Starting phenix.real_space_refine on Sun Mar 24 18:16:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vpx_32074/03_2024/7vpx_32074_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vpx_32074/03_2024/7vpx_32074.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vpx_32074/03_2024/7vpx_32074_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vpx_32074/03_2024/7vpx_32074_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vpx_32074/03_2024/7vpx_32074_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vpx_32074/03_2024/7vpx_32074.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vpx_32074/03_2024/7vpx_32074.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vpx_32074/03_2024/7vpx_32074_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vpx_32074/03_2024/7vpx_32074_neut_updated.pdb" } resolution = 3.0 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= 0.043 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 6 6.06 5 P 316 5.49 5 S 164 5.16 5 C 25154 2.51 5 N 8130 2.21 5 O 9470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "J GLU 207": "OE1" <-> "OE2" Residue "J PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 213": "OE1" <-> "OE2" Residue "J GLU 214": "OE1" <-> "OE2" Residue "J ARG 216": "NH1" <-> "NH2" 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 781": "OD1" <-> "OD2" 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 967": "OE1" <-> "OE2" 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 PHE 1126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 1135": "OE1" <-> "OE2" Residue "1 ARG 1137": "NH1" <-> "NH2" 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 ARG 508": "NH1" <-> "NH2" Residue "2 TYR 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 530": "NH1" <-> "NH2" Residue "2 TYR 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 573": "OD1" <-> "OD2" Residue "2 PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 591": "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 "C TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "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" Residue "O GLU 26": "OE1" <-> "OE2" Residue "O GLU 65": "OE1" <-> "OE2" Residue "O GLU 83": "OE1" <-> "OE2" Residue "m GLU 28": "OE1" <-> "OE2" Residue "m ARG 73": "NH1" <-> "NH2" Residue "h GLU 18": "OE1" <-> "OE2" Residue "h ARG 61": "NH1" <-> "NH2" Residue "h ARG 66": "NH1" <-> "NH2" Residue "k GLU 63": "OE1" <-> "OE2" Residue "M PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 61": "OE1" <-> "OE2" Residue "n ARG 32": "NH1" <-> "NH2" Residue "l GLU 44": "OE1" <-> "OE2" Residue "l ARG 76": "NH1" <-> "NH2" Residue "i ARG 61": "NH1" <-> "NH2" Residue "i GLU 68": "OE1" <-> "OE2" Residue "i ARG 102": "NH1" <-> "NH2" Residue "N ARG 21": "NH1" <-> "NH2" Residue "N GLU 44": "OE1" <-> "OE2" Residue "j ARG 51": "NH1" <-> "NH2" Residue "j TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 43240 Number of models: 1 Model: "" Number of chains: 39 Chain: "B" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 799 Classifications: {'peptide': 147} Incomplete info: {'backbone_only': 89} Link IDs: {'PTRANS': 8, 'TRANS': 138} Chain breaks: 2 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: "D" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 604 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain breaks: 3 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 400 Unresolved non-hydrogen angles: 501 Unresolved non-hydrogen dihedrals: 317 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 8, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 209 Chain: "J" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 369 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'TRANS': 53} Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 9, 'ARG:plan': 6, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 79 Chain: "H" Number of atoms: 2754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 2754 Inner-chain residues flagged as termini: ['pdbres=" U H 69 "', 'pdbres=" G H 81 "'] Classifications: {'RNA': 130} Modifications used: {'5*END': 2, 'rna2p_pur': 8, 'rna2p_pyr': 11, 'rna3p_pur': 55, 'rna3p_pyr': 56} Link IDs: {'rna2p': 19, 'rna3p': 110} Chain breaks: 1 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: 1325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1325 Classifications: {'peptide': 187} Incomplete info: {'backbone_only': 45} Link IDs: {'PTRANS': 22, 'TRANS': 164} Chain breaks: 4 Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 287 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 97 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: "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: "C" Number of atoms: 2127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 2127 Classifications: {'peptide': 425} Incomplete info: {'backbone_only': 293, 'truncation_to_alanine': 22} Link IDs: {'PTRANS': 13, 'TRANS': 411} 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: "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: "I" Number of atoms: 314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 314 Classifications: {'RNA': 15} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 4, 'rna3p_pyr': 7} Link IDs: {'rna2p': 3, 'rna3p': 11} Chain: "K" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 216 Classifications: {'RNA': 10} Modifications used: {'5*END': 1, 'rna3p_pur': 7, 'rna3p_pyr': 3} Link IDs: {'rna3p': 9} Chain: "L" Number of atoms: 3485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 3485 Classifications: {'RNA': 164} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 13, 'rna3p_pur': 68, 'rna3p_pyr': 72} Link IDs: {'rna2p': 24, 'rna3p': 139} Chain: "O" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1643 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 19, 'TRANS': 181} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "m" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 576 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "h" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 641 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "k" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 692 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "M" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 787 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 94} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Chain: "n" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 568 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "l" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 638 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "i" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 764 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 425 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "j" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 637 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "6" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 613 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 40 Unusual residues: {' ZN': 3, 'SJT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 135 SG CYS B 56 74.753 111.826 114.577 1.00166.32 S ATOM 158 SG CYS B 59 77.824 111.267 112.284 1.00166.67 S ATOM 24734 SG CYS C 408 91.555 76.678 105.430 1.00 93.55 S ATOM 41567 SG CYS N 6 92.835 166.628 285.244 1.00175.75 S ATOM 41593 SG CYS N 9 90.952 167.499 282.665 1.00127.41 S ATOM 42609 SG CYS 6 11 111.586 102.516 158.498 1.00 81.38 S ATOM 42872 SG CYS 6 46 112.367 102.494 162.268 1.00 86.33 S ATOM 42895 SG CYS 6 49 111.536 105.427 160.989 1.00 98.99 S ATOM 43166 SG CYS 6 85 108.738 102.666 161.110 1.00 76.95 S ATOM 42747 SG CYS 6 30 95.509 102.858 158.687 1.00 93.84 S ATOM 42768 SG CYS 6 33 92.619 102.706 155.487 1.00 90.47 S ATOM 43063 SG CYS 6 72 91.642 100.675 158.242 1.00 84.61 S ATOM 43087 SG CYS 6 75 94.780 99.667 156.533 1.00 80.84 S ATOM 42696 SG CYS 6 23 99.802 115.957 162.644 1.00106.09 S ATOM 42967 SG CYS 6 58 101.920 112.925 162.468 1.00109.30 S ATOM 42988 SG CYS 6 61 101.825 115.579 159.222 1.00114.85 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ASN 2 624 " occ=0.00 ... (2 atoms not shown) pdb=" O ASN 2 624 " occ=0.00 residue: pdb=" N ALA 2 625 " occ=0.00 ... (2 atoms not shown) pdb=" O ALA 2 625 " occ=0.00 residue: pdb=" N HIS 2 626 " occ=0.00 ... (2 atoms not shown) pdb=" O HIS 2 626 " occ=0.00 residue: pdb=" N LYS 2 627 " occ=0.00 ... (2 atoms not shown) pdb=" O LYS 2 627 " occ=0.00 Time building chain proxies: 23.42, per 1000 atoms: 0.54 Number of scatterers: 43240 At special positions: 0 Unit cell: (168.485, 207.617, 372.841, 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 6 29.99 S 164 16.00 P 316 15.00 O 9470 8.00 N 8130 7.00 C 25154 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 Atom "ATOM 32335 O4' A L 29 .*. O " rejected from bonding due to valence issues. Atom "ATOM 32335 O4' A L 29 .*. O " rejected from bonding due to valence issues. Atom "ATOM 32335 O4' A L 29 .*. O " rejected from bonding due to valence issues. Atom "ATOM 32397 O4' A L 32 .*. O " rejected from bonding due to valence issues. Atom "ATOM 32377 O4' C L 31 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 18.39 Conformation dependent library (CDL) restraints added in 7.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 6 201 " pdb="ZN ZN 6 201 " - pdb=" SG CYS 6 46 " pdb="ZN ZN 6 201 " - pdb=" SG CYS 6 49 " pdb="ZN ZN 6 201 " - pdb=" SG CYS 6 11 " pdb="ZN ZN 6 201 " - pdb=" SG CYS 6 85 " pdb=" ZN 6 202 " pdb="ZN ZN 6 202 " - pdb=" SG CYS 6 75 " pdb="ZN ZN 6 202 " - pdb=" SG CYS 6 30 " pdb="ZN ZN 6 202 " - pdb=" SG CYS 6 33 " pdb="ZN ZN 6 202 " - pdb=" SG CYS 6 72 " pdb=" ZN 6 203 " pdb="ZN ZN 6 203 " - pdb=" SG CYS 6 58 " pdb="ZN ZN 6 203 " - pdb=" SG CYS 6 61 " pdb="ZN ZN 6 203 " - pdb=" SG CYS 6 23 " pdb=" ZN B 500 " pdb="ZN ZN B 500 " - pdb=" NE2 HIS B 72 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 56 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 59 " pdb="ZN ZN B 500 " - pdb=" ND1 HIS B 78 " 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 " pdb=" ZN N 201 " pdb="ZN ZN N 201 " - pdb=" NE2 HIS N 24 " pdb="ZN ZN N 201 " - pdb=" ND1 HIS N 30 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 9 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 6 " Number of angles added : 14 10998 Ramachandran restraints generated. 5499 Oldfield, 0 Emsley, 5499 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6884 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 179 helices and 67 sheets defined 33.3% alpha, 18.4% beta 82 base pairs and 157 stacking pairs defined. Time for finding SS restraints: 19.00 Creating SS restraints... Processing helix chain 'B' and resid 66 through 73 Processing helix chain 'B' and resid 76 through 86 Processing helix chain 'B' and resid 105 through 108 No H-bonds generated for 'chain 'B' and resid 105 through 108' Processing helix chain 'D' and resid 47 through 67 Processing helix chain 'D' and resid 97 through 118 Processing helix chain 'D' and resid 152 through 157 Processing helix chain 'D' and resid 159 through 171 removed outlier: 6.423A pdb=" N THR D 163 " --> pdb=" O ARG D 160 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU D 164 " --> pdb=" O GLY D 161 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU D 168 " --> pdb=" O LYS D 165 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N CYS D 171 " --> pdb=" O GLU D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 228 Processing helix chain 'J' and resid 181 through 214 removed outlier: 3.695A pdb=" N ARG J 206 " --> pdb=" O ALA J 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 216 through 232 Processing helix chain '1' and resid 492 through 505 removed outlier: 5.210A pdb=" N LEU 1 500 " --> pdb=" O LYS 1 496 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N LEU 1 501 " --> pdb=" O ILE 1 497 " (cutoff:3.500A) removed outlier: 4.995A 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: 5.208A 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: 5.382A pdb=" N HIS 1 572 " --> pdb=" O PRO 1 569 " (cutoff:3.500A) Processing helix chain '1' and resid 587 through 603 Processing helix chain '1' and resid 606 through 613 Processing helix chain '1' and resid 615 through 617 No H-bonds generated for 'chain '1' and resid 615 through 617' Processing helix chain '1' and resid 622 through 639 removed outlier: 3.617A 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: 7.429A pdb=" N CYS 1 677 " --> pdb=" O ILE 1 673 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ALA 1 678 " --> pdb=" O LEU 1 674 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ILE 1 679 " --> pdb=" O MET 1 675 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LEU 1 680 " --> pdb=" O GLY 1 676 " (cutoff:3.500A) Proline residue: 1 681 - end of helix removed outlier: 5.217A pdb=" N ARG 1 684 " --> pdb=" O LEU 1 680 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N SER 1 685 " --> pdb=" O PRO 1 681 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N HIS 1 692 " --> pdb=" O GLU 1 688 " (cutoff:3.500A) removed outlier: 6.016A 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 721 through 723 No H-bonds generated for 'chain '1' and resid 721 through 723' 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: 3.651A pdb=" N GLU 1 768 " --> pdb=" O TYR 1 764 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLN 1 778 " --> pdb=" O ILE 1 774 " (cutoff:3.500A) Processing helix chain '1' and resid 784 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: 4.873A pdb=" N ASP 1 856 " --> pdb=" O ARG 1 852 " (cutoff:3.500A) Processing helix chain '1' and resid 862 through 879 Processing helix chain '1' and resid 886 through 901 Processing helix chain '1' and resid 908 through 924 removed