PRO E 227 " model vdw 2.045 3.440 nonbonded pdb=" O LEU C 402 " pdb=" ND2 ASN C 403 " model vdw 2.165 2.520 nonbonded pdb=" O LYS 3 343 " pdb=" OG1 THR 3 344 " model vdw 2.175 2.440 nonbonded pdb=" OD1 ASP 6 27 " pdb=" OG SER 6 67 " model vdw 2.198 2.440 nonbonded pdb=" OD1 ASN 31183 " pdb=" OG SER 31205 " model vdw 2.217 2.440 ... (remaining 235573 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: 1.390 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: 9.090 Check model and map are aligned: 0.600 Set scattering table: 0.430 Process input model: 106.410 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.150 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: 0.020 Load rotamer database and sin/cos tables:12.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6066 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 32944 Z= 0.280 Angle : 0.774 18.198 44527 Z= 0.475 Chirality : 0.049 0.678 3946 Planarity : 0.006 0.106 5945 Dihedral : 18.396 177.728 12442 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.45 % Favored : 96.47 % Rotamer: Outliers : 5.50 % Allowed : 21.66 % Favored : 72.83 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.02 % 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: -3.06 (0.10), residues: 4597 helix: -2.04 (0.10), residues: 1618 sheet: -1.07 (0.16), residues: 999 loop : -2.43 (0.11), residues: 1980 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 0.018 0.001 ARG E 166 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 4095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 423 time to evaluate : 3.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 558 ARG cc_start: 0.7132 (mmp80) cc_final: 0.6756 (mmt90) REVERT: 1 655 LYS cc_start: 0.7741 (mmpt) cc_final: 0.7524 (mptt) REVERT: 1 835 ASP cc_start: 0.7521 (m-30) cc_final: 0.7318 (m-30) REVERT: 1 883 ASP cc_start: 0.5846 (p0) cc_final: 0.5156 (t0) REVERT: 1 890 GLU cc_start: 0.6954 (tt0) cc_final: 0.6669 (tp30) REVERT: 1 926 LYS cc_start: 0.6793 (OUTLIER) cc_final: 0.6411 (mmmm) REVERT: 1 929 LEU cc_start: 0.7498 (mt) cc_final: 0.7254 (tt) REVERT: 1 962 MET cc_start: 0.6448 (OUTLIER) cc_final: 0.6073 (ttm) REVERT: 1 967 GLU cc_start: 0.4676 (OUTLIER) cc_final: 0.4202 (tp30) REVERT: 1 1037 ASP cc_start: 0.7941 (m-30) cc_final: 0.7521 (m-30) REVERT: 1 1053 ARG cc_start: 0.6926 (OUTLIER) cc_final: 0.6713 (ttt180) REVERT: 1 1056 MET cc_start: 0.8357 (mmm) cc_final: 0.8078 (mmm) REVERT: 1 1160 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.7002 (tt0) REVERT: 1 1161 MET cc_start: 0.8315 (ttm) cc_final: 0.7827 (mtp) REVERT: 3 114 ARG cc_start: 0.9157 (OUTLIER) cc_final: 0.8634 (ttp-170) REVERT: 3 191 GLU cc_start: 0.7116 (pm20) cc_final: 0.6705 (pt0) REVERT: 3 316 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7634 (tp30) REVERT: 3 326 ARG cc_start: 0.8641 (mtt180) cc_final: 0.8159 (mtt180) REVERT: 3 377 MET cc_start: 0.8437 (mtt) cc_final: 0.7966 (mtp) REVERT: 3 573 GLN cc_start: 0.2320 (OUTLIER) cc_final: 0.1860 (mm-40) REVERT: 3 583 MET cc_start: 0.2905 (mtm) cc_final: 0.2205 (tmm) REVERT: 3 630 MET cc_start: 0.3854 (ttm) cc_final: 0.3177 (tpp) REVERT: 3 1143 HIS cc_start: 0.7826 (m90) cc_final: 0.7363 (t-90) REVERT: 3 1188 ASN cc_start: 0.6987 (p0) cc_final: 0.6656 (p0) REVERT: 3 1189 LYS cc_start: 0.8053 (mttm) cc_final: 0.7810 (mmtt) REVERT: C 403 ASN cc_start: 0.7206 (p0) cc_final: 0.6841 (p0) REVERT: C 414 TYR cc_start: 0.7080 (t80) cc_final: 0.6799 (t80) REVERT: D 202 ASP cc_start: 0.7369 (t0) cc_final: 0.7010 (t70) REVERT: D 203 GLU cc_start: 0.6971 (mt-10) cc_final: 0.6497 (mt-10) REVERT: D 204 ASP cc_start: 0.7154 (t70) cc_final: 0.6870 (t70) REVERT: D 242 MET cc_start: 0.6155 (mmm) cc_final: 0.5797 (tmm) REVERT: E 205 ASP cc_start: 0.4762 (t0) cc_final: 0.4261 (p0) outliers start: 125 outliers final: 46 residues processed: 530 average time/residue: 1.4365 time to fit residues: 900.9209 Evaluate side-chains 403 residues out of total 4095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 349 time to evaluate : 3.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 576 VAL Chi-restraints excluded: chain 1 residue 705 SER 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 1 residue 926 LYS Chi-restraints excluded: chain 1 residue 956 SER Chi-restraints excluded: chain 1 residue 962 MET Chi-restraints excluded: chain 1 residue 967 GLU Chi-restraints excluded: chain 1 residue 1053 ARG Chi-restraints excluded: chain 1 residue 1160 GLU Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 3 residue 55 THR Chi-restraints excluded: chain 3 residue 64 SER Chi-restraints excluded: chain 3 residue 114 ARG Chi-restraints excluded: chain 3 residue 316 GLU Chi-restraints excluded: chain 3 residue 351 SER Chi-restraints excluded: chain 3 residue 390 ARG Chi-restraints excluded: chain 3 residue 420 THR Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 459 VAL Chi-restraints excluded: chain 3 residue 462 VAL Chi-restraints excluded: chain 3 residue 476 VAL Chi-restraints excluded: chain 3 residue 490 THR Chi-restraints excluded: chain 3 residue 524 ILE Chi-restraints excluded: chain 3 residue 533 VAL Chi-restraints excluded: chain 3 residue 534 ASN Chi-restraints excluded: chain 3 residue 546 LYS Chi-restraints excluded: chain 3 residue 558 LEU Chi-restraints excluded: chain 3 residue 573 GLN Chi-restraints excluded: chain 3 residue 591 SER Chi-restraints excluded: chain 3 residue 629 SER 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 738 THR Chi-restraints excluded: chain 3 residue 755 VAL Chi-restraints excluded: chain 3 residue 865 VAL Chi-restraints excluded: chain 3 residue 890 SER Chi-restraints excluded: chain 3 residue 1008 SER Chi-restraints excluded: chain 3 residue 1065 GLU Chi-restraints excluded: chain 3 residue 1120 THR Chi-restraints excluded: chain 3 residue 1121 THR Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 398 LYS Chi-restraints excluded: chain C residue 472 GLN Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 239 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 401 optimal weight: 50.0000 chunk 360 optimal weight: 0.4980 chunk 199 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 242 optimal weight: 8.9990 chunk 192 optimal weight: 3.9990 chunk 372 optimal weight: 8.9990 chunk 144 optimal weight: 5.9990 chunk 226 optimal weight: 4.9990 chunk 277 optimal weight: 4.9990 chunk 431 optimal weight: 9.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 804 ASN ** 1 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11007 HIS 11032 GLN 11107 GLN 11144 GLN 11194 HIS 11252 GLN 11256 HIS 11293 ASN 2 458 ASN 2 467 GLN 2 490 HIS 3 27 GLN 3 46 ASN ** 3 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 219 HIS 3 264 GLN 3 363 HIS 3 480 ASN 3 575 ASN 3 594 ASN 3 612 ASN ** 3 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 776 GLN 3 796 ASN 3 805 ASN 3 844 ASN 3 846 ASN 3 870 ASN 3 916 ASN 3 941 HIS 3 983 ASN 31017 ASN 31052 ASN C 400 HIS D 179 ASN ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6162 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 32944 Z= 0.342 Angle : 0.689 13.103 44527 Z= 0.356 Chirality : 0.048 0.218 3946 Planarity : 0.005 0.068 5945 Dihedral : 15.487 158.752 7343 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.34 % Favored : 95.62 % Rotamer: Outliers : 8.32 % Allowed : 21.80 % Favored : 69.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.11), residues: 4597 helix: -0.36 (0.12), residues: 1627 sheet: -0.60 (0.16), residues: 1012 loop : -1.98 (0.12), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP 3 903 HIS 0.010 0.002 HIS C 425 PHE 0.021 0.003 PHE 2 575 TYR 0.022 0.003 TYR 3 926 ARG 0.007 0.001 ARG 3 34 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 4095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 356 time to evaluate : 3.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 503 LYS cc_start: 0.5826 (tttp) cc_final: 0.5243 (mmtp) REVERT: 1 558 ARG cc_start: 0.7131 (mmp80) cc_final: 0.6720 (mmt90) REVERT: 1 564 ASP cc_start: 0.7107 (m-30) cc_final: 0.6872 (m-30) REVERT: 1 566 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7220 (mp) REVERT: 1 655 LYS cc_start: 0.7900 (mmpt) cc_final: 0.7630 (mptt) REVERT: 1 656 LYS cc_start: 0.7203 (mmtp) cc_final: 0.6755 (mmtt) REVERT: 1 839 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6879 (mp0) REVERT: 1 883 ASP cc_start: 0.6207 (p0) cc_final: 0.5661 (t0) REVERT: 1 926 LYS cc_start: 0.7019 (OUTLIER) cc_final: 0.6585 (mmmm) REVERT: 1 957 ARG cc_start: 0.7478 (ttm110) cc_final: 0.7000 (mtm-85) REVERT: 1 961 VAL cc_start: 0.8273 (t) cc_final: 0.8029 (p) REVERT: 1 962 MET cc_start: 0.6654 (mtp) cc_final: 0.6410 (ttm) REVERT: 1 967 GLU cc_start: 0.4978 (OUTLIER) cc_final: 0.4274 (tp30) REVERT: 1 1037 ASP cc_start: 0.7935 (m-30) cc_final: 0.7505 (m-30) REVERT: 1 1056 MET cc_start: 0.8519 (mmm) cc_final: 0.8207 (mmm) REVERT: 1 1135 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7236 (tt0) REVERT: 1 1160 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6976 (tt0) REVERT: 1 1235 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7431 (mm-30) REVERT: 2 502 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.6095 (ttp-170) REVERT: 2 572 HIS cc_start: 0.5110 (OUTLIER) cc_final: 0.4040 (t70) REVERT: 3 151 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7026 (mtt-85) REVERT: 3 178 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7195 (mp0) REVERT: 3 273 ARG cc_start: 0.9102 (OUTLIER) cc_final: 0.8831 (mmm160) REVERT: 3 316 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7761 (tp30) REVERT: 3 326 ARG cc_start: 0.8656 (mtt180) cc_final: 0.8175 (mtt180) REVERT: 3 377 MET cc_start: 0.8511 (mtt) cc_final: 0.7981 (mtp) REVERT: 3 447 MET cc_start: 0.1060 (ttt) cc_final: -0.2039 (mmm) REVERT: 3 571 SER cc_start: 0.3090 (OUTLIER) cc_final: 0.2777 (p) REVERT: 3 573 GLN cc_start: 0.2311 (OUTLIER) cc_final: 0.1992 (mm-40) REVERT: 3 574 LEU cc_start: 0.2008 (OUTLIER) cc_final: 0.0970 (pt) REVERT: 3 583 MET cc_start: 0.2787 (mtm) cc_final: 0.2128 (tmm) REVERT: 3 630 MET cc_start: 0.3593 (ttm) cc_final: 0.2912 (tpp) REVERT: 3 715 MET cc_start: 0.6859 (OUTLIER) cc_final: 0.6510 (mmm) REVERT: 3 809 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.6852 (mp0) REVERT: 3 873 GLN cc_start: 0.7443 (OUTLIER) cc_final: 0.6910 (mm-40) REVERT: 3 1048 ASP cc_start: 0.7497 (OUTLIER) cc_final: 0.7197 (t70) REVERT: 3 1143 HIS cc_start: 0.7806 (m90) cc_final: 0.7192 (t-170) REVERT: 3 1188 ASN cc_start: 0.7200 (p0) cc_final: 0.6798 (p0) REVERT: 6 25 LYS cc_start: 0.8135 (ttpt) cc_final: 0.7307 (pttm) REVERT: C 424 ARG cc_start: 0.7202 (mtm180) cc_final: 0.6724 (ptp-110) REVERT: D 143 ASP cc_start: 0.4730 (OUTLIER) cc_final: 0.3975 (p0) REVERT: D 189 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8512 (tp) REVERT: D 202 ASP cc_start: 0.7599 (t0) cc_final: 0.7168 (t70) REVERT: D 203 GLU cc_start: 0.7169 (mt-10) cc_final: 0.6574 (mt-10) REVERT: D 204 ASP cc_start: 0.7414 (t70) cc_final: 0.7088 (t70) REVERT: D 247 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7682 (mt) REVERT: E 196 LYS cc_start: 0.4068 (OUTLIER) cc_final: 0.3485 (mmmt) REVERT: E 205 ASP cc_start: 0.4631 (t0) cc_final: 0.3969 (p0) outliers start: 189 outliers final: 87 residues processed: 506 average time/residue: 1.3102 time to fit residues: 792.7592 Evaluate side-chains 461 residues out of total 4095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 350 time to evaluate : 3.