outlier: 6.514A 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 963 removed outlier: 3.588A pdb=" N GLN 1 950 " --> pdb=" O LYS 1 946 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL 1 960 " --> pdb=" O SER 1 956 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N VAL 1 961 " --> pdb=" O ARG 1 957 " (cutoff:3.500A) Processing helix chain '1' and resid 969 through 982 removed outlier: 3.902A pdb=" N LEU 1 982 " --> pdb=" O LEU 1 978 " (cutoff:3.500A) Processing helix chain '1' and resid 987 through 1001 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 1052 through 1067 removed outlier: 3.551A pdb=" N LEU 11063 " --> pdb=" O PHE 11060 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU 11066 " --> pdb=" O LEU 11063 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS 11067 " --> pdb=" O GLU 11064 " (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 1127 No H-bonds generated for 'chain '1' and resid 1125 through 1127' Processing helix chain '1' and resid 1129 through 1137 removed outlier: 3.575A pdb=" N TYR 11136 " --> pdb=" O LEU 11132 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG 11137 " --> pdb=" O MET 11133 " (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: 5.560A 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: 3.690A 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: 3.602A pdb=" N VAL 11239 " --> pdb=" O GLU 11235 " (cutoff:3.500A) Processing helix chain '1' and resid 1243 through 1253 removed outlier: 5.028A pdb=" N GLN 11252 " --> pdb=" O GLN 11248 " (cutoff:3.500A) removed outlier: 5.124A 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 530 Processing helix chain '2' and resid 568 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: 4.962A pdb=" N ASN 31183 " --> pdb=" O CYS 31179 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER 31184 " --> pdb=" O GLU 31180 " (cutoff:3.500A) Processing helix chain '3' and resid 1187 through 1194 Processing helix chain '3' and resid 1201 through 1215 removed outlier: 3.642A pdb=" N ILE 31211 " --> pdb=" O LYS 31207 " (cutoff:3.500A) removed outlier: 3.667A 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 '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 '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: 4.718A 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 Processing helix chain 'C' and resid 419 through 426 removed outlier: 3.516A pdb=" N ARG C 424 " --> pdb=" O LYS C 420 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE C 426 " --> pdb=" O PHE C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 438 removed outlier: 4.094A 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 '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: 4.492A pdb=" N GLN G 173 " --> pdb=" O MET G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 206 Processing helix chain 'a' and resid 20 through 26 Processing helix chain 'a' and resid 28 through 37 removed outlier: 3.980A pdb=" N GLN a 34 " --> pdb=" O VAL a 31 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL a 36 " --> pdb=" O THR a 33 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LYS a 37 " --> pdb=" O GLN a 34 " (cutoff:3.500A) Processing helix chain 'b' and resid 7 through 13 Processing helix chain 'c' and resid 17 through 27 Processing helix chain 'e' and resid 5 through 12 Processing helix chain 'f' and resid 74 through 76 No H-bonds generated for 'chain 'f' and resid 74 through 76' Processing helix chain 'g' and resid 3 through 8 Processing helix chain 'g' and resid 76 through 79 No H-bonds generated for 'chain 'g' and resid 76 through 79' Processing helix chain 'O' and resid 7 through 12 removed outlier: 4.933A pdb=" N LEU O 12 " --> pdb=" O ASN O 8 " (cutoff:3.500A) Processing helix chain 'O' and resid 29 through 31 No H-bonds generated for 'chain 'O' and resid 29 through 31' Processing helix chain 'O' and resid 42 through 44 No H-bonds generated for 'chain 'O' and resid 42 through 44' Processing helix chain 'O' and resid 50 through 52 No H-bonds generated for 'chain 'O' and resid 50 through 52' Processing helix chain 'O' and resid 64 through 88 removed outlier: 3.580A pdb=" N LYS O 87 " --> pdb=" O GLU O 83 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET O 88 " --> pdb=" O THR O 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 91 through 93 No H-bonds generated for 'chain 'O' and resid 91 through 93' Processing helix chain 'O' and resid 101 through 103 No H-bonds generated for 'chain 'O' and resid 101 through 103' Processing helix chain 'O' and resid 116 through 126 removed outlier: 4.035A pdb=" N VAL O 125 " --> pdb=" O ARG O 121 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N TYR O 126 " --> pdb=" O GLU O 122 " (cutoff:3.500A) Processing helix chain 'O' and resid 154 through 163 Processing helix chain 'O' and resid 190 through 192 No H-bonds generated for 'chain 'O' and resid 190 through 192' Processing helix chain 'm' and resid 7 through 14 Processing helix chain 'm' and resid 66 through 68 No H-bonds generated for 'chain 'm' and resid 66 through 68' Processing helix chain 'h' and resid 4 through 9 removed outlier: 3.502A pdb=" N LYS h 9 " --> pdb=" O ARG h 5 " (cutoff:3.500A) Processing helix chain 'h' and resid 62 through 64 No H-bonds generated for 'chain 'h' and resid 62 through 64' Processing helix chain 'h' and resid 76 through 79 No H-bonds generated for 'chain 'h' and resid 76 through 79' Processing helix chain 'k' and resid 7 through 12 removed outlier: 4.587A pdb=" N HIS k 12 " --> pdb=" O LYS k 8 " (cutoff:3.500A) Processing helix chain 'k' and resid 74 through 76 No H-bonds generated for 'chain 'k' and resid 74 through 76' Processing helix chain 'M' and resid 23 through 37 removed outlier: 4.393A pdb=" N GLN M 36 " --> pdb=" O ALA M 32 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N PHE M 37 " --> pdb=" O ILE M 33 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 72 Processing helix chain 'M' and resid 92 through 98 Processing helix chain 'n' and resid 64 through 66 No H-bonds generated for 'chain 'n' and resid 64 through 66' Processing helix chain 'l' and resid 17 through 27 Processing helix chain 'l' and resid 81 through 83 No H-bonds generated for 'chain 'l' and resid 81 through 83' Processing helix chain 'i' and resid 19 through 26 Processing helix chain 'i' and resid 28 through 38 removed outlier: 4.107A pdb=" N GLN i 34 " --> pdb=" O VAL i 31 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL i 36 " --> pdb=" O THR i 33 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN i 38 " --> pdb=" O SER i 35 " (cutoff:3.500A) Processing helix chain 'i' and resid 103 through 105 No H-bonds generated for 'chain 'i' and resid 103 through 105' Processing helix chain 'N' and resid 18 through 25 Processing helix chain 'N' and resid 28 through 50 removed outlier: 3.629A pdb=" N GLN N 45 " --> pdb=" O TRP N 41 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA N 46 " --> pdb=" O MET N 42 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER N 48 " --> pdb=" O GLU N 44 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU N 49 " --> pdb=" O GLN N 45 " (cutoff:3.500A) Processing helix chain 'j' and resid 5 through 13 Processing helix chain 'j' and resid 65 through 67 No H-bonds generated for 'chain 'j' and resid 65 through 67' Processing helix chain 'j' and resid 75 through 79 Processing helix chain '6' and resid 48 through 50 No H-bonds generated for 'chain '6' and resid 48 through 50' 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 sheet with id= A, first strand: chain 'B' and resid 46 through 48 Processing sheet with id= B, 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= C, first strand: chain 'B' and resid 148 through 153 removed outlier: 4.029A pdb=" N GLN B 167 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 136 through 141 Processing sheet with id= E, 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: 6.543A pdb=" N ILE 31126 " --> pdb=" O LEU 3 8 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N GLU 31115 " --> pdb=" O PRO 31131 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER 31103 " --> pdb=" O THR 31120 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '3' and resid 16 through 20 removed outlier: 3.668A pdb=" N PHE 3 16 " --> pdb=" O SER 3 33 " (cutoff:3.500A) removed outlier: 3.594A 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: 5.754A pdb=" N THR 3 52 " --> pdb=" O ARG 3 42 " (cutoff:3.500A) Processing sheet with id= G, 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: 6.534A pdb=" N TYR 3 77 " --> pdb=" O ALA 3 67 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N SER 3 82 " --> pdb=" O ARG 3 86 " (cutoff:3.500A) removed outlier: 5.910A 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= H, first strand: chain '3' and resid 120 through 123 Processing sheet with id= I, first strand: chain '3' and resid 144 through 146 Processing sheet with id= J, 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: 6.675A pdb=" N ALA 3 183 " --> pdb=" O VAL 3 170 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLY 3 172 " --> pdb=" O MET 3 181 " (cutoff:3.500A) removed outlier: 7.247A 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: 6.581A pdb=" N GLU 3 212 " --> pdb=" O ARG 3 222 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ARG 3 222 " --> pdb=" O GLU 3 212 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ASP 3 214 " --> pdb=" O VAL 3 220 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL 3 220 " --> pdb=" O ASP 3 214 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '3' and resid 235 through 237 Processing sheet with id= L, 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: 4.236A 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: 5.751A 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: 5.605A pdb=" N LEU 3 327 " --> pdb=" O THR 3 314 " (cutoff:3.500A) removed outlier: 6.806A 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= M, first strand: chain '3' and resid 336 through 342 removed outlier: 7.354A pdb=" N ALA 3 350 " --> pdb=" O ALA 3 337 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N MET 3 339 " --> pdb=" O PHE 3 348 " (cutoff:3.500A) removed outlier: 6.699A 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= N, first strand: chain '3' and resid 774 through 780 Processing sheet with id= O, first strand: chain '3' and resid 474 through 477 Processing sheet with id= P, first strand: chain '3' and resid 533 through 537 removed outlier: 3.823A pdb=" N GLN 3 518 " --> pdb=" O ARG 3 525 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain '3' and resid 546 through 548 removed outlier: 4.333A 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= R, first strand: chain '3' and resid 566 through 568 Processing sheet with id= S, 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: 4.263A pdb=" N MET 3 590 " --> pdb=" O ALA 3 606 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ALA 3 606 " --> pdb=" O MET 3 590 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU 3 609 " --> pdb=" O THR 3 613 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N THR 3 613 " --> pdb=" O LEU 3 609 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER 3 629 " --> pdb=" O ILE 3 616 " (cutoff:3.500A) Processing sheet with id= T, 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= U, 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= V, 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: 5.196A pdb=" N GLU 3 446 " --> pdb=" O ALA 3 766 " (cutoff:3.500A) Processing sheet with id= W, 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: 4.377A 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= X, 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: 6.542A pdb=" N LEU 3 906 " --> pdb=" O VAL 3 891 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL 3 893 " --> pdb=" O TYR 3 904 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N TYR 3 904 " --> pdb=" O VAL 3 893 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N HIS 3 941 " --> pdb=" O THR 3 927 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain '3' and resid 949 through 955 removed outlier: 6.776A 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: 6.674A 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= Z, 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: 4.347A pdb=" N ILE 3 993 " --> pdb=" O ILE 31001 " (cutoff:3.500A) removed outlier: 6.642A 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: 6.650A 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: 7.195A pdb=" N LYS 31015 " --> pdb=" O LEU 31021 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LEU 31021 " --> pdb=" O LYS 31015 " (cutoff:3.500A) Processing sheet with id= AA, 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: 6.703A pdb=" N ARG 31057 " --> pdb=" O VAL 31091 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N VAL 31091 " --> pdb=" O ARG 31057 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain '4' and resid 85 through 88 Processing sheet with id= AC, first strand: chain '4' and resid 77 through 79 Processing sheet with id= AD, first strand: chain '4' and resid 144 through 147 Processing sheet with id= AE, 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= AF, first strand: chain 'E' and resid 579 through 581 Processing sheet with id= AG, 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: 6.677A pdb=" N ALA E 719 " --> pdb=" O GLN E 596 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ILE E 598 " --> pdb=" O ALA E 719 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR E 721 " --> pdb=" O ILE E 598 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 13 through 16 removed outlier: 4.137A 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: 