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 566 LEU Chi-restraints excluded: chain 1 residue 576 VAL Chi-restraints excluded: chain 1 residue 585 GLU Chi-restraints excluded: chain 1 residue 602 LYS Chi-restraints excluded: chain 1 residue 612 THR Chi-restraints excluded: chain 1 residue 617 ILE Chi-restraints excluded: chain 1 residue 735 ILE Chi-restraints excluded: chain 1 residue 768 GLU Chi-restraints excluded: chain 1 residue 781 ASP Chi-restraints excluded: chain 1 residue 798 THR Chi-restraints excluded: chain 1 residue 801 VAL Chi-restraints excluded: chain 1 residue 839 GLU Chi-restraints excluded: chain 1 residue 908 SER Chi-restraints excluded: chain 1 residue 926 LYS Chi-restraints excluded: chain 1 residue 967 GLU Chi-restraints excluded: chain 1 residue 1007 HIS Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1063 LEU Chi-restraints excluded: chain 1 residue 1113 THR Chi-restraints excluded: chain 1 residue 1123 CYS Chi-restraints excluded: chain 1 residue 1126 PHE Chi-restraints excluded: chain 1 residue 1135 GLU Chi-restraints excluded: chain 1 residue 1160 GLU Chi-restraints excluded: chain 1 residue 1207 SER Chi-restraints excluded: chain 1 residue 1235 GLU Chi-restraints excluded: chain 2 residue 476 GLU 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 706 THR Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 55 THR Chi-restraints excluded: chain 3 residue 64 SER Chi-restraints excluded: chain 3 residue 128 ARG Chi-restraints excluded: chain 3 residue 146 ARG Chi-restraints excluded: chain 3 residue 151 ARG Chi-restraints excluded: chain 3 residue 156 SER Chi-restraints excluded: chain 3 residue 178 GLU Chi-restraints excluded: chain 3 residue 221 VAL Chi-restraints excluded: chain 3 residue 242 SER Chi-restraints excluded: chain 3 residue 273 ARG Chi-restraints excluded: chain 3 residue 316 GLU Chi-restraints excluded: chain 3 residue 342 LEU Chi-restraints excluded: chain 3 residue 404 LEU Chi-restraints excluded: chain 3 residue 420 THR Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 433 SER Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 459 VAL Chi-restraints excluded: chain 3 residue 462 VAL Chi-restraints excluded: chain 3 residue 463 ARG Chi-restraints excluded: chain 3 residue 476 VAL Chi-restraints excluded: chain 3 residue 490 THR Chi-restraints excluded: chain 3 residue 524 ILE Chi-restraints excluded: chain 3 residue 533 VAL Chi-restraints excluded: chain 3 residue 549 VAL Chi-restraints excluded: chain 3 residue 571 SER Chi-restraints excluded: chain 3 residue 573 GLN Chi-restraints excluded: chain 3 residue 574 LEU Chi-restraints excluded: chain 3 residue 589 CYS Chi-restraints excluded: chain 3 residue 595 VAL Chi-restraints excluded: chain 3 residue 629 SER Chi-restraints excluded: chain 3 residue 639 SER Chi-restraints excluded: chain 3 residue 677 THR Chi-restraints excluded: chain 3 residue 689 THR Chi-restraints excluded: chain 3 residue 704 VAL Chi-restraints excluded: chain 3 residue 715 MET Chi-restraints excluded: chain 3 residue 738 THR Chi-restraints excluded: chain 3 residue 755 VAL Chi-restraints excluded: chain 3 residue 759 THR Chi-restraints excluded: chain 3 residue 809 GLU Chi-restraints excluded: chain 3 residue 821 GLU Chi-restraints excluded: chain 3 residue 838 MET Chi-restraints excluded: chain 3 residue 865 VAL Chi-restraints excluded: chain 3 residue 873 GLN Chi-restraints excluded: chain 3 residue 890 SER Chi-restraints excluded: chain 3 residue 919 SER Chi-restraints excluded: chain 3 residue 965 LYS Chi-restraints excluded: chain 3 residue 1008 SER Chi-restraints excluded: chain 3 residue 1038 LEU Chi-restraints excluded: chain 3 residue 1048 ASP Chi-restraints excluded: chain 3 residue 1065 GLU Chi-restraints excluded: chain 3 residue 1120 THR Chi-restraints excluded: chain 3 residue 1150 SER Chi-restraints excluded: chain 3 residue 1170 VAL Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain 5 residue 17 LYS 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 402 LEU Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 472 GLN Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 166 GLU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 237 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 239 optimal weight: 0.0370 chunk 133 optimal weight: 0.9980 chunk 359 optimal weight: 7.9990 chunk 293 optimal weight: 8.9990 chunk 118 optimal weight: 0.9990 chunk 432 optimal weight: 20.0000 chunk 466 optimal weight: 8.9990 chunk 384 optimal weight: 50.0000 chunk 428 optimal weight: 6.9990 chunk 147 optimal weight: 0.8980 chunk 346 optimal weight: 5.9990 overall best weight: 1.7862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 804 ASN 11007 HIS 11107 GLN 11209 ASN 2 458 ASN ** 3 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 219 HIS 3 363 HIS 3 796 ASN C 400 HIS ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6139 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32944 Z= 0.213 Angle : 0.575 12.063 44527 Z= 0.296 Chirality : 0.043 0.167 3946 Planarity : 0.005 0.072 5945 Dihedral : 14.688 158.895 7313 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.58 % Favored : 96.40 % Rotamer: Outliers : 6.87 % Allowed : 22.81 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.88 (0.12), residues: 4597 helix: 0.59 (0.13), residues: 1623 sheet: -0.33 (0.16), residues: 1000 loop : -1.71 (0.12), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 2 708 HIS 0.018 0.001 HIS 11007 PHE 0.024 0.002 PHE 2 575 TYR 0.021 0.002 TYR D 209 ARG 0.006 0.000 ARG 3 464 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 4095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 355 time to evaluate : 3.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 503 LYS cc_start: 0.5998 (tttp) cc_final: 0.5624 (mmtp) REVERT: 1 558 ARG cc_start: 0.7057 (mmp80) cc_final: 0.6569 (mmp80) REVERT: 1 564 ASP cc_start: 0.6862 (m-30) cc_final: 0.6571 (m-30) REVERT: 1 566 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.7089 (mp) REVERT: 1 592 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7288 (mt-10) REVERT: 1 656 LYS cc_start: 0.7096 (mmtp) cc_final: 0.6828 (mmtm) REVERT: 1 839 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6967 (tm-30) REVERT: 1 860 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7216 (mp0) REVERT: 1 883 ASP cc_start: 0.6019 (p0) cc_final: 0.5715 (t0) REVERT: 1 890 GLU cc_start: 0.6905 (tt0) cc_final: 0.6576 (tp30) REVERT: 1 926 LYS cc_start: 0.6872 (OUTLIER) cc_final: 0.6590 (mmmm) REVERT: 1 942 ASN cc_start: 0.6659 (t0) cc_final: 0.6044 (m-40) REVERT: 1 957 ARG cc_start: 0.7484 (ttm110) cc_final: 0.7195 (mtm-85) REVERT: 1 967 GLU cc_start: 0.4315 (OUTLIER) cc_final: 0.3798 (tp30) REVERT: 1 1037 ASP cc_start: 0.7902 (m-30) cc_final: 0.7487 (m-30) REVERT: 1 1056 MET cc_start: 0.8461 (mmm) cc_final: 0.8209 (mmm) REVERT: 1 1135 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7345 (tt0) REVERT: 1 1160 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7082 (tt0) REVERT: 1 1161 MET cc_start: 0.8358 (ttm) cc_final: 0.7774 (mtp) REVERT: 1 1246 MET cc_start: 0.8784 (mmm) cc_final: 0.8481 (mmm) REVERT: 2 502 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7486 (ptp-170) REVERT: 2 572 HIS cc_start: 0.5149 (OUTLIER) cc_final: 0.4129 (t70) REVERT: 3 151 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7065 (mtt-85) REVERT: 3 178 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7123 (mp0) REVERT: 3 316 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7743 (tp30) REVERT: 3 326 ARG cc_start: 0.8639 (mtt180) cc_final: 0.8143 (mtt180) REVERT: 3 377 MET cc_start: 0.8430 (mtt) cc_final: 0.7944 (mtp) REVERT: 3 447 MET cc_start: 0.0971 (ttt) cc_final: -0.1790 (mmp) REVERT: 3 475 ILE cc_start: 0.4345 (OUTLIER) cc_final: 0.4093 (pp) REVERT: 3 573 GLN cc_start: 0.2623 (OUTLIER) cc_final: 0.2129 (mm-40) REVERT: 3 583 MET cc_start: 0.2583 (mtm) cc_final: 0.2021 (tmm) REVERT: 3 749 GLN cc_start: 0.1555 (OUTLIER) cc_final: 0.0897 (mt0) REVERT: 3 809 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.6809 (mp0) REVERT: 3 1121 THR cc_start: 0.9122 (OUTLIER) cc_final: 0.8861 (m) REVERT: 3 1143 HIS cc_start: 0.7775 (m90) cc_final: 0.7270 (t-90) REVERT: 3 1188 ASN cc_start: 0.7194 (p0) cc_final: 0.6718 (p0) REVERT: 6 25 LYS cc_start: 0.8137 (ttpt) cc_final: 0.7267 (pttm) REVERT: 6 54 TYR cc_start: 0.8047 (m-10) cc_final: 0.7754 (m-80) REVERT: C 424 ARG cc_start: 0.7187 (mtm180) cc_final: 0.6747 (ptp-170) REVERT: C 470 ARG cc_start: 0.6663 (OUTLIER) cc_final: 0.5645 (mtt-85) REVERT: D 143 ASP cc_start: 0.5197 (OUTLIER) cc_final: 0.4347 (p0) REVERT: D 148 GLU cc_start: 0.5966 (OUTLIER) cc_final: 0.5580 (pp20) REVERT: D 153 MET cc_start: 0.8350 (mmm) cc_final: 0.7838 (mmp) REVERT: D 202 ASP cc_start: 0.7555 (t0) cc_final: 0.7263 (t70) REVERT: D 203 GLU cc_start: 0.7199 (mt-10) cc_final: 0.6783 (mt-10) REVERT: D 204 ASP cc_start: 0.7573 (t70) cc_final: 0.7299 (t70) REVERT: E 196 LYS cc_start: 0.3925 (OUTLIER) cc_final: 0.3434 (mmmt) REVERT: E 205 ASP cc_start: 0.4677 (t0) cc_final: 0.4018 (p0) REVERT: E 225 LEU cc_start: 0.2948 (OUTLIER) cc_final: 0.2726 (mt) outliers start: 156 outliers final: 78 residues processed: 476 average time/residue: 1.2941 time to fit residues: 738.8638 Evaluate side-chains 447 residues out of total 4095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 346 time to evaluate : 3.