6.730A 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= AI, first strand: chain 'G' and resid 83 through 86 Processing sheet with id= AJ, 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= AK, first strand: chain 'a' and resid 90 through 96 Processing sheet with id= AL, first strand: chain 'a' and resid 98 through 101 removed outlier: 6.682A pdb=" N GLU a 68 " --> pdb=" O VAL a 56 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N VAL a 56 " --> pdb=" O GLU a 68 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'b' and resid 57 through 60 removed outlier: 3.799A pdb=" N GLY b 57 " --> pdb=" O GLU b 49 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N THR b 47 " --> pdb=" O LEU b 59 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N MET b 27 " --> pdb=" O LEU b 23 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'b' and resid 62 through 64 removed outlier: 6.576A pdb=" N ALA b 45 " --> pdb=" O LEU b 33 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N LEU b 33 " --> pdb=" O ALA b 45 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'c' and resid 84 through 89 removed outlier: 6.760A 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: 4.416A 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: 3.626A 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: 7.423A 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= AP, first strand: chain 'c' and resid 56 through 58 Processing sheet with id= AQ, first strand: chain 'd' and resid 54 through 58 removed outlier: 5.860A 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: 3.779A pdb=" N MET d 69 " --> pdb=" O LYS d 20 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'd' and resid 40 through 42 Processing sheet with id= AS, first strand: chain 'e' and resid 47 through 50 removed outlier: 4.429A pdb=" N GLU e 26 " --> pdb=" O THR e 22 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'e' and resid 60 through 63 removed outlier: 7.056A 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= AU, first strand: chain 'f' and resid 65 through 68 removed outlier: 3.770A pdb=" N LEU f 67 " --> pdb=" O CYS f 45 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N CYS f 45 " --> pdb=" O LEU f 67 " (cutoff:3.500A) removed outlier: 3.742A 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= AV, first strand: chain 'f' and resid 40 through 42 Processing sheet with id= AW, 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= AX, 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: 6.034A pdb=" N ILE g 29 " --> pdb=" O LYS g 41 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'O' and resid 175 through 178 Processing sheet with id= AZ, first strand: chain 'm' and resid 57 through 60 removed outlier: 6.028A pdb=" N THR m 47 " --> pdb=" O LEU m 59 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'm' and resid 62 through 64 removed outlier: 3.714A pdb=" N SER m 35 " --> pdb=" O GLN m 43 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ALA m 45 " --> pdb=" O LEU m 33 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N LEU m 33 " --> pdb=" O ALA m 45 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'h' and resid 53 through 55 Processing sheet with id= BC, first strand: chain 'h' and resid 57 through 60 removed outlier: 6.176A pdb=" N LYS h 41 " --> pdb=" O ILE h 29 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ILE h 29 " --> pdb=" O LYS h 41 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'k' and resid 65 through 68 removed outlier: 5.899A pdb=" N CYS k 45 " --> pdb=" O LEU k 67 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ARG k 18 " --> pdb=" O VAL k 82 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N VAL k 82 " --> pdb=" O ARG k 18 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ILE k 20 " --> pdb=" O MET k 80 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N MET k 80 " --> pdb=" O ILE k 20 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'k' and resid 70 through 72 removed outlier: 3.544A pdb=" N ALA k 33 " --> pdb=" O ILE k 41 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N CYS k 43 " --> pdb=" O PHE k 31 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N PHE k 31 " --> pdb=" O CYS k 43 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'M' and resid 83 through 86 Processing sheet with id= BG, first strand: chain 'n' and resid 67 through 72 removed outlier: 6.910A pdb=" N LYS n 20 " --> pdb=" O ILE n 68 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU n 70 " --> pdb=" O SER n 18 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N SER n 18 " --> pdb=" O LEU n 70 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ALA n 72 " --> pdb=" O LYS n 16 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N LYS n 16 " --> pdb=" O ALA n 72 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL n 41 " --> pdb=" O ARG n 32 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'l' and resid 71 through 75 removed outlier: 6.290A pdb=" N ALA l 61 " --> pdb=" O LEU l 74 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N MET l 41 " --> pdb=" O LEU l 35 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU l 35 " --> pdb=" O MET l 41 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU l 86 " --> pdb=" O TRP l 34 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'l' and resid 77 through 79 Processing sheet with id= BJ, first strand: chain 'i' and resid 90 through 96 Processing sheet with id= BK, first strand: chain 'i' and resid 98 through 101 removed outlier: 3.570A pdb=" N ALA i 58 " --> pdb=" O VAL i 66 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLU i 68 " --> pdb=" O VAL i 56 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N VAL i 56 " --> pdb=" O GLU i 68 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'N' and resid 4 through 6 removed outlier: 3.605A pdb=" N THR N 11 " --> pdb=" O CYS N 6 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'j' and resid 55 through 58 removed outlier: 3.642A pdb=" N PHE j 70 " --> pdb=" O GLU j 21 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'j' and resid 60 through 63 removed outlier: 3.581A pdb=" N GLU j 34 " --> pdb=" O GLN j 42 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N SER j 44 " --> pdb=" O LEU j 32 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N LEU j 32 " --> pdb=" O SER j 44 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain '6' and resid 39 through 42 removed outlier: 6.406A pdb=" N TYR 6 71 " --> pdb=" O CYS 6 40 " (cutoff:3.500A) 1717 hydrogen bonds defined for protein. 4767 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 210 hydrogen bonds 388 hydrogen bond angles 0 basepair planarities 82 basepair parallelities 157 stacking parallelities Total time for adding SS restraints: 24.95 Time building geometry restraints manager: 19.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 7076 1.27 - 1.41: 11451 1.41 - 1.55: 25047 1.55 - 1.69: 785 1.69 - 1.84: 261 Bond restraints: 44620 Sorted by residual: bond pdb=" N PRO C 419 " pdb=" CA PRO C 419 " ideal model delta sigma weight residual 1.469 1.692 -0.223 1.28e-02 6.10e+03 3.04e+02 bond pdb=" C ARG 6 38 " pdb=" N PRO 6 39 " ideal model delta sigma weight residual 1.332 1.517 -0.185 1.33e-02 5.65e+03 1.94e+02 bond pdb=" N PRO 1 718 " pdb=" CA PRO 1 718 " ideal model delta sigma weight residual 1.468 1.660 -0.192 1.70e-02 3.46e+03 1.28e+02 bond pdb=" C CYS 6 30 " pdb=" O CYS 6 30 " ideal model delta sigma weight residual 1.234 1.125 0.109 1.27e-02 6.20e+03 7.32e+01 bond pdb=" C16 SJT 6 204 " pdb=" C18 SJT 6 204 " ideal model delta sigma weight residual 1.575 1.409 0.166 2.00e-02 2.50e+03 6.88e+01 ... (remaining 44615 not shown) Histogram of bond angle deviations from ideal: 85.58 - 96.76: 11 96.76 - 107.95: 4571 107.95 - 119.14: 32346 119.14 - 130.32: 23927 130.32 - 141.51: 291 Bond angle restraints: 61146 Sorted by residual: angle pdb=" N ASP 31064 " pdb=" CA ASP 31064 " pdb=" CB ASP 31064 " ideal model delta sigma weight residual 110.49 141.51 -31.02 1.69e+00 3.50e-01 3.37e+02 angle pdb=" C GLY C 418 " pdb=" N PRO C 419 " pdb=" CA PRO C 419 " ideal model delta sigma weight residual 119.84 139.93 -20.09 1.25e+00 6.40e-01 2.58e+02 angle pdb=" C17 SJT 6 204 " pdb=" C16 SJT 6 204 " pdb=" C18 SJT 6 204 " ideal model delta sigma weight residual 68.17 116.04 -47.87 3.00e+00 1.11e-01 2.55e+02 angle pdb=" N PRO 1 780 " pdb=" CA PRO 1 780 " pdb=" C PRO 1 780 " ideal model delta sigma weight residual 113.40 133.41 -20.01 1.34e+00 5.57e-01 2.23e+02 angle pdb=" C ARG 6 38 " pdb=" N PRO 6 39 " pdb=" CA PRO 6 39 " ideal model delta sigma weight residual 119.89 133.85 -13.96 1.02e+00 9.61e-01 1.87e+02 ... (remaining 61141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.29: 23090 33.29 - 66.59: 1572 66.59 - 99.88: 157 99.88 - 133.18: 13 133.18 - 166.47: 7 Dihedral angle restraints: 24839 sinusoidal: 12274 harmonic: 12565 Sorted by residual: dihedral pdb=" C4' U L 90 " pdb=" C3' U L 90 " pdb=" C2' U L 90 " pdb=" C1' U L 90 " ideal model delta sinusoidal sigma weight residual -35.00 36.06 -71.06 1 8.00e+00 1.56e-02 1.01e+02 dihedral pdb=" C5' U L 90 " pdb=" C4' U L 90 " pdb=" C3' U L 90 " pdb=" O3' U L 90 " ideal model delta sinusoidal sigma weight residual 147.00 83.59 63.41 1 8.00e+00 1.56e-02 8.29e+01 dihedral pdb=" O4' C L 73 " pdb=" C1' C L 73 " pdb=" N1 C L 73 " pdb=" C2 C L 73 " ideal model delta sinusoidal sigma weight residual 200.00 41.62 158.38 1 1.50e+01 4.44e-03 8.23e+01 ... (remaining 24836 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.043: 6008 1.043 - 2.085: 0 2.085 - 3.128: 0 3.128 - 4.171: 0 4.171 - 5.213: 5 Chirality restraints: 6013 Sorted by residual: chirality pdb=" C22 SJT 6 204 " pdb=" C21 SJT 6 204 " pdb=" C23 SJT 6 204 " pdb=" C24 SJT 6 204 " both_signs ideal model delta sigma weight residual False 2.69 -2.53 5.21 2.00e-01 2.50e+01 6.79e+02 chirality pdb=" C25 SJT 6 204 " pdb=" C24 SJT 6 204 " pdb=" C26 SJT 6 204 " pdb=" O6 SJT 6 204 " both_signs ideal model delta sigma weight residual False 2.56 -2.56 5.12 2.00e-01 2.50e+01 6.55e+02 chirality pdb=" C8 SJT 6 204 " pdb=" C7 SJT 6 204 " pdb=" C9 SJT 6 204 " pdb=" O3 SJT 6 204 " both_signs ideal model delta sigma weight residual False -2.59 2.51 -5.10 2.00e-01 2.50e+01 6.51e+02 ... (remaining 6010 not shown) Planarity restraints: 7428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C14 SJT 6 204 " -0.316 2.00e-02 2.50e+03 2.73e-01 9.29e+02 pdb=" C15 SJT 6 204 " 0.486 2.00e-02 2.50e+03 pdb=" C16 SJT 6 204 " 0.075 2.00e-02 2.50e+03 pdb=" C17 SJT 6 204 " -0.113 2.00e-02 2.50e+03 pdb=" C18 SJT 6 204 " -0.133 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N SJT 6 204 " 0.245 2.00e-02 2.50e+03 1.46e-01 2.68e+02 pdb=" C SJT 6 204 " 0.028 2.00e-02 2.50e+03 pdb=" O SJT 6 204 " 0.025 2.00e-02 2.50e+03 pdb=" C1 SJT 6 204 " -0.126 2.00e-02 2.50e+03 pdb=" C7 SJT 6 204 " -0.173 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C16 SJT 6 204 " -0.084 2.00e-02 2.50e+03 1.54e-01 2.38e+02 pdb=" C18 SJT 6 204 " 0.198 2.00e-02 2.50e+03 pdb=" C19 SJT 6 204 " -0.202 2.00e-02 2.50e+03 pdb=" C20 SJT 6 204 " 0.088 2.00e-02 2.50e+03 ... (remaining 7425 not shown) Histogram of nonbonded interaction distances: 1.02 - 1.79: 31 1.79 - 2.57: 443 2.57 - 3.35: 49730 3.35 - 4.12: 105536 4.12 - 4.90: 174197 Nonbonded interactions: 329937 Sorted by model distance: nonbonded pdb=" O4 U L 30 " pdb=" CD1 LEU O 175 " model vdw 1.018 3.460 nonbonded pdb=" O THR O 62 " pdb=" N GLU O 64 " model vdw 1.051 2.520 nonbonded pdb=" O2' G L 164 " pdb=" N ARG h 50 " model vdw 1.115 2.520 nonbonded pdb=" C8 A L 118 " pdb=" N PRO N 2 " model vdw 1.143 3.340 nonbonded pdb=" O2' G L 164 " pdb=" C ASN h 49 " model vdw 1.231 3.270 ... (remaining 329932 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'a' and (resid 19 through 77 or resid 88 through 114)) selection = (chain 'i' and ((resid 19 through 27 and (name N or name CA or name C or name O \ )) or resid 28 or (resid 29 through 88 and (name N or name CA or name C or name \ O )) or resid 89 or (resid 90 through 112 and (name N or name CA or name C or na \ me O )) or resid 113 or (resid 114 and (name N or name CA or name C or name O )) \ )) } ncs_group { reference = chain 'b' selection = (chain 'm' and ((resid 2 through 3 and (name N or name CA or name C or name O )) \ or resid 4 or (resid 5 through 6 and (name N or name CA or name C or name O )) \ or resid 7 or (resid 8 and (name N or name CA or name C or name O )) or resid 9 \ or (resid 10 through 17 and (name N or name CA or name C or name O )) or resid 1 \ 8 or (resid 19 through 75 and (name N or name CA or name C or name O )))) } ncs_group { reference = (chain 'c' and resid 14 through 90) selection = (chain 'l' and ((resid 14 through 16 and (name N or name CA or name C or name O \ )) or resid 17 or (resid 18 through 90 and (name N or name CA or name C or name \ O )))) } ncs_group { reference = (chain 'd' and resid 4 through 76) selection = (chain 'n' and ((resid 4 through 5 and (name N or name CA or name C or name O )) \ or resid 6 through 7 or (resid 8 through 35 and (name N or name CA or name C or \ name O )) or resid 36 or (resid 37 through 76 and (name N or name CA or name C \ or name O )))) } ncs_group { reference = (chain 'e' and resid 3 through 83) selection = (chain 'j' and ((resid 3 through 5 and (name N or name CA or name C or name O )) \ or resid 6 or (resid 7 through 73 and (name N or name CA or name C or name O )) \ or resid 74 or (resid 75 through 80 and (name N or name CA or name C or name O \ )) or resid 81 or (resid 82 through 83 and (name N or name CA or name C or name \ O )))) } ncs_group { reference = (chain 'g' and resid 2 through 82) selection = (chain 'h' and ((resid 2 through 51 and (name N or name CA or name C or name O ) \ ) or resid 52 or (resid 53 through 70 and (name N or name CA or name C or name O \ )) or resid 71 or (resid 72 through 74 and (name N or name CA or name C or name \ O )) or resid 75 or (resid 76 through 82 and (name N or name CA or name C or na \ me O )))) } 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: 6.280 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 25.320 Check model and map are aligned: 0.760 Set scattering table: 0.420 Process input model: 139.110 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 185.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3364 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.223 44620 Z= 0.580 Angle : 1.325 47.873 61146 Z= 0.811 Chirality : 0.170 5.213 6013 Planarity : 0.009 0.273 7428 Dihedral : 19.526 166.473 17955 Min Nonbonded Distance : 1.018 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.47 % Favored : 96.22 % Rotamer: Outliers : 7.75 % Allowed : 17.35 % Favored : 74.90 % Cbeta Deviations : 0.81 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.02 % Twisted Proline : 0.40 % 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: -2.52 (0.10), residues: 5499 helix: -1.53 (0.10), residues: 1877 sheet: -0.94 (0.15), residues: 1170 loop : -2.07 (0.11), residues: 2452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.004 TRP O 187 HIS 0.056 0.003 HIS i 62 PHE 0.052 0.004 PHE O 48 TYR 0.051 0.004 TYR 6 36 ARG 0.032 0.002 ARG n 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10998 Ramachandran restraints generated. 5499 Oldfield, 0 Emsley, 5499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10998 Ramachandran restraints generated. 5499 Oldfield, 0 Emsley, 5499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 839 residues out of total 4942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 602 time to evaluate : 4.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 699 GLN cc_start: 0.5780 (OUTLIER) cc_final: 0.5463 (tm-30) REVERT: 1 869 MET cc_start: 0.6007 (tpt) cc_final: 0.5741 (tpt) REVERT: 1 910 MET cc_start: 0.4240 (mmt) cc_final: 0.3906 (mmp) REVERT: 2 587 HIS cc_start: 0.7786 (OUTLIER) cc_final: 0.6141 (p-80) REVERT: 3 645 MET cc_start: -0.1672 (tmt) cc_final: -0.2538 (tpp) REVERT: 3 664 TYR cc_start: 0.7573 (m-80) cc_final: 0.6992 (m-80) REVERT: C 464 LEU cc_start: 0.7491 (tt) cc_final: 0.7190 (mt) REVERT: E 199 SER cc_start: 0.3705 (t) cc_final: 0.3375 (t) REVERT: O 3 GLN cc_start: 0.0719 (OUTLIER) cc_final: -0.0733 (pt0) REVERT: k 38 MET cc_start: 0.2469 (mmm) cc_final: 0.1978 (mmm) REVERT: M 61 GLU cc_start: 0.0713 (OUTLIER) cc_final: 0.0490 (mm-30) REVERT: l 41 MET cc_start: 0.2191 (ttp) cc_final: 0.0613 (tpt) REVERT: i 114 LEU cc_start: -0.0262 (OUTLIER) cc_final: -0.0858 (mp) REVERT: N 48 SER cc_start: -0.0531 (OUTLIER) cc_final: -0.0738 (p) REVERT: j 78 LYS cc_start: 0.1877 (OUTLIER) cc_final: 0.1585 (ttmm) REVERT: j 83 LEU cc_start: 0.0979 (OUTLIER) cc_final: 0.0659 (mp) outliers start: 237 outliers final: 56 residues processed: 807 average time/residue: 1.3769 time to fit residues: 1381.5010 Evaluate side-chains 409 residues out of total 4942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 345 time to evaluate : 4.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 699 GLN Chi-restraints excluded: chain 1 residue 721 ILE Chi-restraints excluded: chain 1 residue 772 ILE Chi-restraints excluded: chain 1 residue 781 ASP Chi-restraints excluded: chain 1 residue 925 VAL Chi-restraints excluded: chain 1 residue 965 CYS Chi-restraints excluded: chain 1 residue 1004 ILE Chi-restraints excluded: chain 1 residue 1013 ILE Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1137 ARG Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 587 HIS Chi-restraints excluded: chain 3 residue 459 VAL Chi-restraints excluded: chain 3 residue 490 THR Chi-restraints excluded: chain 3 residue 591 SER Chi-restraints excluded: chain 3 residue 670 GLN Chi-restraints excluded: chain 3 residue 712 VAL Chi-restraints excluded: chain 3 residue 713 LEU Chi-restraints excluded: chain 3 residue 755 VAL Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 1017 ASN Chi-restraints excluded: chain 3 residue 1191 LYS Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain 5 residue 49 LEU Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain E residue 198 TRP Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 48 PHE Chi-restraints excluded: chain O residue 140 SER Chi-restraints excluded: chain O residue 172 ARG Chi-restraints excluded: chain m residue 27 MET Chi-restraints excluded: chain k residue 12 HIS Chi-restraints excluded: chain k residue 54 LYS Chi-restraints excluded: chain k residue 56 SER Chi-restraints excluded: chain k residue 57 LYS Chi-restraints excluded: chain k residue 58 GLN Chi-restraints excluded: chain k residue 67 LEU Chi-restraints excluded: chain M residue 8 PRO Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain n residue 21 LEU Chi-restraints excluded: chain n residue 27 VAL Chi-restraints excluded: chain n residue 46 VAL Chi-restraints excluded: chain l residue 62 GLU Chi-restraints excluded: chain l residue 68 THR Chi-restraints excluded: chain l residue 70 SER Chi-restraints excluded: chain l residue 80 LYS Chi-restraints excluded: chain l residue 82 ASP Chi-restraints excluded: chain l residue 86 LEU Chi-restraints excluded: chain i residue 37 LYS Chi-restraints excluded: chain i residue 51 LYS Chi-restraints excluded: chain i residue 114 LEU Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 48 SER Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 34 GLU Chi-restraints excluded: chain j residue 78 LYS Chi-restraints excluded: chain j residue 83 LEU Chi-restraints excluded: chain 6 residue 26 CYS Chi-restraints excluded: chain 6 residue 36 TYR Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain 6 residue 61 CYS Chi-restraints excluded: chain 6 residue 83 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 581 random chunks: chunk 490 optimal weight: 8.9990 chunk 440 optimal weight: 20.0000 chunk 244 optimal weight: 0.8980 chunk 150 optimal weight: 0.0770 chunk 297 optimal weight: 40.0000 chunk 235 optimal weight: 2.9990 chunk 455 optimal weight: 40.0000 chunk 176 optimal weight: 2.9990 chunk 276 optimal weight: 8.9990 chunk 338 optimal weight: 4.9990 chunk 527 optimal weight: 50.0000 overall best weight: 2.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 534 GLN 1 662 HIS 1 778 GLN ** 1 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11069 HIS 11144 GLN 11209 ASN 11252 GLN 2 458 ASN 2 467 GLN 2 490 HIS 2 587 HIS 3 27 GLN 3 138 GLN 3 254 ASN 3 264 GLN ** 3 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 440 HIS 3 480 ASN 3 594 ASN 3 612 ASN 3 636 GLN ** 3 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 916 ASN 3 994 GLN 31020 GLN 31083 ASN C 400 HIS C 445 HIS C 448 ASN O 35 ASN O 96 ASN m 43 GLN h 49 ASN ** k 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 37 HIS k 58 GLN k 76 ASN n 26 HIS l 88 GLN i 62 HIS 6 55 GLN ** 6 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4080 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 44620 Z= 0.413 Angle : 0.891 26.214 61146 Z= 0.444 Chirality : 0.063 1.932 6013 Planarity : 0.007 0.089 7428 Dihedral : 17.688 173.406 11026 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.87 % Favored : 96.05 % Rotamer: Outliers : 8.01 % Allowed : 21.18 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.02 % Twisted Proline : 0.40 % 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: -1.51 (0.10), residues: 5499 helix: -0.26 (0.11), residues: 1886 sheet: -0.61 (0.15), residues: 1145 loop : -1.73 (0.11), residues: 2468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP 3 862 HIS 0.016 0.002 HIS 3 791 PHE 0.055 0.004 PHE 5 66 TYR 0.041 0.004 TYR 3 926 ARG 0.010 0.001 ARG 3 128 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10998 Ramachandran restraints generated. 5499 Oldfield, 0 Emsley, 5499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10998 Ramachandran restraints generated. 5499 Oldfield, 0 Emsley, 5499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 4942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 358 time to evaluate : 4.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 TYR cc_start: 0.4974 (m-80) cc_final: 0.4063 (m-10) REVERT: 1 613 MET cc_start: 0.6193 (OUTLIER) cc_final: 0.5977 (mmm) REVERT: 1 623 TYR cc_start: 0.5752 (OUTLIER) cc_final: 0.4701 (t80) REVERT: 1 760 GLU cc_start: 0.6686 (tm-30) cc_final: 0.6431 (tm-30) REVERT: 1 771 LEU cc_start: 0.6944 (pp) cc_final: 0.6096 (mm) REVERT: 1 964 THR cc_start: 0.7536 (OUTLIER) cc_final: 0.7212 (t) REVERT: 1 1156 GLU cc_start: 0.6367 (OUTLIER) cc_final: 0.4841 (tp30) REVERT: 1 1277 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.7088 (tt0) REVERT: 2 477 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7586 (mpp) REVERT: 3 273 ARG cc_start: 0.6006 (OUTLIER) cc_final: 0.5662 (mtp180) REVERT: 3 573 GLN cc_start: 0.4628 (OUTLIER) cc_final: 0.4103 (mm110) REVERT: 3 574 LEU cc_start: 0.1909 (OUTLIER) cc_final: 0.1550 (tt) REVERT: 3 645 MET cc_start: -0.1312 (tmt) cc_final: -0.2238 (tpp) REVERT: 3 975 LYS cc_start: 0.6984 (tptp) cc_final: 0.6639 (tptp) REVERT: 3 1016 ARG cc_start: 0.3616 (OUTLIER) cc_final: 0.3166 (tpt170) REVERT: C 440 ILE cc_start: 0.7487 (OUTLIER) cc_final: 0.7197 (pt) REVERT: E 160 MET cc_start: 0.2653 (OUTLIER) cc_final: 0.0783 (mpm) REVERT: E 198 TRP cc_start: 0.4929 (OUTLIER) cc_final: 0.4715 (p-90) REVERT: O 3 GLN cc_start: 0.0581 (OUTLIER) cc_final: 0.0135 (tt0) REVERT: O 168 LYS cc_start: -0.1458 (OUTLIER) cc_final: -0.2304 (mmmt) REVERT: k 17 MET cc_start: -0.2060 (OUTLIER) cc_final: -0.2690 (ptm) REVERT: n 69 MET cc_start: 0.2071 (ptm) cc_final: 0.0611 (pmm) REVERT: l 41 MET cc_start: 0.3311 (ttp) cc_final: 0.0677 (tpt) REVERT: l 80 LYS cc_start: 0.1615 (OUTLIER) cc_final: 0.0690 (mptt) REVERT: i 114 LEU cc_start: -0.0565 (OUTLIER) cc_final: -0.1256 (mp) outliers start: 245 outliers final: 84 residues processed: 562 average time/residue: 1.2782 time to fit residues: 910.4373 Evaluate side-chains 400 residues out of total 4942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 298 time to evaluate : 4.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain J residue 230 THR Chi-restraints excluded: chain 1 residue 556 ILE Chi-restraints excluded: chain 1 residue 613 MET Chi-restraints excluded: chain 1 residue 623 TYR Chi-restraints excluded: chain 1 residue 722 GLU Chi-restraints excluded: chain 1 residue 723 SER Chi-restraints excluded: chain 1 residue 772 ILE Chi-restraints excluded: chain 1 residue 781 ASP Chi-restraints excluded: chain 1 residue 804 ASN Chi-restraints excluded: chain 1 residue 837 THR Chi-restraints excluded: chain 1 residue 886 HIS Chi-restraints excluded: chain 1 residue 925 VAL Chi-restraints excluded: chain 1 residue 963 LYS Chi-restraints excluded: chain 1 residue 964 THR Chi-restraints excluded: chain 1 residue 1004 ILE Chi-restraints excluded: chain 1 residue 1021 THR Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1060 PHE Chi-restraints excluded: chain 1 residue 1077 THR Chi-restraints excluded: chain 1 residue 1156 GLU Chi-restraints excluded: chain 1 residue 1200 TYR Chi-restraints excluded: chain 1 residue 1277 GLN Chi-restraints excluded: chain 2 residue 477 MET Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 511 LEU Chi-restraints excluded: chain 3 residue 8 LEU Chi-restraints excluded: chain 3 residue 79 VAL Chi-restraints excluded: chain 3 residue 107 PHE Chi-restraints excluded: chain 3 residue 165 THR Chi-restraints excluded: chain 3 residue 193 ASP Chi-restraints excluded: chain 3 residue 219 HIS Chi-restraints excluded: chain 3 residue 220 VAL Chi-restraints excluded: chain 3 residue 237 THR Chi-restraints excluded: chain 3 residue 250 ILE Chi-restraints excluded: chain 3 residue 273 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 437 VAL Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 468 ASP Chi-restraints excluded: chain 3 residue 476 VAL Chi-restraints excluded: chain 3 residue 497 SER Chi-restraints excluded: chain 3 residue 534 ASN 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 677 THR Chi-restraints excluded: chain 3 residue 721 LEU Chi-restraints excluded: chain 3 residue 789 VAL Chi-restraints excluded: chain 3 residue 790 ILE Chi-restraints excluded: chain 3 residue 906 LEU Chi-restraints excluded: chain 3 residue 919 SER Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 1016 ARG Chi-restraints excluded: chain 3 residue 1043 THR Chi-restraints excluded: chain 3 residue 1121 THR Chi-restraints excluded: chain 3 residue 1162 SER Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain 5 residue 49 LEU Chi-restraints excluded: chain 5 residue 57 GLU Chi-restraints excluded: chain 5 residue 63 ARG Chi-restraints excluded: chain 5 residue 74 GLN Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 403 ASN Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 198 TRP Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 48 PHE Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain O residue 140 SER Chi-restraints excluded: chain O residue 168 LYS Chi-restraints excluded: chain m residue 51 ILE Chi-restraints excluded: chain h residue 82 ASP Chi-restraints excluded: chain k residue 17 MET Chi-restraints excluded: chain k residue 54 LYS Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain n residue 27 VAL Chi-restraints excluded: chain n residue 46 VAL Chi-restraints excluded: chain l residue 62 GLU Chi-restraints excluded: chain l residue 80 LYS Chi-restraints excluded: chain i residue 114 LEU Chi-restraints excluded: chain N residue 3 LYS Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 34 GLU Chi-restraints excluded: chain j residue 47 THR Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain 6 residue 22 LEU Chi-restraints excluded: chain 6 residue 36 TYR Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain 6 residue 41 THR Chi-restraints excluded: chain 6 residue 47 ASP Chi-restraints excluded: chain 6 residue 66 VAL Chi-restraints excluded: chain 6 residue 81 ASP Chi-restraints excluded: chain 6 residue 83 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 581 random chunks: chunk 293 optimal weight: 9.9990 chunk 163 optimal weight: 0.7980 chunk 439 optimal weight: 20.0000 chunk 359 optimal weight: 30.0000 chunk 145 optimal weight: 0.9990 chunk 528 optimal weight: 8.9990 chunk 570 optimal weight: 8.9990 chunk 470 optimal weight: 50.0000 chunk 524 optimal weight: 6.9990 chunk 180 optimal weight: 0.8980 chunk 424 optimal weight: 6.