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 566 LEU Chi-restraints excluded: chain 1 residue 585 GLU Chi-restraints excluded: chain 1 residue 592 GLU Chi-restraints excluded: chain 1 residue 617 ILE Chi-restraints excluded: chain 1 residue 735 ILE Chi-restraints excluded: chain 1 residue 781 ASP Chi-restraints excluded: chain 1 residue 798 THR Chi-restraints excluded: chain 1 residue 801 VAL Chi-restraints excluded: chain 1 residue 839 GLU Chi-restraints excluded: chain 1 residue 860 GLU Chi-restraints excluded: chain 1 residue 908 SER Chi-restraints excluded: chain 1 residue 926 LYS Chi-restraints excluded: chain 1 residue 967 GLU Chi-restraints excluded: chain 1 residue 971 MET Chi-restraints excluded: chain 1 residue 997 LEU Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1059 CYS Chi-restraints excluded: chain 1 residue 1113 THR Chi-restraints excluded: chain 1 residue 1123 CYS Chi-restraints excluded: chain 1 residue 1126 PHE Chi-restraints excluded: chain 1 residue 1135 GLU Chi-restraints excluded: chain 1 residue 1160 GLU Chi-restraints excluded: chain 1 residue 1207 SER 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 706 THR Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 55 THR Chi-restraints excluded: chain 3 residue 64 SER Chi-restraints excluded: chain 3 residue 146 ARG Chi-restraints excluded: chain 3 residue 151 ARG Chi-restraints excluded: chain 3 residue 153 THR Chi-restraints excluded: chain 3 residue 156 SER Chi-restraints excluded: chain 3 residue 178 GLU Chi-restraints excluded: chain 3 residue 223 LYS Chi-restraints excluded: chain 3 residue 242 SER Chi-restraints excluded: chain 3 residue 278 LEU Chi-restraints excluded: chain 3 residue 316 GLU Chi-restraints excluded: chain 3 residue 318 ASP Chi-restraints excluded: chain 3 residue 342 LEU Chi-restraints excluded: chain 3 residue 404 LEU Chi-restraints excluded: chain 3 residue 420 THR Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 459 VAL Chi-restraints excluded: chain 3 residue 463 ARG Chi-restraints excluded: chain 3 residue 475 ILE Chi-restraints excluded: chain 3 residue 476 VAL Chi-restraints excluded: chain 3 residue 524 ILE Chi-restraints excluded: chain 3 residue 533 VAL Chi-restraints excluded: chain 3 residue 546 LYS Chi-restraints excluded: chain 3 residue 549 VAL Chi-restraints excluded: chain 3 residue 573 GLN Chi-restraints excluded: chain 3 residue 589 CYS Chi-restraints excluded: chain 3 residue 629 SER Chi-restraints excluded: chain 3 residue 639 SER Chi-restraints excluded: chain 3 residue 671 ASN Chi-restraints excluded: chain 3 residue 677 THR Chi-restraints excluded: chain 3 residue 689 THR Chi-restraints excluded: chain 3 residue 704 VAL Chi-restraints excluded: chain 3 residue 749 GLN Chi-restraints excluded: chain 3 residue 755 VAL Chi-restraints excluded: chain 3 residue 809 GLU Chi-restraints excluded: chain 3 residue 821 GLU Chi-restraints excluded: chain 3 residue 834 LEU Chi-restraints excluded: chain 3 residue 865 VAL Chi-restraints excluded: chain 3 residue 890 SER Chi-restraints excluded: chain 3 residue 965 LYS Chi-restraints excluded: chain 3 residue 1008 SER Chi-restraints excluded: chain 3 residue 1048 ASP Chi-restraints excluded: chain 3 residue 1065 GLU Chi-restraints excluded: chain 3 residue 1120 THR Chi-restraints excluded: chain 3 residue 1121 THR Chi-restraints excluded: chain 3 residue 1150 SER Chi-restraints excluded: chain 3 residue 1170 VAL Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain 5 residue 17 LYS 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 405 ASN Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 470 ARG Chi-restraints excluded: chain C residue 472 GLN Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 237 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 426 optimal weight: 20.0000 chunk 324 optimal weight: 7.9990 chunk 224 optimal weight: 0.5980 chunk 47 optimal weight: 9.9990 chunk 206 optimal weight: 5.9990 chunk 290 optimal weight: 0.0770 chunk 433 optimal weight: 50.0000 chunk 459 optimal weight: 8.9990 chunk 226 optimal weight: 0.0270 chunk 411 optimal weight: 30.0000 chunk 123 optimal weight: 0.9990 overall best weight: 1.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 534 GLN 1 804 ASN 1 973 HIS 11107 GLN 2 458 ASN ** 3 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 219 HIS 3 363 HIS ** 3 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 796 ASN C 400 HIS ** C 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6139 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32944 Z= 0.193 Angle : 0.558 12.023 44527 Z= 0.285 Chirality : 0.042 0.174 3946 Planarity : 0.004 0.068 5945 Dihedral : 14.502 157.523 7307 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.03 % Favored : 95.94 % Rotamer: Outliers : 7.05 % Allowed : 22.68 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 (0.12), residues: 4597 helix: 1.19 (0.13), residues: 1620 sheet: -0.14 (0.17), residues: 1003 loop : -1.49 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 1 938 HIS 0.008 0.001 HIS C 425 PHE 0.017 0.002 PHE 11153 TYR 0.017 0.002 TYR 3 926 ARG 0.007 0.000 ARG 1 739 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 4095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 367 time to evaluate : 3.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 558 ARG cc_start: 0.7019 (mmp80) cc_final: 0.6505 (mmp80) REVERT: 1 564 ASP cc_start: 0.7031 (m-30) cc_final: 0.6778 (m-30) REVERT: 1 656 LYS cc_start: 0.7112 (mmtp) cc_final: 0.6779 (mmtp) REVERT: 1 770 MET cc_start: 0.7963 (mmm) cc_final: 0.7556 (mmt) REVERT: 1 839 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.6999 (tm-30) REVERT: 1 860 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7199 (mp0) REVERT: 1 883 ASP cc_start: 0.6042 (p0) cc_final: 0.5817 (t0) REVERT: 1 890 GLU cc_start: 0.6917 (tt0) cc_final: 0.6598 (tp30) REVERT: 1 926 LYS cc_start: 0.6874 (OUTLIER) cc_final: 0.6590 (mmmm) REVERT: 1 942 ASN cc_start: 0.6621 (t0) cc_final: 0.6182 (m-40) REVERT: 1 957 ARG cc_start: 0.7513 (ttm110) cc_final: 0.6864 (mtp-110) REVERT: 1 967 GLU cc_start: 0.4439 (OUTLIER) cc_final: 0.3947 (tp30) REVERT: 1 1037 ASP cc_start: 0.7906 (m-30) cc_final: 0.7491 (m-30) REVERT: 1 1041 ARG cc_start: 0.7285 (mmm160) cc_final: 0.7000 (mmm160) REVERT: 1 1056 MET cc_start: 0.8428 (mmm) cc_final: 0.8139 (mmm) REVERT: 1 1135 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7340 (tt0) REVERT: 1 1160 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7056 (tt0) REVERT: 1 1161 MET cc_start: 0.8359 (ttm) cc_final: 0.7793 (mtp) REVERT: 1 1246 MET cc_start: 0.8834 (mmm) cc_final: 0.8559 (mmm) REVERT: 2 502 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7520 (ptp-170) REVERT: 2 572 HIS cc_start: 0.5195 (OUTLIER) cc_final: 0.4354 (t70) REVERT: 3 9 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.7841 (tt0) REVERT: 3 114 ARG cc_start: 0.9301 (OUTLIER) cc_final: 0.8949 (ttp-170) REVERT: 3 151 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7083 (mtt-85) REVERT: 3 178 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7206 (mp0) REVERT: 3 316 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7755 (tp30) REVERT: 3 326 ARG cc_start: 0.8637 (mtt180) cc_final: 0.8182 (mtt180) REVERT: 3 377 MET cc_start: 0.8415 (mtt) cc_final: 0.7947 (mtp) REVERT: 3 447 MET cc_start: 0.1406 (ttt) cc_final: -0.1486 (mmp) REVERT: 3 574 LEU cc_start: 0.2022 (OUTLIER) cc_final: 0.1137 (pt) REVERT: 3 583 MET cc_start: 0.2173 (mtm) cc_final: 0.1831 (tmm) REVERT: 3 630 MET cc_start: 0.3305 (ttm) cc_final: 0.2561 (mmm) REVERT: 3 749 GLN cc_start: 0.1388 (OUTLIER) cc_final: 0.0806 (mt0) REVERT: 3 770 LEU cc_start: 0.4782 (OUTLIER) cc_final: 0.4576 (tp) REVERT: 3 809 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.6797 (mp0) REVERT: 3 821 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6906 (mp0) REVERT: 3 1048 ASP cc_start: 0.7317 (OUTLIER) cc_final: 0.7087 (t70) REVERT: 3 1143 HIS cc_start: 0.7737 (m90) cc_final: 0.7268 (t-90) REVERT: 3 1188 ASN cc_start: 0.7333 (p0) cc_final: 0.6780 (p0) REVERT: 6 25 LYS cc_start: 0.8094 (ttpt) cc_final: 0.7270 (pttm) REVERT: C 417 ARG cc_start: 0.5769 (mmt90) cc_final: 0.5514 (mmt180) REVERT: C 424 ARG cc_start: 0.7169 (mtm180) cc_final: 0.6738 (ptp-170) REVERT: D 143 ASP cc_start: 0.5385 (p0) cc_final: 0.4569 (p0) REVERT: D 148 GLU cc_start: 0.5923 (OUTLIER) cc_final: 0.5540 (pp20) REVERT: D 191 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.6922 (tmt170) REVERT: D 202 ASP cc_start: 0.7531 (t0) cc_final: 0.7245 (t70) REVERT: D 203 GLU cc_start: 0.7192 (mt-10) cc_final: 0.6739 (mt-10) REVERT: D 204 ASP cc_start: 0.7336 (t70) cc_final: 0.7071 (t70) REVERT: D 247 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7504 (mt) REVERT: E 169 LYS cc_start: 0.7024 (mttt) cc_final: 0.6166 (ttpt) REVERT: E 196 LYS cc_start: 0.3930 (OUTLIER) cc_final: 0.3456 (mmmt) REVERT: E 205 ASP cc_start: 0.4265 (t0) cc_final: 0.3804 (p0) REVERT: E 237 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6249 (tm-30) outliers start: 160 outliers final: 81 residues processed: 492 average time/residue: 1.3356 time to fit residues: 786.5921 Evaluate side-chains 456 residues out of total 4095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 351 time to evaluate : 3.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 576 VAL Chi-restraints excluded: chain 1 residue 585 GLU Chi-restraints excluded: chain 1 residue 617 ILE Chi-restraints excluded: chain 1 residue 798 THR Chi-restraints excluded: chain 1 residue 839 GLU Chi-restraints excluded: chain 1 residue 860 GLU Chi-restraints excluded: chain 1 residue 925 VAL Chi-restraints excluded: chain 1 residue 926 LYS Chi-restraints excluded: chain 1 residue 964 THR Chi-restraints excluded: chain 1 residue 967 GLU Chi-restraints excluded: chain 1 residue 971 MET Chi-restraints excluded: chain 1 residue 997 LEU Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1059 CYS Chi-restraints excluded: chain 1 residue 1113 THR Chi-restraints excluded: chain 1 residue 1123 CYS Chi-restraints excluded: chain 1 residue 1126 PHE Chi-restraints excluded: chain 1 residue 1135 GLU Chi-restraints excluded: chain 1 residue 1160 GLU Chi-restraints excluded: chain 1 residue 1207 SER Chi-restraints excluded: chain 1 residue 1241 ILE 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 572 HIS Chi-restraints excluded: chain 2 residue 706 THR Chi-restraints excluded: chain 3 residue 9 GLN Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 55 THR Chi-restraints excluded: chain 3 residue 64 SER Chi-restraints excluded: chain 3 residue 114 ARG Chi-restraints excluded: chain 3 residue 146 ARG Chi-restraints excluded: chain 3 residue 151 ARG Chi-restraints excluded: chain 3 residue 156 SER Chi-restraints excluded: chain 3 residue 178 GLU Chi-restraints excluded: chain 3 residue 223 LYS Chi-restraints excluded: chain 3 residue 242 SER Chi-restraints excluded: chain 3 residue 278 LEU Chi-restraints excluded: chain 3 residue 316 GLU Chi-restraints excluded: chain 3 residue 342 LEU Chi-restraints excluded: chain 3 residue 404 LEU Chi-restraints excluded: chain 3 residue 420 THR Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 459 VAL Chi-restraints excluded: chain 3 residue 462 VAL Chi-restraints excluded: chain 3 residue 463 ARG Chi-restraints excluded: chain 3 residue 476 VAL Chi-restraints excluded: chain 3 residue 490 THR Chi-restraints excluded: chain 3 residue 524 ILE Chi-restraints excluded: chain 3 residue 533 VAL Chi-restraints excluded: chain 3 residue 534 ASN Chi-restraints excluded: chain 3 residue 546 LYS Chi-restraints excluded: chain 3 residue 549 VAL Chi-restraints excluded: chain 3 residue 574 LEU Chi-restraints excluded: chain 3 residue 591 SER Chi-restraints excluded: chain 3 residue 629 SER Chi-restraints excluded: chain 3 residue 639 SER Chi-restraints excluded: chain 3 residue 671 ASN Chi-restraints excluded: chain 3 residue 677 THR Chi-restraints excluded: chain 3 residue 704 VAL Chi-restraints excluded: chain 3 residue 713 LEU Chi-restraints excluded: chain 3 residue 738 THR Chi-restraints excluded: chain 3 residue 749 GLN Chi-restraints excluded: chain 3 residue 755 VAL Chi-restraints excluded: chain 3 residue 770 LEU Chi-restraints excluded: chain 3 residue 809 GLU Chi-restraints excluded: chain 3 residue 821 GLU Chi-restraints excluded: chain 3 residue 834 LEU Chi-restraints excluded: chain 3 residue 838 MET Chi-restraints excluded: chain 3 residue 865 VAL Chi-restraints excluded: chain 3 residue 890 SER Chi-restraints excluded: chain 3 residue 897 SER