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11028 HIS ** 11108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11293 ASN 3 28 GLN 3 138 GLN 3 844 ASN 3 861 GLN ** 5 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN m 43 GLN l 88 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4245 moved from start: 0.4930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.108 44620 Z= 0.508 Angle : 0.874 24.752 61146 Z= 0.441 Chirality : 0.064 2.074 6013 Planarity : 0.007 0.086 7428 Dihedral : 17.451 176.591 10941 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.84 % Favored : 95.11 % Rotamer: Outliers : 8.79 % Allowed : 23.56 % Favored : 67.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.02 % Twisted Proline : 0.40 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.11), residues: 5499 helix: 0.20 (0.12), residues: 1864 sheet: -0.64 (0.15), residues: 1125 loop : -1.66 (0.11), residues: 2510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP 3 903 HIS 0.011 0.002 HIS 11283 PHE 0.038 0.004 PHE 3 788 TYR 0.064 0.004 TYR 3 970 ARG 0.009 0.001 ARG E 161 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10998 Ramachandran restraints generated. 5499 Oldfield, 0 Emsley, 5499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10998 Ramachandran restraints generated. 5499 Oldfield, 0 Emsley, 5499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 4942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 309 time to evaluate : 4.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 TYR cc_start: 0.5009 (m-80) cc_final: 0.4567 (m-10) REVERT: 1 538 LEU cc_start: 0.7621 (tp) cc_final: 0.7420 (mp) REVERT: 1 613 MET cc_start: 0.6826 (OUTLIER) cc_final: 0.6604 (mmm) REVERT: 1 620 MET cc_start: 0.6459 (OUTLIER) cc_final: 0.5998 (pmm) REVERT: 1 623 TYR cc_start: 0.5920 (OUTLIER) cc_final: 0.5049 (t80) REVERT: 1 928 TYR cc_start: 0.7156 (OUTLIER) cc_final: 0.5537 (m-80) REVERT: 1 1003 VAL cc_start: 0.8684 (p) cc_final: 0.8461 (p) REVERT: 1 1029 GLU cc_start: 0.5420 (OUTLIER) cc_final: 0.4515 (pm20) REVERT: 1 1156 GLU cc_start: 0.6398 (OUTLIER) cc_final: 0.4511 (tp30) REVERT: 1 1160 GLU cc_start: 0.7035 (mp0) cc_final: 0.6775 (mp0) REVERT: 1 1287 ILE cc_start: 0.8141 (OUTLIER) cc_final: 0.7561 (mp) REVERT: 2 586 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8654 (mt) REVERT: 3 9 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.8043 (tm-30) REVERT: 3 100 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6527 (tp30) REVERT: 3 181 MET cc_start: 0.7108 (OUTLIER) cc_final: 0.6727 (mtt) REVERT: 3 219 HIS cc_start: 0.7070 (OUTLIER) cc_final: 0.6802 (p90) REVERT: 3 250 ILE cc_start: 0.7151 (OUTLIER) cc_final: 0.6722 (mt) REVERT: 3 273 ARG cc_start: 0.6432 (OUTLIER) cc_final: 0.6164 (mtp180) REVERT: 3 331 ASP cc_start: 0.7140 (OUTLIER) cc_final: 0.6877 (m-30) REVERT: 3 468 ASP cc_start: 0.0761 (OUTLIER) cc_final: 0.0522 (t0) REVERT: 3 525 ARG cc_start: 0.4999 (OUTLIER) cc_final: 0.4608 (ptp-170) REVERT: 3 534 ASN cc_start: 0.2887 (OUTLIER) cc_final: 0.2593 (p0) REVERT: 3 583 MET cc_start: -0.2129 (mmt) cc_final: -0.2632 (mtt) REVERT: 3 645 MET cc_start: -0.0115 (tmt) cc_final: -0.0673 (tpt) REVERT: 3 688 ASP cc_start: 0.4053 (OUTLIER) cc_final: 0.3380 (t0) REVERT: 3 849 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6791 (mm-30) REVERT: 3 1115 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6587 (pm20) REVERT: E 158 GLU cc_start: 0.5124 (OUTLIER) cc_final: 0.4799 (tm-30) REVERT: E 198 TRP cc_start: 0.4997 (OUTLIER) cc_final: 0.4458 (p90) REVERT: E 204 ASP cc_start: 0.4080 (OUTLIER) cc_final: 0.2142 (p0) REVERT: E 241 LYS cc_start: 0.7139 (OUTLIER) cc_final: 0.6178 (tppt) REVERT: h 45 MET cc_start: 0.0733 (OUTLIER) cc_final: 0.0410 (tpt) REVERT: h 50 ARG cc_start: 0.1413 (OUTLIER) cc_final: 0.0853 (mtt90) REVERT: l 41 MET cc_start: 0.2989 (ttp) cc_final: 0.0536 (tpt) REVERT: i 73 MET cc_start: 0.4119 (OUTLIER) cc_final: 0.3609 (ttm) REVERT: i 114 LEU cc_start: -0.0394 (OUTLIER) cc_final: -0.0797 (mt) REVERT: j 43 MET cc_start: 0.0991 (OUTLIER) cc_final: 0.0460 (tmm) outliers start: 269 outliers final: 106 residues processed: 534 average time/residue: 1.1634 time to fit residues: 804.8057 Evaluate side-chains 412 residues out of total 4942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 276 time to evaluate : 4.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 230 THR Chi-restraints excluded: chain 1 residue 494 GLU Chi-restraints excluded: chain 1 residue 613 MET Chi-restraints excluded: chain 1 residue 620 MET Chi-restraints excluded: chain 1 residue 623 TYR Chi-restraints excluded: chain 1 residue 680 LEU Chi-restraints excluded: chain 1 residue 682 HIS Chi-restraints excluded: chain 1 residue 722 GLU Chi-restraints excluded: chain 1 residue 772 ILE Chi-restraints excluded: chain 1 residue 781 ASP Chi-restraints excluded: chain 1 residue 796 CYS Chi-restraints excluded: chain 1 residue 821 HIS Chi-restraints excluded: chain 1 residue 837 THR Chi-restraints excluded: chain 1 residue 925 VAL Chi-restraints excluded: chain 1 residue 928 TYR Chi-restraints excluded: chain 1 residue 960 VAL Chi-restraints excluded: chain 1 residue 1004 ILE Chi-restraints excluded: chain 1 residue 1021 THR Chi-restraints excluded: chain 1 residue 1029 GLU Chi-restraints excluded: chain 1 residue 1030 LYS Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1060 PHE Chi-restraints excluded: chain 1 residue 1063 LEU Chi-restraints excluded: chain 1 residue 1096 THR Chi-restraints excluded: chain 1 residue 1156 GLU Chi-restraints excluded: chain 1 residue 1169 VAL Chi-restraints excluded: chain 1 residue 1200 TYR Chi-restraints excluded: chain 1 residue 1241 ILE Chi-restraints excluded: chain 1 residue 1267 LYS Chi-restraints excluded: chain 1 residue 1287 ILE Chi-restraints excluded: chain 1 residue 1292 LYS Chi-restraints excluded: chain 1 residue 1294 THR Chi-restraints excluded: chain 2 residue 462 VAL Chi-restraints excluded: chain 2 residue 477 MET Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 500 VAL Chi-restraints excluded: chain 2 residue 512 GLN Chi-restraints excluded: chain 2 residue 564 ILE Chi-restraints excluded: chain 2 residue 586 ILE Chi-restraints excluded: chain 3 residue 8 LEU Chi-restraints excluded: chain 3 residue 9 GLN Chi-restraints excluded: chain 3 residue 39 GLU Chi-restraints excluded: chain 3 residue 56 VAL Chi-restraints excluded: chain 3 residue 79 VAL Chi-restraints excluded: chain 3 residue 87 ILE Chi-restraints excluded: chain 3 residue 100 GLU Chi-restraints excluded: chain 3 residue 107 PHE Chi-restraints excluded: chain 3 residue 156 SER Chi-restraints excluded: chain 3 residue 181 MET Chi-restraints excluded: chain 3 residue 197 THR Chi-restraints excluded: chain 3 residue 219 HIS Chi-restraints excluded: chain 3 residue 229 GLU Chi-restraints excluded: chain 3 residue 250 ILE Chi-restraints excluded: chain 3 residue 257 THR Chi-restraints excluded: chain 3 residue 273 ARG Chi-restraints excluded: chain 3 residue 314 THR Chi-restraints excluded: chain 3 residue 331 ASP Chi-restraints excluded: chain 3 residue 393 LYS Chi-restraints excluded: chain 3 residue 404 LEU Chi-restraints excluded: chain 3 residue 425 VAL 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 468 ASP Chi-restraints excluded: chain 3 residue 475 ILE Chi-restraints excluded: chain 3 residue 476 VAL Chi-restraints excluded: chain 3 residue 491 VAL Chi-restraints excluded: chain 3 residue 497 SER Chi-restraints excluded: chain 3 residue 505 THR Chi-restraints excluded: chain 3 residue 525 ARG Chi-restraints excluded: chain 3 residue 534 ASN Chi-restraints excluded: chain 3 residue 640 LEU Chi-restraints excluded: chain 3 residue 641 CYS Chi-restraints excluded: chain 3 residue 677 THR Chi-restraints excluded: chain 3 residue 688 ASP Chi-restraints excluded: chain 3 residue 712 VAL Chi-restraints excluded: chain 3 residue 718 ARG Chi-restraints excluded: chain 3 residue 719 SER Chi-restraints excluded: chain 3 residue 762 LEU Chi-restraints excluded: chain 3 residue 777 VAL Chi-restraints excluded: chain 3 residue 790 ILE Chi-restraints excluded: chain 3 residue 799 ILE Chi-restraints excluded: chain 3 residue 803 ASP Chi-restraints excluded: chain 3 residue 849 GLU Chi-restraints excluded: chain 3 residue 893 VAL Chi-restraints excluded: chain 3 residue 906 LEU Chi-restraints excluded: chain 3 residue 936 LYS Chi-restraints excluded: chain 3 residue 945 VAL Chi-restraints excluded: chain 3 residue 963 VAL Chi-restraints excluded: chain 3 residue 1016 ARG Chi-restraints excluded: chain 3 residue 1037 SER Chi-restraints excluded: chain 3 residue 1043 THR Chi-restraints excluded: chain 3 residue 1066 VAL Chi-restraints excluded: chain 3 residue 1115 GLU Chi-restraints excluded: chain 3 residue 1121 THR Chi-restraints excluded: chain 3 residue 1133 THR Chi-restraints excluded: chain 3 residue 1162 SER Chi-restraints excluded: chain 3 residue 1200 THR Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain 5 residue 21 THR Chi-restraints excluded: chain 5 residue 49 LEU Chi-restraints excluded: chain 5 residue 57 GLU Chi-restraints excluded: chain 5 residue 63 ARG Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 198 TRP Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 241 LYS Chi-restraints excluded: chain O residue 45 ILE Chi-restraints excluded: chain O residue 48 PHE Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain m residue 51 ILE Chi-restraints excluded: chain h residue 45 MET Chi-restraints excluded: chain h residue 50 ARG Chi-restraints excluded: chain k residue 54 LYS Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain n residue 27 VAL Chi-restraints excluded: chain n residue 46 VAL Chi-restraints excluded: chain l residue 82 ASP Chi-restraints excluded: chain i residue 42 VAL Chi-restraints excluded: chain i residue 73 MET Chi-restraints excluded: chain i residue 114 LEU Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 43 MET Chi-restraints excluded: chain j residue 47 THR Chi-restraints excluded: chain 6 residue 36 TYR Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain 6 residue 41 THR Chi-restraints excluded: chain 6 residue 47 ASP Chi-restraints excluded: chain 6 residue 59 VAL Chi-restraints excluded: chain 6 residue 66 VAL Chi-restraints excluded: chain 6 residue 81 ASP Chi-restraints excluded: chain 6 residue 83 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 581 random chunks: chunk 522 optimal weight: 50.0000 chunk 397 optimal weight: 7.9990 chunk 274 optimal weight: 40.0000 chunk 58 optimal weight: 0.6980 chunk 252 optimal weight: 0.7980 chunk 354 optimal weight: 20.0000 chunk 530 optimal weight: 20.0000 chunk 561 optimal weight: 50.0000 chunk 277 optimal weight: 0.7980 chunk 502 optimal weight: 30.0000 chunk 151 optimal weight: 0.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 587 HIS 3 194 ASN 3 422 GLN 3 612 ASN 3 636 GLN 3 796 ASN ** 3 844 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN m 43 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4230 moved from start: 0.5388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 44620 Z= 0.356 Angle : 0.749 24.837 61146 Z= 0.370 Chirality : 0.058 2.009 6013 Planarity : 0.006 0.069 7428 Dihedral : 17.213 174.238 10924 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.91 % Favored : 95.04 % Rotamer: Outliers : 7.22 % Allowed : 26.11 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -0.81 (0.11), residues: 5499 helix: 0.68 (0.12), residues: 1859 sheet: -0.50 (0.16), residues: 1103 loop : -1.47 (0.11), residues: 2537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP 3 903 HIS 0.008 0.001 HIS 3 804 PHE 0.038 0.003 PHE 3 788 TYR 0.051 0.003 TYR 3 970 ARG 0.009 0.001 ARG 3 10 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10998 Ramachandran restraints generated. 5499 Oldfield, 0 Emsley, 5499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10998 Ramachandran restraints generated. 5499 Oldfield, 0 Emsley, 5499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 4942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 303 time to evaluate : 4.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 TYR cc_start: 0.4989 (m-80) cc_final: 0.4669 (m-10) REVERT: 1 623 TYR cc_start: 0.6130 (OUTLIER) cc_final: 0.5066 (t80) REVERT: 1 714 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.6579 (tp30) REVERT: 1 928 TYR cc_start: 0.7013 (OUTLIER) cc_final: 0.5725 (m-80) REVERT: 1 964 THR cc_start: 0.7885 (p) cc_final: 0.7609 (t) REVERT: 1 1156 GLU cc_start: 0.6342 (OUTLIER) cc_final: 0.4508 (tp30) REVERT: 1 1287 ILE cc_start: 0.8176 (OUTLIER) cc_final: 0.7539 (mp) REVERT: 3 143 ILE cc_start: 0.6871 (OUTLIER) cc_final: 0.6503 (mm) REVERT: 3 146 ARG cc_start: 0.6930 (OUTLIER) cc_final: 0.5814 (ptm-80) REVERT: 3 181 MET cc_start: 0.6818 (OUTLIER) cc_final: 0.6419 (mtt) REVERT: 3 273 ARG cc_start: 0.6688 (OUTLIER) cc_final: 0.6391 (mtp180) REVERT: 3 274 ARG cc_start: 0.6304 (OUTLIER) cc_final: 0.5621 (mtm180) REVERT: 3 331 ASP cc_start: 0.7027 (OUTLIER) cc_final: 0.6773 (m-30) REVERT: 3 468 ASP cc_start: 0.0555 (OUTLIER) cc_final: 0.0308 (t0) REVERT: 3 525 ARG cc_start: 0.4616 (OUTLIER) cc_final: 0.4373 (ptp-170) REVERT: 3 534 ASN cc_start: 0.2697 (OUTLIER) cc_final: 0.2479 (p0) REVERT: 3 583 MET cc_start: -0.1872 (mmt) cc_final: -0.2406 (mtt) REVERT: 3 645 MET cc_start: -0.0381 (tmt) cc_final: -0.0969 (tpt) REVERT: 3 666 ASN cc_start: 0.6860 (OUTLIER) cc_final: 0.6631 (m110) REVERT: 3 734 LEU cc_start: 0.6946 (mt) cc_final: 0.6736 (mp) REVERT: 3 776 GLN cc_start: 0.4923 (OUTLIER) cc_final: 0.4655 (mt0) REVERT: 3 936 LYS cc_start: 0.6362 (OUTLIER) cc_final: 0.6149 (pttt) REVERT: 3 998 HIS cc_start: 0.5204 (OUTLIER) cc_final: 0.4700 (t-90) REVERT: 3 1001 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.7920 (mm) REVERT: E 155 LYS cc_start: 0.3217 (OUTLIER) cc_final: 0.2978 (ptmt) REVERT: E 158 GLU cc_start: 0.5127 (tm-30) cc_final: 0.4704 (tm-30) REVERT: E 207 GLU cc_start: 0.4579 (OUTLIER) cc_final: 0.4334 (mp0) REVERT: E 231 TYR cc_start: 0.4271 (OUTLIER) cc_final: 0.3991 (m-10) REVERT: E 238 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6980 (mm-30) REVERT: O 67 MET cc_start: 0.2432 (tpp) cc_final: 0.1964 (mtt) REVERT: m 20 MET cc_start: -0.0685 (tmm) cc_final: -0.0987 (tmm) REVERT: h 45 MET cc_start: 0.0567 (OUTLIER) cc_final: 0.0315 (tpt) REVERT: n 69 MET cc_start: 0.2056 (ptm) cc_final: 0.0062 (pmm) REVERT: l 41 MET cc_start: 0.2826 (ttp) cc_final: 0.0575 (tpt) REVERT: i 73 MET cc_start: 0.4083 (OUTLIER) cc_final: 0.3408 (ttm) REVERT: i 114 LEU cc_start: -0.0178 (OUTLIER) cc_final: -0.0504 (mt) outliers start: 221 outliers final: 103 residues processed: 486 average time/residue: 1.1515 time to fit residues: 732.0749 Evaluate side-chains 415 residues out of total 4942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 287 time to evaluate : 3.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain 1 residue 549 ARG Chi-restraints excluded: chain 1 residue 609 MET Chi-restraints excluded: chain 1 residue 617 ILE Chi-restraints excluded: chain 1 residue 623 TYR Chi-restraints excluded: chain 1 residue 680 LEU Chi-restraints excluded: chain 1 residue 714 GLU Chi-restraints excluded: chain 1 residue 772 ILE Chi-restraints excluded: chain 1 residue 781 ASP Chi-restraints excluded: chain 1 residue 796 CYS Chi-restraints excluded: chain 1 residue 821 HIS Chi-restraints excluded: chain 1 residue 837 THR Chi-restraints excluded: chain 1 residue 884 ILE Chi-restraints excluded: chain 1 residue 914 PHE Chi-restraints excluded: chain 1 residue 925 VAL Chi-restraints excluded: chain 1 residue 928 TYR Chi-restraints excluded: chain 1 residue 960 VAL Chi-restraints excluded: chain 1 residue 1004 ILE Chi-restraints excluded: chain 1 residue 1021 THR Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1060 PHE Chi-restraints excluded: chain 1 residue 1063 LEU Chi-restraints excluded: chain 1 residue 1093 VAL Chi-restraints excluded: chain 1 residue 1141 LEU Chi-restraints excluded: chain 1 residue 1156 GLU Chi-restraints excluded: chain 1 residue 1221 GLU Chi-restraints excluded: chain 1 residue 1287 ILE Chi-restraints excluded: chain 1 residue 1292 LYS Chi-restraints excluded: chain 1 residue 1294 THR Chi-restraints excluded: chain 2 residue 477 MET Chi-restraints excluded: chain 2 residue 483 GLN Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 564 ILE Chi-restraints excluded: chain 3 residue 8 LEU Chi-restraints excluded: chain 3 residue 39 GLU Chi-restraints excluded: chain 3 residue 56 VAL Chi-restraints excluded: chain 3 residue 79 VAL Chi-restraints excluded: chain 3 residue 107 PHE Chi-restraints excluded: chain 3 residue 143 ILE Chi-restraints excluded: chain 3 residue 146 ARG Chi-restraints excluded: chain 3 residue 156 SER Chi-restraints excluded: chain 3 residue 165 THR Chi-restraints excluded: chain 3 residue 181 MET Chi-restraints excluded: chain 3 residue 197 THR Chi-restraints excluded: chain 3 residue 257 THR Chi-restraints excluded: chain 3 residue 273 ARG Chi-restraints excluded: chain 3 residue 274 ARG Chi-restraints excluded: chain 3 residue 280 ASP Chi-restraints excluded: chain 3 residue 331 ASP Chi-restraints excluded: chain 3 residue 398 VAL Chi-restraints excluded: chain 3 residue 404 LEU Chi-restraints excluded: chain 3 residue 425 VAL Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 468 ASP Chi-restraints excluded: chain 3 residue 475 ILE Chi-restraints excluded: chain 3 residue 476 VAL Chi-restraints excluded: chain 3 residue 497 SER Chi-restraints excluded: chain 3 residue 525 ARG Chi-restraints excluded: chain 3 residue 534 ASN Chi-restraints excluded: chain 3 residue 641 CYS Chi-restraints excluded: chain 3 residue 666 ASN Chi-restraints excluded: chain 3 residue 677 THR Chi-restraints excluded: chain 3 residue 712 VAL Chi-restraints excluded: chain 3 residue 718 ARG Chi-restraints excluded: chain 3 residue 719 SER Chi-restraints excluded: chain 3 residue 747 SER Chi-restraints excluded: chain 3 residue 776 GLN Chi-restraints excluded: chain 3 residue 777 VAL Chi-restraints excluded: chain 3 residue 789 VAL Chi-restraints excluded: chain 3 residue 803 ASP Chi-restraints excluded: chain 3 residue 893 VAL Chi-restraints excluded: chain 3 residue 906 LEU Chi-restraints excluded: chain 3 residue 936 LYS Chi-restraints excluded: chain 3 residue 945 VAL Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 963 VAL Chi-restraints excluded: chain 3 residue 998 HIS Chi-restraints excluded: chain 3 residue 1000 VAL Chi-restraints excluded: chain 3 residue 1001 ILE Chi-restraints excluded: chain 3 residue 1016 ARG Chi-restraints excluded: chain 3 residue 1037 SER Chi-restraints excluded: chain 3 residue 1043 THR Chi-restraints excluded: chain 3 residue 1116 SER Chi-restraints excluded: chain 3 residue 1121 THR Chi-restraints excluded: chain 3 residue 1133 THR Chi-restraints excluded: chain 3 residue 1162 SER Chi-restraints excluded: chain 3 residue 1217 PHE Chi-restraints excluded: chain 5 residue 21 THR Chi-restraints excluded: chain 5 residue 49 LEU Chi-restraints excluded: chain 5 residue 57 GLU Chi-restraints excluded: chain 5 residue 63 ARG Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 425 HIS Chi-restraints excluded: chain C residue 469 GLU Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 231 TYR Chi-restraints excluded: chain O residue 19 ILE Chi-restraints excluded: chain O residue 45 ILE Chi-restraints excluded: chain O residue 48 PHE Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain O residue 176 VAL Chi-restraints excluded: chain m residue 51 ILE Chi-restraints excluded: chain h residue 23 THR Chi-restraints excluded: chain h residue 34 VAL Chi-restraints excluded: chain h residue 45 MET Chi-restraints excluded: chain h residue 46 THR Chi-restraints excluded: chain k residue 54 LYS Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain n residue 27 VAL Chi-restraints excluded: chain n residue 46 VAL Chi-restraints excluded: chain i residue 42 VAL Chi-restraints excluded: chain i residue 73 MET Chi-restraints excluded: chain i residue 114 LEU Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 43 MET Chi-restraints excluded: chain j residue 47 THR Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain 6 residue 36 TYR Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain 6 residue 41 THR Chi-restraints excluded: chain 6 residue 47 ASP Chi-restraints excluded: chain 6 residue 66 VAL Chi-restraints excluded: chain 6 residue 81 ASP Chi-restraints excluded: chain 6 residue 83 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 581 random chunks: chunk 467 optimal weight: 10.0000 chunk 318 optimal weight: 50.0000 chunk 8 optimal weight: 7.9990 chunk 418 optimal weight: 1.9990 chunk 231 optimal weight: 0.8980 chunk 479 optimal weight: 40.0000 chunk 388 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 286 optimal weight: 40.0000 chunk 504 optimal weight: 30.0000 chunk 141 optimal weight: 0.0670 overall best weight: 4.1926 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 662 HIS ** 1 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 138 GLN 3 219 HIS 3 254 ASN ** 3 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 670 GLN 3 776 GLN 3 791 HIS ** 3 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 844 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN O 133 HIS m 43 GLN n 5 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4347 moved from start: 0.6188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.110 44620 Z= 0.616 Angle : 0.946 25.201 61146 Z= 0.478 Chirality : 0.066 2.063 6013 Planarity : 0.008 0.116 7428 Dihedral : 17.360 174.552 10922 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.86 % Favored : 93.05 % Rotamer: Outliers : 9.35 % Allowed : 25.16 % Favored : 65.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.20 (0.11), residues: 5499 helix: 0.29 (0.12), residues: 1854 sheet: -0.63 (0.16), residues: 1095 loop : -1.67 (0.11), residues: 2550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP 3 903 HIS 0.019 0.002 HIS 3 804 PHE 0.047 0.004 PHE 3 788 TYR 0.075 0.004 TYR 3 970 ARG 0.013 0.001 ARG 2 495 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10998 Ramachandran restraints generated. 5499 Oldfield, 0 Emsley, 5499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10998 Ramachandran restraints generated. 5499 Oldfield, 0 Emsley, 5499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 4942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 289 time to evaluate : 4.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 TYR cc_start: 0.5133 (m-80) cc_final: 0.4862 (m-10) REVERT: 1 549 ARG cc_start: 0.5913 (OUTLIER) cc_final: 0.5423 (ptt-90) REVERT: 1 620 MET cc_start: 0.6550 (OUTLIER) cc_final: 0.6242 (pmm) REVERT: 1 623 TYR cc_start: 0.5922 (OUTLIER) cc_final: 0.5172 (t80) REVERT: 1 714 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.6411 (tp30) REVERT: 1 784 MET cc_start: 0.5260 (mmt) cc_final: 0.4745 (mmt) REVERT: 1 910 MET cc_start: 0.4241 (OUTLIER) cc_final: 0.3894 (mmp) REVERT: 1 1156 GLU cc_start: 0.6414 (OUTLIER) cc_final: 0.4513 (tp30) REVERT: 1 1287 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7600 (mp) REVERT: 2 586 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8696 (mt) REVERT: 3 9 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7712 (tt0) REVERT: 3 100 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6558 (tp30) REVERT: 3 128 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.6912 (mtt180) REVERT: 3 146 ARG cc_start: 0.7116 (OUTLIER) cc_final: 0.5980 (ptm-80) REVERT: 3 181 MET cc_start: 0.6955 (OUTLIER) cc_final: 0.6267 (mtt) REVERT: 3 219 HIS cc_start: 0.7060 (OUTLIER) cc_final: 0.6799 (p90) REVERT: 3 273 ARG cc_start: 0.6758 (OUTLIER) cc_final: 0.6553 (mtp180) REVERT: 3 274 ARG cc_start: 0.6651 (OUTLIER) cc_final: 0.5871 (mtm180) REVERT: 3 386 PHE cc_start: 0.6707 (OUTLIER) cc_final: 0.6359 (m-80) REVERT: 3 534 ASN cc_start: 0.2953 (OUTLIER) cc_final: 0.2542 (p0) REVERT: 3 553 GLN cc_start: 0.4397 (OUTLIER) cc_final: 0.2312 (pt0) REVERT: 3 640 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7614 (pt) REVERT: 3 645 MET cc_start: -0.0045 (tmt) cc_final: -0.0754 (tmt) REVERT: 3 998 HIS cc_start: 0.5641 (OUTLIER) cc_final: 0.5118 (t-90) REVERT: 3 1001 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.8076 (mm) REVERT: 3 1040 ASP cc_start: 0.7250 (OUTLIER) cc_final: 0.7003 (p0) REVERT: 3 1117 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7916 (tp) REVERT: E 160 MET cc_start: 0.3855 (OUTLIER) cc_final: 0.2632 (mpt) REVERT: E 231 TYR cc_start: 0.4324 (OUTLIER) cc_final: 0.3917 (m-10) REVERT: E 232 MET cc_start: -0.0880 (tpt) cc_final: -0.1242 (tpt) REVERT: E 238 GLU cc_start: 0.7366 (mm-30) cc_final: 0.7158 (mm-30) REVERT: E 241 LYS cc_start: 0.7361 (OUTLIER) cc_final: 0.6497 (tppt) REVERT: E 242 PHE cc_start: 0.0598 (t80) cc_final: -0.0314 (t80) REVERT: O 67 MET cc_start: 0.2750 (tpp) cc_final: 0.2513 (mtt) REVERT: O 168 LYS cc_start: -0.1750 (OUTLIER) cc_final: -0.2175 (mmmt) REVERT: m 20 MET cc_start: -0.0225 (tmm) cc_final: -0.0512 (tmm) REVERT: h 45 MET cc_start: 0.0573 (OUTLIER) cc_final: -0.0147 (tpt) REVERT: n 13 MET cc_start: -0.0820 (OUTLIER) cc_final: -0.1419 (tpp) REVERT: l 41 MET cc_start: 0.2764 (ttp) cc_final: 0.0525 (tpt) REVERT: N 3 LYS cc_start: 0.0009 (OUTLIER) cc_final: -0.0819 (tmtt) outliers start: 286 outliers final: 139 residues processed: 530 average time/residue: 1.1490 time to fit residues: 791.0609 Evaluate side-chains 448 residues out of total 4942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 278 time to evaluate : 4.