Chi-restraints excluded: chain 3 residue 965 LYS Chi-restraints excluded: chain 3 residue 1008 SER Chi-restraints excluded: chain 3 residue 1048 ASP Chi-restraints excluded: chain 3 residue 1065 GLU Chi-restraints excluded: chain 3 residue 1120 THR Chi-restraints excluded: chain 3 residue 1150 SER Chi-restraints excluded: chain 3 residue 1170 VAL Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain 5 residue 17 LYS 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 405 ASN Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 472 GLN 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 148 GLU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 191 ARG Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 237 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 382 optimal weight: 40.0000 chunk 260 optimal weight: 2.9990 chunk 6 optimal weight: 40.0000 chunk 341 optimal weight: 0.0030 chunk 189 optimal weight: 0.1980 chunk 391 optimal weight: 20.0000 chunk 317 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 234 optimal weight: 0.0370 chunk 412 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 overall best weight: 0.7870 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 692 HIS 1 804 ASN 1 973 HIS 11194 HIS 2 458 ASN ** 3 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 219 HIS 3 363 HIS 3 636 GLN 3 796 ASN C 400 HIS ** C 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6113 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 32944 Z= 0.142 Angle : 0.522 10.567 44527 Z= 0.264 Chirality : 0.041 0.223 3946 Planarity : 0.004 0.067 5945 Dihedral : 14.335 157.483 7299 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.32 % Favored : 96.66 % Rotamer: Outliers : 5.86 % Allowed : 24.00 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.02 % 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: 0.03 (0.13), residues: 4597 helix: 1.55 (0.14), residues: 1625 sheet: 0.11 (0.17), residues: 979 loop : -1.34 (0.13), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 1 938 HIS 0.008 0.001 HIS C 425 PHE 0.017 0.001 PHE D 168 TYR 0.015 0.001 TYR D 136 ARG 0.008 0.000 ARG 1 739 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 4095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 355 time to evaluate : 3.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 558 ARG cc_start: 0.6858 (mmp80) cc_final: 0.6557 (mmp80) REVERT: 1 564 ASP cc_start: 0.6986 (m-30) cc_final: 0.6748 (m-30) REVERT: 1 651 VAL cc_start: 0.8360 (t) cc_final: 0.8153 (t) REVERT: 1 656 LYS cc_start: 0.7128 (mmtp) cc_final: 0.6741 (mmtt) REVERT: 1 835 ASP cc_start: 0.7439 (m-30) cc_final: 0.7238 (m-30) REVERT: 1 839 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7002 (tm-30) REVERT: 1 860 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.7189 (mp0) REVERT: 1 890 GLU cc_start: 0.6870 (tt0) cc_final: 0.6529 (tp30) REVERT: 1 926 LYS cc_start: 0.6919 (OUTLIER) cc_final: 0.6657 (mmmm) REVERT: 1 942 ASN cc_start: 0.6635 (t0) cc_final: 0.6243 (m-40) REVERT: 1 957 ARG cc_start: 0.7480 (ttm110) cc_final: 0.7220 (mmm-85) REVERT: 1 967 GLU cc_start: 0.4355 (OUTLIER) cc_final: 0.3775 (tp30) REVERT: 1 971 MET cc_start: 0.5990 (OUTLIER) cc_final: 0.5767 (ttm) REVERT: 1 1037 ASP cc_start: 0.7906 (m-30) cc_final: 0.7477 (m-30) REVERT: 1 1056 MET cc_start: 0.8333 (mmm) cc_final: 0.8128 (mmm) REVERT: 1 1061 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7026 (mp0) REVERT: 1 1135 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7376 (tt0) REVERT: 1 1160 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7006 (tt0) REVERT: 1 1161 MET cc_start: 0.8288 (ttm) cc_final: 0.7712 (mtp) REVERT: 2 572 HIS cc_start: 0.5367 (OUTLIER) cc_final: 0.4557 (t70) REVERT: 3 114 ARG cc_start: 0.9276 (OUTLIER) cc_final: 0.8916 (ttp-170) REVERT: 3 136 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.6297 (mt-10) REVERT: 3 151 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7052 (mtt-85) REVERT: 3 178 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7184 (mp0) REVERT: 3 316 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7649 (tp30) REVERT: 3 326 ARG cc_start: 0.8614 (mtt180) cc_final: 0.8100 (mtt180) REVERT: 3 377 MET cc_start: 0.8380 (mtt) cc_final: 0.7973 (mtp) REVERT: 3 447 MET cc_start: 0.1411 (ttt) cc_final: -0.1443 (mmp) REVERT: 3 574 LEU cc_start: 0.2176 (OUTLIER) cc_final: 0.1383 (pt) REVERT: 3 583 MET cc_start: 0.2171 (mtm) cc_final: 0.1888 (tmm) REVERT: 3 630 MET cc_start: 0.3451 (ttm) cc_final: 0.2743 (mmm) REVERT: 3 645 MET cc_start: 0.0852 (pp-130) cc_final: 0.0036 (mtt) REVERT: 3 721 LEU cc_start: 0.7336 (tt) cc_final: 0.6989 (tp) REVERT: 3 809 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.6889 (mp0) REVERT: 3 821 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6888 (mp0) REVERT: 3 1048 ASP cc_start: 0.7225 (OUTLIER) cc_final: 0.7003 (t70) REVERT: 3 1143 HIS cc_start: 0.7715 (m90) cc_final: 0.7290 (t-90) REVERT: 3 1188 ASN cc_start: 0.7214 (OUTLIER) cc_final: 0.6663 (p0) REVERT: 6 25 LYS cc_start: 0.7989 (ttpt) cc_final: 0.7157 (pttm) REVERT: D 143 ASP cc_start: 0.5300 (p0) cc_final: 0.4476 (p0) REVERT: D 148 GLU cc_start: 0.5898 (OUTLIER) cc_final: 0.5522 (pp20) REVERT: D 189 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8494 (tp) REVERT: D 191 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.6846 (tmt170) REVERT: D 202 ASP cc_start: 0.7480 (t0) cc_final: 0.7136 (t70) REVERT: D 203 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6893 (mt-10) REVERT: D 247 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7283 (mt) REVERT: E 169 LYS cc_start: 0.7009 (mttt) cc_final: 0.6152 (ttpt) REVERT: E 176 LYS cc_start: 0.5466 (tmtt) cc_final: 0.4809 (tmtp) REVERT: E 196 LYS cc_start: 0.3947 (OUTLIER) cc_final: 0.3596 (tppt) REVERT: E 205 ASP cc_start: 0.4244 (t0) cc_final: 0.3768 (p0) REVERT: E 237 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6249 (tm-30) outliers start: 133 outliers final: 71 residues processed: 460 average time/residue: 1.3170 time to fit residues: 726.0154 Evaluate side-chains 443 residues out of total 4095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 347 time to evaluate : 3.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 576 VAL Chi-restraints excluded: chain 1 residue 585 GLU Chi-restraints excluded: chain 1 residue 617 ILE Chi-restraints excluded: chain 1 residue 705 SER Chi-restraints excluded: chain 1 residue 735 ILE Chi-restraints excluded: chain 1 residue 781 ASP Chi-restraints excluded: chain 1 residue 798 THR Chi-restraints excluded: chain 1 residue 801 VAL Chi-restraints excluded: chain 1 residue 839 GLU Chi-restraints excluded: chain 1 residue 860 GLU Chi-restraints excluded: chain 1 residue 925 VAL Chi-restraints excluded: chain 1 residue 926 LYS Chi-restraints excluded: chain 1 residue 964 THR Chi-restraints excluded: chain 1 residue 967 GLU Chi-restraints excluded: chain 1 residue 971 MET Chi-restraints excluded: chain 1 residue 1059 CYS Chi-restraints excluded: chain 1 residue 1061 GLU Chi-restraints excluded: chain 1 residue 1063 LEU Chi-restraints excluded: chain 1 residue 1123 CYS Chi-restraints excluded: chain 1 residue 1126 PHE Chi-restraints excluded: chain 1 residue 1135 GLU Chi-restraints excluded: chain 1 residue 1160 GLU Chi-restraints excluded: chain 1 residue 1207 SER Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 572 HIS 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 64 SER Chi-restraints excluded: chain 3 residue 114 ARG Chi-restraints excluded: chain 3 residue 136 GLU Chi-restraints excluded: chain 3 residue 146 ARG Chi-restraints excluded: chain 3 residue 151 ARG Chi-restraints excluded: chain 3 residue 178 GLU Chi-restraints excluded: chain 3 residue 181 MET Chi-restraints excluded: chain 3 residue 316 GLU Chi-restraints excluded: chain 3 residue 342 LEU Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 433 SER Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 459 VAL Chi-restraints excluded: chain 3 residue 462 VAL Chi-restraints excluded: chain 3 residue 463 ARG Chi-restraints excluded: chain 3 residue 476 VAL Chi-restraints excluded: chain 3 residue 490 THR Chi-restraints excluded: chain 3 residue 524 ILE Chi-restraints excluded: chain 3 residue 533 VAL Chi-restraints excluded: chain 3 residue 534 ASN Chi-restraints excluded: chain 3 residue 546 LYS Chi-restraints excluded: chain 3 residue 549 VAL Chi-restraints excluded: chain 3 residue 574 LEU Chi-restraints excluded: chain 3 residue 591 SER Chi-restraints excluded: chain 3 residue 595 VAL Chi-restraints excluded: chain 3 residue 629 SER Chi-restraints excluded: chain 3 residue 671 ASN Chi-restraints excluded: chain 3 residue 677 THR Chi-restraints excluded: chain 3 residue 704 VAL Chi-restraints excluded: chain 3 residue 713 LEU Chi-restraints excluded: chain 3 residue 728 ARG Chi-restraints excluded: chain 3 residue 755 VAL Chi-restraints excluded: chain 3 residue 809 GLU Chi-restraints excluded: chain 3 residue 821 GLU Chi-restraints excluded: chain 3 residue 834 LEU Chi-restraints excluded: chain 3 residue 865 VAL Chi-restraints excluded: chain 3 residue 890 SER Chi-restraints excluded: chain 3 residue 1008 SER Chi-restraints excluded: chain 3 residue 1048 ASP Chi-restraints excluded: chain 3 residue 1065 GLU Chi-restraints excluded: chain 3 residue 1120 THR Chi-restraints excluded: chain 3 residue 1150 SER Chi-restraints excluded: chain 3 residue 1188 ASN Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain 5 residue 17 LYS 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 402 LEU Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 472 GLN Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 191 ARG Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 232 MET Chi-restraints excluded: chain E residue 237 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 154 optimal weight: 0.9990 chunk 413 optimal weight: 30.0000 chunk 90 optimal weight: 2.9990 chunk 269 optimal weight: 8.9990 chunk 113 optimal weight: 4.9990 chunk 459 optimal weight: 30.0000 chunk 381 optimal weight: 50.0000 chunk 212 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 152 optimal weight: 2.9990 chunk 241 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 534 GLN 1 692 HIS 1 804 ASN 1 973 HIS 2 478 HIS ** 3 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 219 HIS 3 363 HIS 3 796 ASN C 400 HIS ** C 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6143 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32944 Z= 0.191 Angle : 0.548 11.522 44527 Z= 0.280 Chirality : 0.042 0.186 3946 Planarity : 0.004 0.061 5945 Dihedral : 14.337 154.904 7298 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.03 % Favored : 95.94 % Rotamer: Outliers : 6.38 % Allowed : 23.21 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.02 % 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: 0.18 (0.13), residues: 4597 helix: 1.69 (0.14), residues: 1625 sheet: 0.18 (0.17), residues: 1001 loop : -1.28 (0.13), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 1 938 HIS 0.008 0.001 HIS C 425 PHE 0.020 0.002 PHE 11153 TYR 0.017 0.002 TYR 3 520 ARG 0.006 0.000 ARG 31164 