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain J residue 230 THR Chi-restraints excluded: chain 1 residue 549 ARG Chi-restraints excluded: chain 1 residue 609 MET Chi-restraints excluded: chain 1 residue 617 ILE Chi-restraints excluded: chain 1 residue 620 MET Chi-restraints excluded: chain 1 residue 623 TYR Chi-restraints excluded: chain 1 residue 680 LEU Chi-restraints excluded: chain 1 residue 682 HIS Chi-restraints excluded: chain 1 residue 683 LEU Chi-restraints excluded: chain 1 residue 714 GLU Chi-restraints excluded: chain 1 residue 722 GLU Chi-restraints excluded: chain 1 residue 772 ILE Chi-restraints excluded: chain 1 residue 781 ASP Chi-restraints excluded: chain 1 residue 796 CYS Chi-restraints excluded: chain 1 residue 837 THR Chi-restraints excluded: chain 1 residue 884 ILE Chi-restraints excluded: chain 1 residue 910 MET Chi-restraints excluded: chain 1 residue 925 VAL Chi-restraints excluded: chain 1 residue 928 TYR Chi-restraints excluded: chain 1 residue 960 VAL Chi-restraints excluded: chain 1 residue 981 TYR Chi-restraints excluded: chain 1 residue 989 VAL Chi-restraints excluded: chain 1 residue 1004 ILE Chi-restraints excluded: chain 1 residue 1013 ILE Chi-restraints excluded: chain 1 residue 1021 THR Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1060 PHE Chi-restraints excluded: chain 1 residue 1063 LEU Chi-restraints excluded: chain 1 residue 1077 THR Chi-restraints excluded: chain 1 residue 1093 VAL Chi-restraints excluded: chain 1 residue 1096 THR Chi-restraints excluded: chain 1 residue 1103 VAL Chi-restraints excluded: chain 1 residue 1141 LEU Chi-restraints excluded: chain 1 residue 1156 GLU Chi-restraints excluded: chain 1 residue 1200 TYR Chi-restraints excluded: chain 1 residue 1221 GLU Chi-restraints excluded: chain 1 residue 1267 LYS Chi-restraints excluded: chain 1 residue 1287 ILE Chi-restraints excluded: chain 1 residue 1292 LYS Chi-restraints excluded: chain 1 residue 1294 THR Chi-restraints excluded: chain 2 residue 462 VAL Chi-restraints excluded: chain 2 residue 477 MET Chi-restraints excluded: chain 2 residue 483 GLN Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 564 ILE Chi-restraints excluded: chain 2 residue 573 ASP Chi-restraints excluded: chain 2 residue 586 ILE Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 8 LEU Chi-restraints excluded: chain 3 residue 9 GLN Chi-restraints excluded: chain 3 residue 39 GLU Chi-restraints excluded: chain 3 residue 56 VAL Chi-restraints excluded: chain 3 residue 74 THR Chi-restraints excluded: chain 3 residue 79 VAL Chi-restraints excluded: chain 3 residue 100 GLU Chi-restraints excluded: chain 3 residue 107 PHE Chi-restraints excluded: chain 3 residue 128 ARG Chi-restraints excluded: chain 3 residue 146 ARG Chi-restraints excluded: chain 3 residue 156 SER Chi-restraints excluded: chain 3 residue 165 THR Chi-restraints excluded: chain 3 residue 170 VAL Chi-restraints excluded: chain 3 residue 171 VAL Chi-restraints excluded: chain 3 residue 181 MET Chi-restraints excluded: chain 3 residue 197 THR Chi-restraints excluded: chain 3 residue 217 LEU Chi-restraints excluded: chain 3 residue 219 HIS Chi-restraints excluded: chain 3 residue 257 THR Chi-restraints excluded: chain 3 residue 273 ARG Chi-restraints excluded: chain 3 residue 274 ARG Chi-restraints excluded: chain 3 residue 280 ASP Chi-restraints excluded: chain 3 residue 317 THR Chi-restraints excluded: chain 3 residue 363 HIS Chi-restraints excluded: chain 3 residue 386 PHE Chi-restraints excluded: chain 3 residue 398 VAL Chi-restraints excluded: chain 3 residue 400 GLU Chi-restraints excluded: chain 3 residue 404 LEU Chi-restraints excluded: chain 3 residue 422 GLN Chi-restraints excluded: chain 3 residue 425 VAL 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 476 VAL Chi-restraints excluded: chain 3 residue 491 VAL Chi-restraints excluded: chain 3 residue 497 SER Chi-restraints excluded: chain 3 residue 505 THR Chi-restraints excluded: chain 3 residue 534 ASN Chi-restraints excluded: chain 3 residue 553 GLN Chi-restraints excluded: chain 3 residue 589 CYS Chi-restraints excluded: chain 3 residue 640 LEU Chi-restraints excluded: chain 3 residue 641 CYS Chi-restraints excluded: chain 3 residue 677 THR Chi-restraints excluded: chain 3 residue 700 LYS Chi-restraints excluded: chain 3 residue 718 ARG Chi-restraints excluded: chain 3 residue 719 SER Chi-restraints excluded: chain 3 residue 747 SER Chi-restraints excluded: chain 3 residue 763 ARG Chi-restraints excluded: chain 3 residue 777 VAL Chi-restraints excluded: chain 3 residue 789 VAL Chi-restraints excluded: chain 3 residue 799 ILE Chi-restraints excluded: chain 3 residue 865 VAL Chi-restraints excluded: chain 3 residue 893 VAL Chi-restraints excluded: chain 3 residue 906 LEU Chi-restraints excluded: chain 3 residue 919 SER Chi-restraints excluded: chain 3 residue 945 VAL Chi-restraints excluded: chain 3 residue 952 ILE Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 963 VAL Chi-restraints excluded: chain 3 residue 998 HIS Chi-restraints excluded: chain 3 residue 1000 VAL Chi-restraints excluded: chain 3 residue 1001 ILE Chi-restraints excluded: chain 3 residue 1016 ARG Chi-restraints excluded: chain 3 residue 1037 SER Chi-restraints excluded: chain 3 residue 1040 ASP Chi-restraints excluded: chain 3 residue 1043 THR Chi-restraints excluded: chain 3 residue 1058 LEU Chi-restraints excluded: chain 3 residue 1062 THR Chi-restraints excluded: chain 3 residue 1066 VAL Chi-restraints excluded: chain 3 residue 1091 VAL Chi-restraints excluded: chain 3 residue 1115 GLU Chi-restraints excluded: chain 3 residue 1116 SER Chi-restraints excluded: chain 3 residue 1117 LEU Chi-restraints excluded: chain 3 residue 1133 THR Chi-restraints excluded: chain 3 residue 1146 MET Chi-restraints excluded: chain 3 residue 1162 SER Chi-restraints excluded: chain 3 residue 1200 THR Chi-restraints excluded: chain 5 residue 21 THR Chi-restraints excluded: chain 5 residue 38 ASP Chi-restraints excluded: chain 5 residue 49 LEU Chi-restraints excluded: chain 5 residue 57 GLU Chi-restraints excluded: chain 5 residue 63 ARG Chi-restraints excluded: chain 5 residue 70 GLU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 469 GLU Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 231 TYR Chi-restraints excluded: chain E residue 241 LYS Chi-restraints excluded: chain O residue 45 ILE Chi-restraints excluded: chain O residue 48 PHE Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain O residue 168 LYS Chi-restraints excluded: chain O residue 176 VAL Chi-restraints excluded: chain m residue 51 ILE Chi-restraints excluded: chain h residue 23 THR Chi-restraints excluded: chain h residue 34 VAL Chi-restraints excluded: chain h residue 45 MET Chi-restraints excluded: chain h residue 46 THR Chi-restraints excluded: chain k residue 13 ILE Chi-restraints excluded: chain k residue 54 LYS Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain n residue 13 MET Chi-restraints excluded: chain n residue 46 VAL Chi-restraints excluded: chain i residue 73 MET Chi-restraints excluded: chain N residue 3 LYS Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 43 MET Chi-restraints excluded: chain j residue 47 THR Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain 6 residue 36 TYR Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain 6 residue 41 THR Chi-restraints excluded: chain 6 residue 47 ASP Chi-restraints excluded: chain 6 residue 59 VAL Chi-restraints excluded: chain 6 residue 66 VAL Chi-restraints excluded: chain 6 residue 81 ASP Chi-restraints excluded: chain 6 residue 83 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 581 random chunks: chunk 188 optimal weight: 5.9990 chunk 505 optimal weight: 20.0000 chunk 111 optimal weight: 0.7980 chunk 329 optimal weight: 1.9990 chunk 138 optimal weight: 0.4980 chunk 562 optimal weight: 9.9990 chunk 466 optimal weight: 1.9990 chunk 260 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 185 optimal weight: 0.9980 chunk 295 optimal weight: 20.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 670 GLN 1 738 HIS ** 1 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11002 ASN 11108 ASN 11209 ASN ** 3 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 138 GLN 3 422 GLN ** 3 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 707 GLN ** 3 844 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 873 GLN C 448 ASN m 43 GLN l 19 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4223 moved from start: 0.6188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 44620 Z= 0.207 Angle : 0.689 24.486 61146 Z= 0.334 Chirality : 0.055 1.996 6013 Planarity : 0.005 0.068 7428 Dihedral : 17.048 173.645 10915 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.31 % Favored : 95.65 % Rotamer: Outliers : 5.65 % Allowed : 28.30 % Favored : 66.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -0.60 (0.11), residues: 5499 helix: 0.96 (0.13), residues: 1858 sheet: -0.41 (0.16), residues: 1100 loop : -1.42 (0.12), residues: 2541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP 1 732 HIS 0.019 0.001 HIS 3 219 PHE 0.033 0.002 PHE 3 788 TYR 0.031 0.002 TYR 3 970 ARG 0.008 0.001 ARG 3 10 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10998 Ramachandran restraints generated. 5499 Oldfield, 0 Emsley, 5499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10998 Ramachandran restraints generated. 5499 Oldfield, 0 Emsley, 5499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 4942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 301 time to evaluate : 4.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 TYR cc_start: 0.4956 (m-80) cc_final: 0.4684 (m-10) REVERT: B 57 LYS cc_start: 0.5115 (pptt) cc_final: 0.4886 (pttt) REVERT: 1 549 ARG cc_start: 0.5692 (OUTLIER) cc_final: 0.5480 (ptt-90) REVERT: 1 562 LYS cc_start: 0.5957 (OUTLIER) cc_final: 0.5649 (ttpt) REVERT: 1 620 MET cc_start: 0.6397 (mpp) cc_final: 0.6150 (pmm) REVERT: 1 623 TYR cc_start: 0.6111 (OUTLIER) cc_final: 0.4939 (t80) REVERT: 1 910 MET cc_start: 0.4289 (OUTLIER) cc_final: 0.3956 (mmp) REVERT: 1 928 TYR cc_start: 0.6791 (OUTLIER) cc_final: 0.5310 (m-80) REVERT: 1 1000 ILE cc_start: 0.6694 (OUTLIER) cc_final: 0.6400 (tp) REVERT: 1 1156 GLU cc_start: 0.6301 (OUTLIER) cc_final: 0.4347 (tp30) REVERT: 1 1209 ASN cc_start: 0.7604 (OUTLIER) cc_final: 0.7377 (m-40) REVERT: 1 1287 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7433 (mp) REVERT: 3 128 ARG cc_start: 0.6972 (OUTLIER) cc_final: 0.6498 (mtt180) REVERT: 3 146 ARG cc_start: 0.6792 (OUTLIER) cc_final: 0.5719 (ptm-80) REVERT: 3 274 ARG cc_start: 0.6425 (OUTLIER) cc_final: 0.6069 (mtt180) REVERT: 3 534 ASN cc_start: 0.2842 (OUTLIER) cc_final: 0.2587 (p0) REVERT: 3 583 MET cc_start: -0.2068 (mmt) cc_final: -0.2740 (mtt) REVERT: 3 645 MET cc_start: -0.0064 (tmt) cc_final: -0.0570 (tpt) REVERT: 3 688 ASP cc_start: 0.4138 (OUTLIER) cc_final: 0.3155 (p0) REVERT: 3 741 PHE cc_start: 0.7596 (t80) cc_final: 0.7321 (m-80) REVERT: 3 998 HIS cc_start: 0.5203 (OUTLIER) cc_final: 0.4440 (t-90) REVERT: 3 1016 ARG cc_start: 0.4088 (OUTLIER) cc_final: 0.3564 (tpt170) REVERT: E 160 MET cc_start: 0.3897 (OUTLIER) cc_final: 0.2742 (mpt) REVERT: E 231 TYR cc_start: 0.4037 (OUTLIER) cc_final: 0.3669 (m-10) REVERT: E 232 MET cc_start: -0.0683 (tpt) cc_final: -0.0989 (tpt) REVERT: E 238 GLU cc_start: 0.7292 (mm-30) cc_final: 0.7041 (mm-30) REVERT: E 241 LYS cc_start: 0.7041 (OUTLIER) cc_final: 0.6334 (tppt) REVERT: E 242 PHE cc_start: 0.0517 (t80) cc_final: -0.0328 (t80) REVERT: m 20 MET cc_start: -0.0591 (tmm) cc_final: -0.0842 (tmm) REVERT: h 45 MET cc_start: 0.0841 (OUTLIER) cc_final: 0.0119 (tpt) REVERT: k 17 MET cc_start: -0.0952 (mmm) cc_final: -0.2592 (ptp) REVERT: n 13 MET cc_start: -0.0907 (OUTLIER) cc_final: -0.1474 (tpp) REVERT: n 69 MET cc_start: 0.2265 (ptm) cc_final: 0.0269 (pmm) REVERT: l 41 MET cc_start: 0.2497 (ttp) cc_final: 0.0421 (tpt) REVERT: i 73 MET cc_start: 0.4071 (OUTLIER) cc_final: 0.3425 (ttm) outliers start: 173 outliers final: 84 residues processed: 435 average time/residue: 1.2658 time to fit residues: 706.9381 Evaluate side-chains 388 residues out of total 4942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 282 time to evaluate : 4.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain 1 residue 511 MET Chi-restraints excluded: chain 1 residue 549 ARG Chi-restraints excluded: chain 1 residue 562 LYS Chi-restraints excluded: chain 1 residue 609 MET Chi-restraints excluded: chain 1 residue 623 TYR Chi-restraints excluded: chain 1 residue 627 THR Chi-restraints excluded: chain 1 residue 844 VAL Chi-restraints excluded: chain 1 residue 910 MET Chi-restraints excluded: chain 1 residue 925 VAL Chi-restraints excluded: chain 1 residue 928 TYR Chi-restraints excluded: chain 1 residue 960 VAL Chi-restraints excluded: chain 1 residue 1000 ILE Chi-restraints excluded: chain 1 residue 1004 ILE Chi-restraints excluded: chain 1 residue 1010 THR Chi-restraints excluded: chain 1 residue 1013 ILE Chi-restraints excluded: chain 1 residue 1021 THR Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1060 PHE Chi-restraints excluded: chain 1 residue 1063 LEU Chi-restraints excluded: chain 1 residue 1093 VAL Chi-restraints excluded: chain 1 residue 1097 LEU Chi-restraints excluded: chain 1 residue 1141 LEU Chi-restraints excluded: chain 1 residue 1156 GLU Chi-restraints excluded: chain 1 residue 1169 VAL Chi-restraints excluded: chain 1 residue 1209 ASN Chi-restraints excluded: chain 1 residue 1241 ILE Chi-restraints excluded: chain 1 residue 1287 ILE Chi-restraints excluded: chain 1 residue 1292 LYS Chi-restraints excluded: chain 1 residue 1294 THR Chi-restraints excluded: chain 2 residue 461 THR Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 564 ILE Chi-restraints excluded: chain 3 residue 8 LEU Chi-restraints excluded: chain 3 residue 39 GLU Chi-restraints excluded: chain 3 residue 56 VAL Chi-restraints excluded: chain 3 residue 79 VAL Chi-restraints excluded: chain 3 residue 96 LYS Chi-restraints excluded: chain 3 residue 107 PHE Chi-restraints excluded: chain 3 residue 128 ARG Chi-restraints excluded: chain 3 residue 146 ARG Chi-restraints excluded: chain 3 residue 156 SER Chi-restraints excluded: chain 3 residue 170 VAL Chi-restraints excluded: chain 3 residue 197 THR Chi-restraints excluded: chain 3 residue 220 VAL Chi-restraints excluded: chain 3 residue 274 ARG Chi-restraints excluded: chain 3 residue 363 HIS Chi-restraints excluded: chain 3 residue 398 VAL Chi-restraints excluded: chain 3 residue 404 