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 4095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 359 time to evaluate : 3.475 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: 1 558 ARG cc_start: 0.6767 (mmp80) cc_final: 0.6475 (mmp80) REVERT: 1 564 ASP cc_start: 0.7125 (m-30) cc_final: 0.6888 (m-30) REVERT: 1 656 LYS cc_start: 0.7208 (mmtp) cc_final: 0.6780 (mttt) REVERT: 1 770 MET cc_start: 0.7885 (mmm) cc_final: 0.7428 (mmt) REVERT: 1 839 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.6985 (tm-30) REVERT: 1 890 GLU cc_start: 0.6897 (tt0) cc_final: 0.6534 (tp30) REVERT: 1 926 LYS cc_start: 0.6929 (OUTLIER) cc_final: 0.6697 (mmmm) REVERT: 1 942 ASN cc_start: 0.6765 (t0) cc_final: 0.6475 (m-40) REVERT: 1 957 ARG cc_start: 0.7469 (ttm110) cc_final: 0.7204 (mmm-85) REVERT: 1 967 GLU cc_start: 0.4655 (OUTLIER) cc_final: 0.4132 (tp30) REVERT: 1 1037 ASP cc_start: 0.7905 (m-30) cc_final: 0.7488 (m-30) REVERT: 1 1056 MET cc_start: 0.8264 (mmm) cc_final: 0.7981 (mmm) REVERT: 1 1135 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7263 (tt0) REVERT: 1 1160 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7014 (tt0) REVERT: 1 1161 MET cc_start: 0.8336 (ttm) cc_final: 0.7775 (mtp) REVERT: 2 502 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7520 (ptp-170) REVERT: 2 572 HIS cc_start: 0.5349 (OUTLIER) cc_final: 0.4644 (t70) REVERT: 3 96 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7854 (tptt) REVERT: 3 114 ARG cc_start: 0.9295 (OUTLIER) cc_final: 0.8951 (ttp-170) REVERT: 3 136 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6374 (mt-10) REVERT: 3 151 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7015 (mtt-85) REVERT: 3 178 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7105 (mp0) REVERT: 3 273 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.8799 (mmm160) REVERT: 3 316 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7707 (tp30) REVERT: 3 326 ARG cc_start: 0.8626 (mtt180) cc_final: 0.8131 (mtt180) REVERT: 3 377 MET cc_start: 0.8385 (mtt) cc_final: 0.7933 (mtp) REVERT: 3 390 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.7643 (ptt90) REVERT: 3 447 MET cc_start: 0.1465 (ttt) cc_final: -0.1423 (mmp) REVERT: 3 546 LYS cc_start: 0.3364 (OUTLIER) cc_final: 0.3018 (mtmm) REVERT: 3 574 LEU cc_start: 0.2504 (OUTLIER) cc_final: 0.1816 (pt) REVERT: 3 583 MET cc_start: 0.2164 (mtm) cc_final: 0.1887 (tmm) REVERT: 3 645 MET cc_start: 0.0262 (pp-130) cc_final: -0.0212 (mtt) REVERT: 3 721 LEU cc_start: 0.7385 (tt) cc_final: 0.7024 (tp) REVERT: 3 749 GLN cc_start: 0.1805 (OUTLIER) cc_final: 0.1164 (mt0) REVERT: 3 754 ILE cc_start: 0.6582 (OUTLIER) cc_final: 0.6277 (mt) REVERT: 3 770 LEU cc_start: 0.4755 (OUTLIER) cc_final: 0.4514 (tp) REVERT: 3 809 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.6822 (mp0) REVERT: 3 1048 ASP cc_start: 0.7315 (OUTLIER) cc_final: 0.7104 (t70) REVERT: 3 1143 HIS cc_start: 0.7736 (m90) cc_final: 0.7289 (t-90) REVERT: 3 1188 ASN cc_start: 0.7271 (OUTLIER) cc_final: 0.6696 (p0) REVERT: 6 25 LYS cc_start: 0.8071 (ttpt) cc_final: 0.7232 (pttm) REVERT: D 143 ASP cc_start: 0.5453 (p0) cc_final: 0.4694 (p0) REVERT: D 189 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8528 (tp) REVERT: D 202 ASP cc_start: 0.7542 (t0) cc_final: 0.7177 (t70) REVERT: D 203 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7009 (mt-10) REVERT: D 247 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7581 (mt) REVERT: E 169 LYS cc_start: 0.7005 (mttt) cc_final: 0.6146 (ttpt) REVERT: E 176 LYS cc_start: 0.5536 (tmtt) cc_final: 0.4849 (tmtp) REVERT: E 196 LYS cc_start: 0.4147 (OUTLIER) cc_final: 0.3544 (mmmt) REVERT: E 205 ASP cc_start: 0.4325 (t0) cc_final: 0.3858 (p0) REVERT: E 237 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6240 (tm-30) outliers start: 145 outliers final: 81 residues processed: 471 average time/residue: 1.3306 time to fit residues: 749.0182 Evaluate side-chains 457 residues out of total 4095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 349 time to evaluate : 3.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 576 VAL Chi-restraints excluded: chain 1 residue 585 GLU Chi-restraints excluded: chain 1 residue 602 LYS Chi-restraints excluded: chain 1 residue 617 ILE Chi-restraints excluded: chain 1 residue 705 SER Chi-restraints excluded: chain 1 residue 735 ILE Chi-restraints excluded: chain 1 residue 781 ASP Chi-restraints excluded: chain 1 residue 798 THR Chi-restraints excluded: chain 1 residue 801 VAL Chi-restraints excluded: chain 1 residue 839 GLU Chi-restraints excluded: chain 1 residue 925 VAL Chi-restraints excluded: chain 1 residue 926 LYS Chi-restraints excluded: chain 1 residue 964 THR Chi-restraints excluded: chain 1 residue 967 GLU Chi-restraints excluded: chain 1 residue 997 LEU Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1059 CYS Chi-restraints excluded: chain 1 residue 1063 LEU Chi-restraints excluded: chain 1 residue 1123 CYS Chi-restraints excluded: chain 1 residue 1126 PHE Chi-restraints excluded: chain 1 residue 1135 GLU Chi-restraints excluded: chain 1 residue 1160 GLU Chi-restraints excluded: chain 1 residue 1207 SER Chi-restraints excluded: chain 1 residue 1241 ILE 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 581 LYS 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 64 SER Chi-restraints excluded: chain 3 residue 96 LYS Chi-restraints excluded: chain 3 residue 114 ARG Chi-restraints excluded: chain 3 residue 136 GLU Chi-restraints excluded: chain 3 residue 146 ARG Chi-restraints excluded: chain 3 residue 151 ARG Chi-restraints excluded: chain 3 residue 178 GLU Chi-restraints excluded: chain 3 residue 223 LYS Chi-restraints excluded: chain 3 residue 273 ARG Chi-restraints excluded: chain 3 residue 316 GLU Chi-restraints excluded: chain 3 residue 342 LEU Chi-restraints excluded: chain 3 residue 390 ARG Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 433 SER Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 459 VAL Chi-restraints excluded: chain 3 residue 462 VAL Chi-restraints excluded: chain 3 residue 463 ARG Chi-restraints excluded: chain 3 residue 476 VAL Chi-restraints excluded: chain 3 residue 490 THR Chi-restraints excluded: chain 3 residue 524 ILE Chi-restraints excluded: chain 3 residue 533 VAL Chi-restraints excluded: chain 3 residue 534 ASN Chi-restraints excluded: chain 3 residue 546 LYS Chi-restraints excluded: chain 3 residue 549 VAL Chi-restraints excluded: chain 3 residue 574 LEU Chi-restraints excluded: chain 3 residue 591 SER Chi-restraints excluded: chain 3 residue 595 VAL Chi-restraints excluded: chain 3 residue 629 SER Chi-restraints excluded: chain 3 residue 639 SER Chi-restraints excluded: chain 3 residue 671 ASN Chi-restraints excluded: chain 3 residue 677 THR Chi-restraints excluded: chain 3 residue 704 VAL Chi-restraints excluded: chain 3 residue 705 ARG Chi-restraints excluded: chain 3 residue 713 LEU Chi-restraints excluded: chain 3 residue 728 ARG Chi-restraints excluded: chain 3 residue 738 THR Chi-restraints excluded: chain 3 residue 749 GLN Chi-restraints excluded: chain 3 residue 754 ILE Chi-restraints excluded: chain 3 residue 755 VAL Chi-restraints excluded: chain 3 residue 770 LEU Chi-restraints excluded: chain 3 residue 809 GLU Chi-restraints excluded: chain 3 residue 834 LEU Chi-restraints excluded: chain 3 residue 865 VAL Chi-restraints excluded: chain 3 residue 890 SER Chi-restraints excluded: chain 3 residue 1008 SER Chi-restraints excluded: chain 3 residue 1048 ASP Chi-restraints excluded: chain 3 residue 1065 GLU Chi-restraints excluded: chain 3 residue 1120 THR Chi-restraints excluded: chain 3 residue 1150 SER Chi-restraints excluded: chain 3 residue 1188 ASN Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain 5 residue 17 LYS 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 402 LEU Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 472 GLN Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 232 MET Chi-restraints excluded: chain E residue 237 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 443 optimal weight: 0.0980 chunk 51 optimal weight: 3.9990 chunk 261 optimal weight: 5.9990 chunk 335 optimal weight: 0.9980 chunk 260 optimal weight: 0.6980 chunk 386 optimal weight: 0.5980 chunk 256 optimal weight: 5.9990 chunk 457 optimal weight: 50.0000 chunk 286 optimal weight: 0.9990 chunk 279 optimal weight: 5.9990 chunk 211 optimal weight: 3.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 692 HIS 1 804 ASN 1 973 HIS 11002 ASN 2 503 HIS ** 3 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 219 HIS 3 363 HIS 3 796 ASN ** C 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6109 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 32944 Z= 0.134 Angle : 0.508 11.542 44527 Z= 0.257 Chirality : 0.040 0.206 3946 Planarity : 0.004 0.064 5945 Dihedral : 14.268 155.394 7298 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 5.20 % Allowed : 24.44 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.02 % 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: 0.41 (0.13), residues: 4597 helix: 1.89 (0.14), residues: 1626 sheet: 0.29 (0.17), residues: 995 loop : -1.14 (0.13), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 1 938 HIS 0.008 0.001 HIS C 425 PHE 0.016 0.001 PHE D 168 TYR 0.014 0.001 TYR 6 54 ARG 0.008 0.000 ARG 1 739 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 4095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 351 time to evaluate : 3.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 558 ARG cc_start: 0.6875 (mmp80) cc_final: 0.6569 (mmp80) REVERT: 1 564 ASP cc_start: 0.7053 (m-30) cc_final: 0.6840 (m-30) REVERT: 1 656 LYS cc_start: 0.7177 (mmtp) cc_final: 0.6796 (mmtt) REVERT: 1 770 MET cc_start: 0.7811 (mmm) cc_final: 0.7432 (mmt) REVERT: 1 839 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.7079 (tm-30) REVERT: 1 867 MET cc_start: 0.7223 (OUTLIER) cc_final: 0.6980 (ttt) REVERT: 1 890 GLU cc_start: 0.6847 (tt0) cc_final: 0.6522 (tp30) REVERT: 1 926 LYS cc_start: 0.6999 (OUTLIER) cc_final: 0.6706 (mmmm) REVERT: 1 957 ARG cc_start: 0.7462 (ttm110) cc_final: 0.7064 (mtp-110) REVERT: 1 967 GLU cc_start: 0.4745 (OUTLIER) cc_final: 0.4104 (tp30) REVERT: 1 1037 ASP cc_start: 0.7905 (m-30) cc_final: 0.7486 (m-30) REVERT: 1 1056 MET cc_start: 0.8197 (mmm) cc_final: 0.7851 (mmm) REVERT: 1 1061 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7051 (mp0) REVERT: 1 1086 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7950 (tttt) REVERT: 1 1135 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7391 (tt0) REVERT: 1 1160 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6990 (tt0) REVERT: 1 1161 MET cc_start: 0.8306 (ttm) cc_final: 0.7762 (mtp) REVERT: 3 114 ARG cc_start: 0.9274 (OUTLIER) cc_final: 0.8917 (ttp-170) REVERT: 3 136 GLU cc_start: 0.6701 (OUTLIER) cc_final: 0.6199 (mt-10) REVERT: 3 151 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.7024 (mtt-85) REVERT: 3 178 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7174 (mp0) REVERT: 3 316 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7729 (tp30) REVERT: 3 326 ARG cc_start: 0.8607 (mtt180) cc_final: 0.8173 (mtt180) REVERT: 3 377 MET cc_start: 0.8352 (mtt) cc_final: 0.7904 (mtp) REVERT: 3 390 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.7508 (ptt90) REVERT: 3 447 MET cc_start: 0.1304 (ttt) cc_final: -0.1501 (mmp) REVERT: 3 546 LYS cc_start: 0.3089 (OUTLIER) cc_final: 0.2738 (mtmm) REVERT: 3 574 LEU cc_start: 0.2315 (OUTLIER) cc_final: 0.1749 (pt) REVERT: 3 583 MET cc_start: 0.2208 (mtm) cc_final: 0.1864 (tmm) REVERT: 3 721 LEU cc_start: 0.7246 (tt) cc_final: 0.6936 (tp) REVERT: 3 749 GLN cc_start: 0.1860 (OUTLIER) cc_final: 0.1175 (mt0) REVERT: 3 754 ILE cc_start: 0.6531 (OUTLIER) cc_final: 0.6230 (mt) REVERT: 3 770 LEU cc_start: 0.4653 (OUTLIER) cc_final: 0.4444 (tp) REVERT: 3 809 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.6881 (mp0) REVERT: 3 1143 HIS cc_start: 0.7708 (m90) cc_final: 0.7291 (t-90) REVERT: 3 1188 ASN cc_start: 0.7116 (OUTLIER) cc_final: 0.6567 (p0) REVERT: 6 25 LYS cc_start: 0.7977 (ttpt) cc_final: 0.7148 (pttm) REVERT: C 465 GLN cc_start: 0.7596 (tt0) cc_final: 0.7309 (tt0) REVERT: D 143 ASP cc_start: 0.5485 (p0) cc_final: 0.4679 (p0) REVERT: D 148 GLU cc_start: 0.5953 (OUTLIER) cc_final: 0.5641 (pp20) REVERT: D 189 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8500 (tp) REVERT: D 202 ASP cc_start: 0.7531 (t0) cc_final: 0.7188 (t70) REVERT: D 203 GLU cc_start: 0.7337 (mt-10) cc_final: 0.7036 (mt-10) REVERT: D 247 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7269 (mt) REVERT: E 169 LYS cc_start: 0.6977 (mttt) cc_final: 0.6115 (ttpt) REVERT: E 176 LYS cc_start: 0.5536 (tmtt) cc_final: 0.4855 (tmtp) REVERT: E 196 LYS cc_start: 0.4165 (OUTLIER) cc_final: 0.3654 (tppt) REVERT: E 205 ASP cc_start: 0.4205 (t0) cc_final: 0.3755 (p0) REVERT: E 237 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.6184 (tm-30) outliers start: 118 outliers final: 68 residues processed: 442 average time/residue: 1.3480 time to fit residues: 714.2065 Evaluate side-chains 436 residues out of total 4095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 342 time to evaluate : 3.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 576 VAL Chi-restraints excluded: chain 1 residue 585 GLU Chi-restraints excluded: chain 1 residue 617 ILE Chi-restraints excluded: chain 1 residue 705 SER Chi-restraints excluded: chain 1 residue 735 ILE Chi-restraints excluded: chain 1 residue 781 ASP Chi-restraints excluded: chain 1 residue 801 VAL Chi-restraints excluded: chain 1 residue 839 GLU Chi-restraints excluded: chain 1 residue 867 MET Chi-restraints excluded: chain 1 residue 925 VAL Chi-restraints excluded: chain 1 residue 926 LYS Chi-restraints excluded: chain 1 residue 956 SER Chi-restraints excluded: chain 1 residue 964 THR Chi-restraints excluded: chain 1 residue 967 GLU Chi-restraints excluded: chain 1 residue 997 LEU Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1059 CYS Chi-restraints excluded: chain 1 residue 1061 GLU Chi-restraints excluded: chain 1 residue 1063 LEU Chi-restraints excluded: chain 1 residue 1086 LYS Chi-restraints excluded: chain 1 residue 1123 CYS Chi-restraints excluded: chain 1 residue 1126 PHE Chi-restraints excluded: chain 1 residue 1135 GLU Chi-restraints excluded: chain 1 residue 1160 GLU Chi-restraints excluded: chain 1 residue 1207 SER Chi-restraints excluded: chain 2 residue 498 VAL 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 64 SER Chi-restraints excluded: chain 3 residue 114 ARG Chi-restraints excluded: chain 3 residue 136 GLU Chi-restraints excluded: chain 3 residue 151 ARG Chi-restraints excluded: chain 3 residue 178 GLU Chi-restraints excluded: chain 3 residue 181 MET Chi-restraints excluded: chain 3 residue 316 GLU Chi-restraints excluded: chain 3 residue 342 LEU Chi-restraints excluded: chain 3 residue 390 ARG Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 433 SER Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 459 VAL Chi-restraints excluded: chain 3 residue 462 VAL Chi-restraints excluded: chain 3 residue 476 VAL Chi-restraints excluded: chain 3 residue 490 THR Chi-restraints excluded: chain 3 residue 524 ILE Chi-restraints excluded: chain 3 residue 533 VAL Chi-restraints excluded: chain 3 residue 534 ASN Chi-restraints excluded: chain 3 residue 546 LYS Chi-restraints excluded: chain 3 residue 549 VAL Chi-restraints excluded: chain 3 residue 574 LEU Chi-restraints excluded: chain 3 residue 595 VAL Chi-restraints excluded: chain 3 residue 677 THR Chi-restraints excluded: chain 3 residue 704 VAL Chi-restraints excluded: chain 3 residue 713 LEU Chi-restraints excluded: chain 3 residue 728 ARG Chi-restraints excluded: chain 3 residue 749 GLN Chi-restraints excluded: chain 3 residue 754 ILE Chi-restraints excluded: chain 3 residue 755 VAL Chi-restraints excluded: chain 3 residue 759 THR Chi-restraints excluded: chain 3 residue 770 LEU Chi-restraints excluded: chain 3 residue 809 GLU Chi-restraints excluded: chain 3 residue 834 LEU Chi-restraints excluded: chain 3 residue 838 MET Chi-restraints excluded: chain 3 residue 865 VAL Chi-restraints excluded: chain 3 residue 965 LYS Chi-restraints excluded: chain 3 residue 1008 SER Chi-restraints excluded: chain 3 residue 1065 GLU Chi-restraints excluded: chain 3 residue 1120 THR Chi-restraints excluded: chain 3 residue 1150 SER Chi-restraints excluded: chain 3 residue 1188 ASN Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain 5 residue 17 LYS 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 405 ASN Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 472 GLN Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 232 MET Chi-restraints excluded: chain E residue 237 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 283 optimal weight: 5.9990 chunk 182 optimal weight: 6.9990 chunk 273 optimal weight: 30.0000 chunk 137 optimal weight: 0.5980 chunk 89 optimal weight: 0.3980 chunk 88 optimal weight: 0.6980 chunk 291 optimal weight: 5.9990 chunk 311 optimal weight: 8.9990 chunk 226 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 359 optimal weight: 30.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 804 ASN 1 973 HIS ** 3 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 206 GLN 3 219 HIS 3 363 HIS ** 3 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 796 ASN 6 78 GLN ** C 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6118 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 32944 Z= 0.148 Angle : 0.512 11.332 44527 Z= 0.259 Chirality : 0.040 0.198 3946 Planarity : 0.004 0.061 5945 Dihedral : 14.246 154.152 7295 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 5.06 % Allowed : 24.66 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.02 % 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: 0.49 (0.13), residues: 4597 helix: 1.96 (0.14), residues: 1622 sheet: 0.34 (0.17), residues: 993 loop : -1.10 (0.13), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 1 938 HIS 0.007 0.001 HIS C 425 PHE 0.016 0.001 PHE D 168 TYR 0.014 0.001 TYR 3 926 ARG 0.009 0.000 ARG 3 463 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 4095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 346 time to evaluate : 3.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 522 LYS cc_start: 0.4971 (ptpt) cc_final: 0.4687 (ptmt) REVERT: 1 558 ARG cc_start: 0.6877 (mmp80) cc_final: 0.6566 (mmp80) REVERT: 1 656 LYS cc_start: 0.7225 (mmtp) cc_final: 0.6846 (mmtt) REVERT: 1 770 MET cc_start: 0.7722 (mmm) cc_final: 0.7363 (mmt) REVERT: 1 839 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.7101 (tm-30) REVERT: 1 867 MET cc_start: 0.7174 (OUTLIER) cc_final: 0.6912 (ttt) REVERT: 1 942 ASN cc_start: 0.6641 (t0) cc_final: 0.6411 (m-40) REVERT: 1 957 ARG cc_start: 0.7489 (ttm110) cc_final: 0.6790 (mtp-110) REVERT: 1 967 GLU cc_start: 0.4819 (OUTLIER) cc_final: 0.4187 (tp30) REVERT: 1 1037 ASP cc_start: 0.7925 (m-30) cc_final: 0.7501 (m-30) REVERT: 1 1061 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7054 (mp0) REVERT: 1 1086 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7969 (tttt) REVERT: 1 1135 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7394 (tt0) REVERT: 1 1160 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6981 (tt0) REVERT: 1 1161 MET cc_start: 0.8287 (ttm) cc_final: 0.7762 (mtp) REVERT: 2 502 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.7203 (ptp-170) REVERT: 3 114 ARG cc_start: 0.9275 (OUTLIER) cc_final: 0.8916 (ttp-170) REVERT: 3 151 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.6993 (mtt-85) REVERT: 3 178 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7082 (mp0) REVERT: 3 316 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7707 (tp30) REVERT: 3 326 ARG cc_start: 0.8613 (mtt180) cc_final: 0.8175 (mtt180) REVERT: 3 377 MET cc_start: 0.8368 (mtt) cc_final: 0.7932 (mtp) REVERT: 3 390 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.7539 (ptt90) REVERT: 3 447 MET cc_start: 0.1370 (ttt) cc_final: -0.1447 (mmp) REVERT: 3 546 LYS cc_start: 0.2900 (OUTLIER) cc_final: 0.2594 (mtmm) REVERT: 3 574 LEU cc_start: 0.2300 (OUTLIER) cc_final: 0.1772 (pt) REVERT: 3 583 MET cc_start: 0.2334 (mtm) cc_final: 0.1914 (tmm) REVERT: 3 715 MET cc_start: 0.6193 (mmm) cc_final: 0.5818 (mmt) REVERT: 3 721 LEU cc_start: 0.7289 (tt) cc_final: 0.6957 (tp) REVERT: 3 749 GLN cc_start: 0.1835 (OUTLIER) cc_final: 0.1153 (mt0) REVERT: 3 754 ILE cc_start: 0.6542 (OUTLIER) cc_final: 0.6256 (mt) REVERT: 3 809 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.6900 (mp0) REVERT: 3 1143 HIS cc_start: 0.7720 (m90) cc_final: 0.7297 (t-90) REVERT: 3 1188 ASN cc_start: 0.7144 (OUTLIER) cc_final: 0.6616 (p0) REVERT: 6 25 LYS cc_start: 0.7935 (ttpt) cc_final: 0.7113 (pttm) REVERT: C 465 GLN cc_start: 0.7608 (tt0) cc_final: 0.7317 (tt0) REVERT: D 143 ASP cc_start: 0.5478 (p0) cc_final: 0.4674 (p0) REVERT: D 148 GLU cc_start: 0.5848 (OUTLIER) cc_final: 0.5533 (pp20) REVERT: D 189 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8479 (tp) REVERT: D 202 ASP cc_start: 0.7516 (t0) cc_final: 0.7173 (t70) REVERT: D 203 GLU cc_start: 0.7285 (mt-10) cc_final: 0.6983 (mt-10) REVERT: E 169 LYS cc_start: 0.6976 (mttt) cc_final: 0.6112 (ttpt) REVERT: E 176 LYS cc_start: 0.5655 (OUTLIER) cc_final: 0.4979 (tmtp) REVERT: E 196 LYS cc_start: 0.4195 (OUTLIER) cc_final: 0.3655 (tppt) REVERT: E 205 ASP cc_start: 0.4234 (t0) cc_final: 0.3779 (p0) REVERT: E 237 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6180 (tm-30) REVERT: E 241 LYS cc_start: 0.4497 (tptm) cc_final: 0.3581 (ttpp) outliers start: 115 outliers final: 75 residues processed: 433 average time/residue: 1.3497 time to fit residues: 699.1607 Evaluate side-chains 438 residues out of total 4095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 339 time to evaluate : 3.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 576 VAL Chi-restraints excluded: chain 1 residue 585 GLU Chi-restraints excluded: chain 1 residue 617 ILE Chi-restraints excluded: chain 1 residue 705 SER Chi-restraints excluded: chain 1 residue 735 ILE Chi-restraints excluded: chain 1 residue 781 ASP Chi-restraints excluded: chain 1 residue 801 VAL Chi-restraints excluded: chain 1 residue 839 GLU Chi-restraints excluded: chain 1 residue 850 ILE Chi-restraints excluded: chain 1 residue 867 MET Chi-restraints excluded: chain 1 residue 925 VAL Chi-restraints excluded: chain 1 residue 964 THR Chi-restraints excluded: chain 1 residue 967 GLU Chi-restraints excluded: chain 1 residue 997 LEU Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1059 CYS Chi-restraints excluded: chain 1 residue 1061 GLU Chi-restraints excluded: chain 1 residue 1063 LEU Chi-restraints excluded: chain 1 residue 1086 LYS Chi-restraints excluded: chain 1 residue 1123 CYS Chi-restraints excluded: chain 1 residue 1126 PHE Chi-restraints excluded: chain 1 residue 1135 GLU Chi-restraints excluded: chain 1 residue 1160 GLU Chi-restraints excluded: chain 1 residue 1207 SER 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 12 THR Chi-restraints excluded: chain 3 residue 55 THR Chi-restraints excluded: chain 3 residue 64 SER Chi-restraints excluded: chain 3 residue 114 ARG Chi-restraints excluded: chain 3 residue 146 ARG Chi-restraints excluded: chain 3 residue 151 ARG Chi-restraints excluded: chain 3 residue 178 GLU Chi-restraints excluded: chain 3 residue 181 MET Chi-restraints excluded: chain 3 residue 316 GLU Chi-restraints excluded: chain 3 residue 342 LEU Chi-restraints excluded: chain 3 residue 390 ARG Chi-restraints excluded: chain 3 residue 419 ASP Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 433 SER Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 459 VAL Chi-restraints excluded: chain 3 residue 462 VAL Chi-restraints excluded: chain 3 residue 476 VAL Chi-restraints excluded: chain 3 residue 490 THR Chi-restraints excluded: chain 3 residue 524 ILE Chi-restraints excluded: chain 3 residue 533 VAL Chi-restraints excluded: chain 3 residue 534 ASN Chi-restraints excluded: chain 3 residue 546 LYS Chi-restraints excluded: chain 3 residue 549 VAL Chi-restraints excluded: chain 3 residue 574 LEU Chi-restraints excluded: chain 3 residue 595 VAL Chi-restraints excluded: chain 3 residue 677 THR Chi-restraints excluded: chain 3 residue 704 VAL Chi-restraints excluded: chain 3 residue 713 LEU Chi-restraints excluded: chain 3 residue 728 ARG Chi-restraints excluded: chain 3 residue 749 GLN Chi-restraints excluded: chain 3 residue 754 ILE Chi-restraints excluded: chain 3 residue 755 VAL Chi-restraints excluded: chain 3 residue 759 THR Chi-restraints excluded: chain 3 residue 809 GLU Chi-restraints excluded: chain 3 residue 824 VAL Chi-restraints excluded: chain 3 residue 834 LEU Chi-restraints excluded: chain 3 residue 865 VAL Chi-restraints excluded: chain 3 residue 965 LYS Chi-restraints excluded: chain 3 residue 1008 SER Chi-restraints excluded: chain 3 residue 1065 GLU Chi-restraints excluded: chain 3 residue 1120 THR Chi-restraints excluded: chain 3 residue 1150 SER Chi-restraints excluded: chain 3 residue 1170 VAL Chi-restraints excluded: chain 3 residue 1188 ASN Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain 5 residue 17 LYS 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 402 LEU Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 472 GLN 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 148 GLU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 176 LYS Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 232 MET Chi-restraints excluded: chain E residue 237 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 416 optimal weight: 5.9990 chunk 438 optimal weight: 0.9990 chunk 400 optimal weight: 0.0000 chunk 426 optimal weight: 20.0000 chunk 256 optimal weight: 5.9990 chunk 185 optimal weight: 7.9990 chunk 335 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 385 optimal weight: 20.0000 chunk 403 optimal weight: 5.9990 chunk 425 optimal weight: 6.9990 overall best weight: 2.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 692 HIS 1 804 ASN 1 973 HIS ** 3 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 219 HIS 3 363 HIS ** 3 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6169 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 32944 Z= 0.261 Angle : 0.592 8.899 44527 Z= 0.305 Chirality : 0.044 0.211 3946 Planarity : 0.004 0.067 5945 Dihedral : 14.348 148.086 7291 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.47 % Favored : 95.51 % Rotamer: Outliers : 5.02 % Allowed : 24.66 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.35 (0.13), residues: 4597 helix: 1.83 (0.14), residues: 1622 sheet: 0.27 (0.17), residues: 1006 loop : -1.17 (0.13), residues: 1969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP 1 938 HIS 0.008 0.001 HIS C 425 PHE 0.020 0.002 PHE 11153 TYR 0.021 0.002 TYR 3 926 ARG 0.007 0.001 ARG 3 274 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 4095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 353 time to evaluate : 3.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 558 ARG cc_start: 0.6909 (mmp80) cc_final: 0.6620 (mmp80) REVERT: 1 656 LYS cc_start: 0.7317 (mmtp) cc_final: 0.6902 (mttt) REVERT: 1 839 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7077 (tm-30) REVERT: 1 867 MET cc_start: 0.7228 (OUTLIER) cc_final: 0.6971 (ttt) REVERT: 1 890 GLU cc_start: 0.6898 (tt0) cc_final: 0.6579 (tp30) REVERT: 1 942 ASN cc_start: 0.6732 (t0) cc_final: 0.6504 (m-40) REVERT: 1 957 ARG cc_start: 0.7479 (ttm110) cc_final: 0.6750 (mtp-110) REVERT: 1 967 GLU cc_start: 0.4616 (OUTLIER) cc_final: 0.3979 (tp30) REVERT: 1 1037 ASP cc_start: 0.7892 (m-30) cc_final: 0.7474 (m-30) REVERT: 1 1061 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.6935 (mp0) REVERT: 1 1086 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.8016 (tttt) REVERT: 1 1135 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7300 (tt0) REVERT: 1 1160 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7079 (tt0) REVERT: 1 1161 MET cc_start: 0.8388 (ttm) cc_final: 0.7854 (mtp) REVERT: 3 114 ARG cc_start: 0.9310 (OUTLIER) cc_final: 0.8982 (ttp-170) REVERT: 3 136 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6454 (mt-10) REVERT: 3 151 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.7038 (mtt-85) REVERT: 3 178 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7120 (mp0) REVERT: 3 253 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7512 (tp30) REVERT: 3 326 ARG cc_start: 0.8626 (mtt180) cc_final: 0.8149 (mtt180) REVERT: 3 377 MET cc_start: 0.8397 (mtt) cc_final: 0.7920 (mtp) REVERT: 3 390 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.7727 (ptt90) REVERT: 3 447 MET cc_start: 0.1545 (ttt) cc_final: -0.1430 (mmp) REVERT: 3 546 LYS cc_start: 0.2934 (OUTLIER) cc_final: 0.2614 (mtmm) REVERT: 3 574 LEU cc_start: 0.2339 (OUTLIER) cc_final: 0.1841 (pt) REVERT: 3 583 MET cc_start: 0.2337 (mtm) cc_final: 0.1265 (pmm) REVERT: 3 630 MET cc_start: 0.3313 (ttm) cc_final: 0.2729 (tpp) REVERT: 3 721 LEU cc_start: 0.7399 (tt) cc_final: 0.7029 (tp) REVERT: 3 749 GLN cc_start: 0.1946 (OUTLIER) cc_final: 0.1269 (mt0) REVERT: 3 754 ILE cc_start: 0.6584 (OUTLIER) cc_final: 0.6301 (mt) REVERT: 3 809 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.6830 (mp0) REVERT: 3 817 GLN cc_start: 0.7884 (tp40) cc_final: 0.7304 (tp40) REVERT: 3 821 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6232 (mp0) REVERT: 3 1143 HIS cc_start: 0.7795 (m90) cc_final: 0.7292 (t-90) REVERT: 3 1188 ASN cc_start: 0.7213 (OUTLIER) cc_final: 0.6656 (p0) REVERT: D 143 ASP cc_start: 0.5471 (p0) cc_final: 0.4729 (p0) REVERT: D 189 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8496 (tp) REVERT: E 169 LYS cc_start: 0.7002 (mttt) cc_final: 0.6147 (ttpt) REVERT: E 176 LYS cc_start: 0.5503 (OUTLIER) cc_final: 0.4811 (tmtp) REVERT: E 177 LYS cc_start: 0.4923 (tptt) cc_final: 0.3769 (ttpm) REVERT: E 196 LYS cc_start: 0.4386 (OUTLIER) cc_final: 0.3636 (mmmt) REVERT: E 205 ASP cc_start: 0.4366 (t0) cc_final: 0.3871 (p0) REVERT: E 237 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.6223 (tm-30) REVERT: E 241 LYS cc_start: 0.4404 (tptm) cc_final: 0.3477 (ttpp) outliers start: 114 outliers final: 77 residues processed: 439 average time/residue: 1.3377 time to fit residues: 702.5264 Evaluate side-chains 448 residues out of total 4095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 347 time to evaluate : 3.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 576 VAL Chi-restraints excluded: chain 1 residue 585 GLU Chi-restraints excluded: chain 1 residue 617 ILE Chi-restraints excluded: chain 1 residue 705 SER Chi-restraints excluded: chain 1 residue 735 ILE Chi-restraints excluded: chain 1 residue 781 ASP Chi-restraints excluded: chain 1 residue 801 VAL Chi-restraints excluded: chain 1 residue 839 GLU Chi-restraints excluded: chain 1 residue 867 MET Chi-restraints excluded: chain 1 residue 925 VAL Chi-restraints excluded: chain 1 residue 964 THR Chi-restraints excluded: chain 1 residue 967 GLU Chi-restraints excluded: chain 1 residue 997 LEU Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1059 CYS Chi-restraints excluded: chain 1 residue 1061 GLU Chi-restraints excluded: chain 1 residue 1063 LEU Chi-restraints excluded: chain 1 residue 1086 LYS Chi-restraints excluded: chain 1 residue 1113 THR Chi-restraints excluded: chain 1 residue 1123 CYS Chi-restraints excluded: chain 1 residue 1126 PHE Chi-restraints excluded: chain 1 residue 1135 GLU Chi-restraints excluded: chain 1 residue 1160 GLU Chi-restraints excluded: chain 1 residue 1207 SER Chi-restraints excluded: chain 1 residue 1241 ILE Chi-restraints excluded: chain 1 residue 1260 LYS Chi-restraints excluded: chain 2 residue 498 VAL 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 64 SER Chi-restraints excluded: chain 3 residue 114 ARG Chi-restraints excluded: chain 3 residue 136 GLU Chi-restraints excluded: chain 3 residue 146 ARG Chi-restraints excluded: chain 3 residue 151 ARG Chi-restraints excluded: chain 3 residue 178 GLU Chi-restraints excluded: chain 3 residue 223 LYS Chi-restraints excluded: chain 3 residue 253 GLU Chi-restraints excluded: chain 3 residue 342 LEU Chi-restraints excluded: chain 3 residue 390 ARG Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 433 SER Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 459 VAL Chi-restraints excluded: chain 3 residue 462 VAL Chi-restraints excluded: chain 3 residue 476 VAL Chi-restraints excluded: chain 3 residue 490 THR Chi-restraints excluded: chain 3 residue 524 ILE Chi-restraints excluded: chain 3 residue 533 VAL Chi-restraints excluded: chain 3 residue 534 ASN Chi-restraints excluded: chain 3 residue 546 LYS Chi-restraints excluded: chain 3 residue 549 VAL Chi-restraints excluded: chain 3 residue 574 LEU Chi-restraints excluded: chain 3 residue 677 THR Chi-restraints excluded: chain 3 residue 704 VAL Chi-restraints excluded: chain 3 residue 705 ARG Chi-restraints excluded: chain 3 residue 713 LEU Chi-restraints excluded: chain 3 residue 728 ARG Chi-restraints excluded: chain 3 residue 738 THR Chi-restraints excluded: chain 3 residue 749 GLN Chi-restraints excluded: chain 3 residue 754 ILE Chi-restraints excluded: chain 3 residue 755 VAL Chi-restraints excluded: chain 3 residue 759 THR Chi-restraints excluded: chain 3 residue 809 GLU Chi-restraints excluded: chain 3 residue 821 GLU Chi-restraints excluded: chain 3 residue 834 LEU Chi-restraints excluded: chain 3 residue 865 VAL Chi-restraints excluded: chain 3 residue 897 SER Chi-restraints excluded: chain 3 residue 965 LYS Chi-restraints excluded: chain 3 residue 1008 SER Chi-restraints excluded: chain 3 residue 1065 GLU Chi-restraints excluded: chain 3 residue 1120 THR Chi-restraints excluded: chain 3 residue 1150 SER Chi-restraints excluded: chain 3 residue 1170 VAL Chi-restraints excluded: chain 3 residue 1188 ASN Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain 5 residue 17 LYS 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 402 LEU Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 472 GLN 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 148 GLU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 176 LYS Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 232 MET Chi-restraints excluded: chain E residue 237 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 280 optimal weight: 50.0000 chunk 451 optimal weight: 8.9990 chunk 275 optimal weight: 40.0000 chunk 214 optimal weight: 1.9990 chunk 313 optimal weight: 4.9990 chunk 473 optimal weight: 0.0370 chunk 435 optimal weight: 50.0000 chunk 376 optimal weight: 50.0000 chunk 39 optimal weight: 3.9990 chunk 291 optimal weight: 10.0000 chunk 231 optimal weight: 50.0000 overall best weight: 4.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 804 ASN 1 973 HIS ** 3 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 219 HIS ** 3 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6210 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 32944 Z= 0.394 Angle : 0.713 14.748 44527 Z= 0.368 Chirality : 0.050 0.277 3946 Planarity : 0.005 0.073 5945 Dihedral : 14.525 132.389 7288 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.97 % Favored : 94.96 % Rotamer: Outliers : 4.67 % Allowed : 25.23 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.03 (0.12), residues: 4597 helix: 1.51 (0.13), residues: 1606 sheet: 0.09 (0.17), residues: 973 loop : -1.25 (0.13), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP 1 938 HIS 0.010 0.002 HIS 31135 PHE 0.028 0.003 PHE 11153 TYR 0.024 0.003 TYR 3 926 ARG 0.008 0.001 ARG 3 274 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9194 Ramachandran restraints generated. 4597 Oldfield, 0 Emsley, 4597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 4095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 352 time to evaluate : 3.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 558 ARG cc_start: 0.6918 (mmp80) cc_final: 0.6647 (mmp80) REVERT: 1 656 LYS cc_start: 0.7296 (mmtp) cc_final: 0.6881 (mttt) REVERT: 1 839 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6978 (mp0) REVERT: 1 942 ASN cc_start: 0.6829 (t0) cc_final: 0.6580 (m-40) REVERT: 1 957 ARG cc_start: 0.7504 (ttm110) cc_final: 0.6793 (mtp-110) REVERT: 1 961 VAL cc_start: 0.8158 (t) cc_final: 0.7868 (p) REVERT: 1 967 GLU cc_start: 0.4603 (OUTLIER) cc_final: 0.3852 (tp30) REVERT: 1 1037 ASP cc_start: 0.7933 (m-30) cc_final: 0.7520 (m-30) REVERT: 1 1041 ARG cc_start: 0.7516 (mmm160) cc_final: 0.7236 (tpt90) REVERT: 1 1135 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7325 (tt0) REVERT: 1 1160 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.6939 (tt0) REVERT: 3 114 ARG cc_start: 0.9328 (OUTLIER) cc_final: 0.9032 (ttp-170) REVERT: 3 136 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6600 (mt-10) REVERT: 3 151 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7097 (mtt-85) REVERT: 3 178 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7202 (mp0) REVERT: 3 253 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7126 (tp30) REVERT: 3 326 ARG cc_start: 0.8624 (mtt180) cc_final: 0.8226 (mtt180) REVERT: 3 377 MET cc_start: 0.8435 (mtt) cc_final: 0.7933 (mtp) REVERT: 3 390 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.7650 (ptt90) REVERT: 3 447 MET cc_start: 0.1679 (ttt) cc_final: -0.1532 (mmp) REVERT: 3 546 LYS cc_start: 0.3083 (OUTLIER) cc_final: 0.2752 (mtmm) REVERT: 3 574 LEU cc_start: 0.2345 (OUTLIER) cc_final: 0.1798 (pt) REVERT: 3 583 MET cc_start: 0.2588 (mtm) cc_final: 0.2102 (tmm) REVERT: 3 721 LEU cc_start: 0.7480 (tt) cc_final: 0.7148 (tp) REVERT: 3 749 GLN cc_start: 0.1708 (OUTLIER) cc_final: 0.1078 (mt0) REVERT: 3 754 ILE cc_start: 0.6396 (OUTLIER) cc_final: 0.6125 (mt) REVERT: 3 809 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.6802 (mp0) REVERT: 3 817 GLN cc_start: 0.7930 (tp40) cc_final: 0.7270 (tp40) REVERT: 3 821 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6317 (mp0) REVERT: 3 1143 HIS cc_start: 0.7847 (m90) cc_final: 0.7320 (t-90) REVERT: 3 1188 ASN cc_start: 0.7086 (OUTLIER) cc_final: 0.6513 (p0) REVERT: 6 25 LYS cc_start: 0.8182 (ttpt) cc_final: 0.7360 (pttm) REVERT: C 417 ARG cc_start: 0.5791 (mmt90) cc_final: 0.5550 (mmt180) REVERT: D 143 ASP cc_start: 0.5304 (p0) cc_final: 0.4365 (p0) REVERT: D 189 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8516 (tp) REVERT: D 202 ASP cc_start: 0.7608 (t70) cc_final: 0.6933 (t70) REVERT: D 203 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6620 (mt-10) REVERT: E 169 LYS cc_start: 0.7013 (mttt) cc_final: 0.6155 (ttpt) REVERT: E 177 LYS cc_start: 0.4877 (tptt) cc_final: 0.3749 (ttpm) REVERT: E 196 LYS cc_start: 0.4417 (OUTLIER) cc_final: 0.3594 (mmmt) REVERT: E 205 ASP cc_start: 0.4274 (t0) cc_final: 0.3821 (p0) REVERT: E 237 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6240 (tm-30) outliers start: 106 outliers final: 74 residues processed: 436 average time/residue: 1.3397 time to fit residues: 700.9687 Evaluate side-chains 440 residues out of total 4095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 346 time to evaluate : 3.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 576 VAL Chi-restraints excluded: chain 1 residue 585 GLU Chi-restraints excluded: chain 1 residue 602 LYS Chi-restraints excluded: chain 1 residue 617 ILE Chi-restraints excluded: chain 1 residue 705 SER Chi-restraints excluded: chain 1 residue 735 ILE Chi-restraints excluded: chain 1 residue 781 ASP Chi-restraints excluded: chain 1 residue 801 VAL Chi-restraints excluded: chain 1 residue 839 GLU Chi-restraints excluded: chain 1 residue 925 VAL Chi-restraints excluded: chain 1 residue 964 THR Chi-restraints excluded: chain 1 residue 967 GLU Chi-restraints excluded: chain 1 residue 997 LEU Chi-restraints excluded: chain 1 residue 1020 LEU Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1059 CYS Chi-restraints excluded: chain 1 residue 1063 LEU Chi-restraints excluded: chain 1 residue 1113 THR Chi-restraints excluded: chain 1 residue 1123 CYS Chi-restraints excluded: chain 1 residue 1126 PHE Chi-restraints excluded: chain 1 residue 1135 GLU Chi-restraints excluded: chain 1 residue 1160 GLU Chi-restraints excluded: chain 1 residue 1170 THR Chi-restraints excluded: chain 1 residue 1207 SER Chi-restraints excluded: chain 1 residue 1241 ILE Chi-restraints excluded: chain 2 residue 498 VAL 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 64 SER Chi-restraints excluded: chain 3 residue 114 ARG Chi-restraints excluded: chain 3 residue 136 GLU Chi-restraints excluded: chain 3 residue 146 ARG Chi-restraints excluded: chain 3 residue 151 ARG Chi-restraints excluded: chain 3 residue 178 GLU Chi-restraints excluded: chain 3 residue 223 LYS Chi-restraints excluded: chain 3 residue 253 GLU Chi-restraints excluded: chain 3 residue 342 LEU Chi-restraints excluded: chain 3 residue 390 ARG Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 433 SER Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 459 VAL Chi-restraints excluded: chain 3 residue 462 VAL Chi-restraints excluded: chain 3 residue 476 VAL Chi-restraints excluded: chain 3 residue 490 THR Chi-restraints excluded: chain 3 residue 524 ILE Chi-restraints excluded: chain 3 residue 531 LYS Chi-restraints excluded: chain 3 residue 533 VAL Chi-restraints excluded: chain 3 residue 546 LYS Chi-restraints excluded: chain 3 residue 549 VAL Chi-restraints excluded: chain 3 residue 574 LEU Chi-restraints excluded: chain 3 residue 677 THR Chi-restraints excluded: chain 3 residue 704 VAL Chi-restraints excluded: chain 3 residue 705 ARG Chi-restraints excluded: chain 3 residue 728 ARG Chi-restraints excluded: chain 3 residue 738 THR Chi-restraints excluded: chain 3 residue 749 GLN Chi-restraints excluded: chain 3 residue 754 ILE Chi-restraints excluded: chain 3 residue 755 VAL Chi-restraints excluded: chain 3 residue 759 THR Chi-restraints excluded: chain 3 residue 809 GLU Chi-restraints excluded: chain 3 residue 821 GLU Chi-restraints excluded: chain 3 residue 834 LEU Chi-restraints excluded: chain 3 residue 865 VAL Chi-restraints excluded: chain 3 residue 897 SER Chi-restraints excluded: chain 3 residue 919 SER Chi-restraints excluded: chain 3 residue 965 LYS Chi-restraints excluded: chain 3 residue 1008 SER Chi-restraints excluded: chain 3 residue 1065 GLU Chi-restraints excluded: chain 3 residue 1120 THR Chi-restraints excluded: chain 3 residue 1150 SER Chi-restraints excluded: chain 3 residue 1170 VAL Chi-restraints excluded: chain 3 residue 1188 ASN 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 402 LEU Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 472 GLN 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 148 GLU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 196 LYS Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 232 MET Chi-restraints excluded: chain E residue 237 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 475 random chunks: chunk 299 optimal weight: 50.0000 chunk 401 optimal weight: 50.0000 chunk 115 optimal weight: 0.8980 chunk 347 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 377 optimal weight: 6.9990 chunk 157 optimal weight: 8.9990 chunk 387 optimal weight: 50.0000 chunk 47 optimal weight: 0.0670 chunk 69 optimal weight: 3.9990 overall best weight: 2.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 804 ASN 1 973 HIS 11107 GLN ** 3 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 219 HIS 3 363 HIS ** 3 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 GLN D 244 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.251608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.205593 restraints weight = 53586.751| |-----------------------------------------------------------------------------| r_work (start): 0.4270 rms_B_bonded: 2.90 r_work: 0.3325 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 32944 Z= 0.281 Angle : 0.616 13.341 44527 Z= 0.316 Chirality : 0.045 0.226 3946 Planarity : 0.005 0.068 5945 Dihedral : 14.429 126.325 7286 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.41 % Favored : 95.57 % Rotamer: Outliers : 4.49 % Allowed : 25.50 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.11 (0.13), residues: 4597 helix: 1.63 (0.14), residues: 1610 sheet: 0.13 (0.17), residues: 967 loop : -1.26 (0.13), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP 1 938 HIS 0.010 0.002 HIS C 425 PHE 0.022 0.002 PHE 11153 TYR 0.021 0.002 TYR 3 926 ARG 0.006 0.001 ARG 31013 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12469.36 seconds wall clock time: 221 minutes 24.28 seconds (13284.28 seconds total)