LEU Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 476 VAL Chi-restraints excluded: chain 3 residue 491 VAL Chi-restraints excluded: chain 3 residue 497 SER Chi-restraints excluded: chain 3 residue 505 THR Chi-restraints excluded: chain 3 residue 534 ASN Chi-restraints excluded: chain 3 residue 671 ASN Chi-restraints excluded: chain 3 residue 677 THR Chi-restraints excluded: chain 3 residue 688 ASP Chi-restraints excluded: chain 3 residue 718 ARG Chi-restraints excluded: chain 3 residue 747 SER Chi-restraints excluded: chain 3 residue 757 ILE Chi-restraints excluded: chain 3 residue 777 VAL Chi-restraints excluded: chain 3 residue 865 VAL Chi-restraints excluded: chain 3 residue 893 VAL Chi-restraints excluded: chain 3 residue 945 VAL Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 963 VAL Chi-restraints excluded: chain 3 residue 996 ILE Chi-restraints excluded: chain 3 residue 998 HIS Chi-restraints excluded: chain 3 residue 1005 VAL Chi-restraints excluded: chain 3 residue 1016 ARG Chi-restraints excluded: chain 3 residue 1037 SER Chi-restraints excluded: chain 3 residue 1043 THR Chi-restraints excluded: chain 3 residue 1116 SER Chi-restraints excluded: chain 3 residue 1146 MET Chi-restraints excluded: chain 3 residue 1162 SER Chi-restraints excluded: chain 5 residue 26 THR Chi-restraints excluded: chain 5 residue 49 LEU Chi-restraints excluded: chain 5 residue 57 GLU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 469 GLU Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 231 TYR Chi-restraints excluded: chain E residue 241 LYS Chi-restraints excluded: chain O residue 19 ILE Chi-restraints excluded: chain O residue 45 ILE Chi-restraints excluded: chain O residue 48 PHE Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain O residue 176 VAL Chi-restraints excluded: chain m residue 51 ILE Chi-restraints excluded: chain h residue 23 THR Chi-restraints excluded: chain h residue 45 MET Chi-restraints excluded: chain h residue 46 THR Chi-restraints excluded: chain k residue 54 LYS Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain n residue 13 MET Chi-restraints excluded: chain i residue 73 MET Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 43 MET Chi-restraints excluded: chain 6 residue 36 TYR Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain 6 residue 41 THR Chi-restraints excluded: chain 6 residue 81 ASP Chi-restraints excluded: chain 6 residue 83 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 581 random chunks: chunk 541 optimal weight: 7.9990 chunk 63 optimal weight: 0.0770 chunk 320 optimal weight: 50.0000 chunk 410 optimal weight: 20.0000 chunk 318 optimal weight: 3.9990 chunk 473 optimal weight: 40.0000 chunk 313 optimal weight: 4.9990 chunk 559 optimal weight: 50.0000 chunk 350 optimal weight: 4.9990 chunk 341 optimal weight: 4.9990 chunk 258 optimal weight: 0.0980 overall best weight: 2.8344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 534 GLN 1 794 GLN ** 1 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 478 HIS ** 3 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 138 GLN ** 3 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 795 ASN ** 3 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 870 ASN C 448 ASN m 43 GLN h 39 HIS ** 6 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4316 moved from start: 0.6570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 44620 Z= 0.433 Angle : 0.811 24.866 61146 Z= 0.402 Chirality : 0.060 2.029 6013 Planarity : 0.006 0.077 7428 Dihedral : 17.087 173.111 10910 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.53 % Favored : 93.40 % Rotamer: Outliers : 7.09 % Allowed : 27.25 % Favored : 65.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -0.73 (0.11), residues: 5499 helix: 0.86 (0.13), residues: 1831 sheet: -0.48 (0.16), residues: 1119 loop : -1.49 (0.12), residues: 2549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP 3 903 HIS 0.014 0.002 HIS 3 804 PHE 0.041 0.003 PHE 3 788 TYR 0.051 0.003 TYR 3 970 ARG 0.012 0.001 ARG 3 815 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10998 Ramachandran restraints generated. 5499 Oldfield, 0 Emsley, 5499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10998 Ramachandran restraints generated. 5499 Oldfield, 0 Emsley, 5499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 4942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 290 time to evaluate : 4.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 TYR cc_start: 0.4924 (m-80) cc_final: 0.4583 (m-10) REVERT: B 57 LYS cc_start: 0.5114 (pptt) cc_final: 0.4906 (pptt) REVERT: 1 549 ARG cc_start: 0.5676 (OUTLIER) cc_final: 0.5276 (ptt-90) REVERT: 1 623 TYR cc_start: 0.6138 (OUTLIER) cc_final: 0.5044 (t80) REVERT: 1 714 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6490 (tp30) REVERT: 1 722 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7929 (mp0) REVERT: 1 1054 GLU cc_start: 0.5744 (tp30) cc_final: 0.5219 (tp30) REVERT: 1 1060 PHE cc_start: 0.6191 (OUTLIER) cc_final: 0.5844 (t80) REVERT: 1 1156 GLU cc_start: 0.6320 (OUTLIER) cc_final: 0.4452 (tp30) REVERT: 1 1160 GLU cc_start: 0.6915 (mp0) cc_final: 0.6580 (mp0) REVERT: 1 1193 GLN cc_start: 0.7244 (OUTLIER) cc_final: 0.5934 (tt0) REVERT: 1 1287 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7486 (mp) REVERT: 2 502 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.7185 (ptp-170) REVERT: 2 566 ILE cc_start: 0.4984 (OUTLIER) cc_final: 0.4694 (pp) REVERT: 2 586 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8689 (mt) REVERT: 3 9 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7505 (tt0) REVERT: 3 10 ARG cc_start: 0.7851 (mtt90) cc_final: 0.7612 (mtt90) REVERT: 3 98 MET cc_start: 0.7735 (OUTLIER) cc_final: 0.7498 (ptp) REVERT: 3 128 ARG cc_start: 0.7292 (OUTLIER) cc_final: 0.6865 (mtt180) REVERT: 3 146 ARG cc_start: 0.6801 (OUTLIER) cc_final: 0.5713 (ptm-80) REVERT: 3 229 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6833 (tp30) REVERT: 3 274 ARG cc_start: 0.6716 (OUTLIER) cc_final: 0.5969 (mtm180) REVERT: 3 400 GLU cc_start: 0.6458 (OUTLIER) cc_final: 0.6063 (tm-30) REVERT: 3 534 ASN cc_start: 0.2966 (OUTLIER) cc_final: 0.2669 (p0) REVERT: 3 553 GLN cc_start: 0.4595 (OUTLIER) cc_final: 0.2497 (pm20) REVERT: 3 640 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7811 (pt) REVERT: 3 645 MET cc_start: -0.0201 (tmt) cc_final: -0.0739 (tpt) REVERT: 3 741 PHE cc_start: 0.7642 (t80) cc_final: 0.7442 (m-80) REVERT: 3 977 LEU cc_start: 0.5994 (OUTLIER) cc_final: 0.5742 (mt) REVERT: 3 998 HIS cc_start: 0.5654 (OUTLIER) cc_final: 0.5016 (t-90) REVERT: 3 1001 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.7947 (mm) REVERT: 3 1040 ASP cc_start: 0.7098 (OUTLIER) cc_final: 0.6787 (p0) REVERT: 5 25 ASP cc_start: 0.5710 (OUTLIER) cc_final: 0.4963 (t0) REVERT: E 158 GLU cc_start: 0.5186 (tm-30) cc_final: 0.4678 (tm-30) REVERT: E 160 MET cc_start: 0.3531 (OUTLIER) cc_final: 0.2607 (mpt) REVERT: E 232 MET cc_start: -0.0733 (tpt) cc_final: -0.1119 (tpt) REVERT: E 241 LYS cc_start: 0.7139 (OUTLIER) cc_final: 0.6397 (tppt) REVERT: O 168 LYS cc_start: -0.1470 (OUTLIER) cc_final: -0.2012 (mmmt) REVERT: m 20 MET cc_start: -0.0650 (tmm) cc_final: -0.0984 (tmm) REVERT: h 45 MET cc_start: 0.0745 (OUTLIER) cc_final: 0.0087 (tpt) REVERT: M 51 MET cc_start: 0.2866 (mmm) cc_final: 0.2083 (mmm) REVERT: n 13 MET cc_start: -0.0755 (OUTLIER) cc_final: -0.1414 (tpp) REVERT: n 69 MET cc_start: 0.2022 (ptm) cc_final: 0.0366 (pmm) REVERT: i 73 MET cc_start: 0.4081 (OUTLIER) cc_final: 0.3424 (ttm) REVERT: N 3 LYS cc_start: -0.0380 (OUTLIER) cc_final: -0.1146 (tmtt) outliers start: 217 outliers final: 118 residues processed: 475 average time/residue: 1.1965 time to fit residues: 736.3998 Evaluate side-chains 433 residues out of total 4942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 282 time to evaluate : 4.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain 1 residue 511 MET Chi-restraints excluded: chain 1 residue 549 ARG Chi-restraints excluded: chain 1 residue 562 LYS Chi-restraints excluded: chain 1 residue 609 MET Chi-restraints excluded: chain 1 residue 617 ILE Chi-restraints excluded: chain 1 residue 623 TYR Chi-restraints excluded: chain 1 residue 627 THR Chi-restraints excluded: chain 1 residue 714 GLU Chi-restraints excluded: chain 1 residue 722 GLU Chi-restraints excluded: chain 1 residue 726 SER Chi-restraints excluded: chain 1 residue 772 ILE Chi-restraints excluded: chain 1 residue 781 ASP Chi-restraints excluded: chain 1 residue 796 CYS Chi-restraints excluded: chain 1 residue 837 THR Chi-restraints excluded: chain 1 residue 844 VAL Chi-restraints excluded: chain 1 residue 925 VAL Chi-restraints excluded: chain 1 residue 928 TYR Chi-restraints excluded: chain 1 residue 960 VAL Chi-restraints excluded: chain 1 residue 989 VAL Chi-restraints excluded: chain 1 residue 1004 ILE Chi-restraints excluded: chain 1 residue 1010 THR Chi-restraints excluded: chain 1 residue 1021 THR Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1060 PHE Chi-restraints excluded: chain 1 residue 1063 LEU Chi-restraints excluded: chain 1 residue 1093 VAL Chi-restraints excluded: chain 1 residue 1097 LEU Chi-restraints excluded: chain 1 residue 1141 LEU Chi-restraints excluded: chain 1 residue 1156 GLU Chi-restraints excluded: chain 1 residue 1169 VAL Chi-restraints excluded: chain 1 residue 1193 GLN Chi-restraints excluded: chain 1 residue 1200 TYR Chi-restraints excluded: chain 1 residue 1241 ILE Chi-restraints excluded: chain 1 residue 1271 SER Chi-restraints excluded: chain 1 residue 1287 ILE Chi-restraints excluded: chain 1 residue 1292 LYS Chi-restraints excluded: chain 1 residue 1294 THR Chi-restraints excluded: chain 2 residue 461 THR Chi-restraints excluded: chain 2 residue 462 VAL Chi-restraints excluded: chain 2 residue 478 HIS Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 502 ARG Chi-restraints excluded: chain 2 residue 512 GLN Chi-restraints excluded: chain 2 residue 533 ILE Chi-restraints excluded: chain 2 residue 564 ILE Chi-restraints excluded: chain 2 residue 566 ILE Chi-restraints excluded: chain 2 residue 586 ILE Chi-restraints excluded: chain 3 residue 8 LEU Chi-restraints excluded: chain 3 residue 9 GLN Chi-restraints excluded: chain 3 residue 39 GLU Chi-restraints excluded: chain 3 residue 56 VAL Chi-restraints excluded: chain 3 residue 64 SER Chi-restraints excluded: chain 3 residue 79 VAL Chi-restraints excluded: chain 3 residue 98 MET Chi-restraints excluded: chain 3 residue 107 PHE Chi-restraints excluded: chain 3 residue 128 ARG Chi-restraints excluded: chain 3 residue 146 ARG Chi-restraints excluded: chain 3 residue 156 SER Chi-restraints excluded: chain 3 residue 170 VAL Chi-restraints excluded: chain 3 residue 171 VAL Chi-restraints excluded: chain 3 residue 188 ASP Chi-restraints excluded: chain 3 residue 197 THR Chi-restraints excluded: chain 3 residue 229 GLU Chi-restraints excluded: chain 3 residue 274 ARG Chi-restraints excluded: chain 3 residue 280 ASP Chi-restraints excluded: chain 3 residue 314 THR Chi-restraints excluded: chain 3 residue 363 HIS Chi-restraints excluded: chain 3 residue 398 VAL Chi-restraints excluded: chain 3 residue 400 GLU Chi-restraints excluded: chain 3 residue 404 LEU Chi-restraints excluded: chain 3 residue 422 GLN Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 444 VAL Chi-restraints excluded: chain 3 residue 476 VAL Chi-restraints excluded: chain 3 residue 491 VAL Chi-restraints excluded: chain 3 residue 497 SER Chi-restraints excluded: chain 3 residue 505 THR Chi-restraints excluded: chain 3 residue 534 ASN Chi-restraints excluded: chain 3 residue 553 GLN Chi-restraints excluded: chain 3 residue 640 LEU Chi-restraints excluded: chain 3 residue 665 LEU Chi-restraints excluded: chain 3 residue 677 THR Chi-restraints excluded: chain 3 residue 688 ASP Chi-restraints excluded: chain 3 residue 718 ARG Chi-restraints excluded: chain 3 residue 747 SER Chi-restraints excluded: chain 3 residue 757 ILE Chi-restraints excluded: chain 3 residue 777 VAL Chi-restraints excluded: chain 3 residue 823 MET Chi-restraints excluded: chain 3 residue 865 VAL Chi-restraints excluded: chain 3 residue 893 VAL Chi-restraints excluded: chain 3 residue 919 SER Chi-restraints excluded: chain 3 residue 945 VAL Chi-restraints excluded: chain 3 residue 959 VAL Chi-restraints excluded: chain 3 residue 963 VAL Chi-restraints excluded: chain 3 residue 977 LEU Chi-restraints excluded: chain 3 residue 998 HIS Chi-restraints excluded: chain 3 residue 1001 ILE Chi-restraints excluded: chain 3 residue 1005 VAL Chi-restraints excluded: chain 3 residue 1016 ARG Chi-restraints excluded: chain 3 residue 1037 SER Chi-restraints excluded: chain 3 residue 1040 ASP Chi-restraints excluded: chain 3 residue 1043 THR Chi-restraints excluded: chain 3 residue 1066 VAL Chi-restraints excluded: chain 3 residue 1091 VAL Chi-restraints excluded: chain 3 residue 1116 SER Chi-restraints excluded: chain 3 residue 1133 THR Chi-restraints excluded: chain 3 residue 1162 SER Chi-restraints excluded: chain 3 residue 1200 THR Chi-restraints excluded: chain 5 residue 25 ASP Chi-restraints excluded: chain 5 residue 26 THR Chi-restraints excluded: chain 5 residue 49 LEU Chi-restraints excluded: chain 5 residue 57 GLU Chi-restraints excluded: chain 5 residue 63 ARG Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 465 GLN Chi-restraints excluded: chain C residue 469 GLU Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 241 LYS Chi-restraints excluded: chain O residue 19 ILE Chi-restraints excluded: chain O residue 45 ILE Chi-restraints excluded: chain O residue 48 PHE Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain O residue 168 LYS Chi-restraints excluded: chain O residue 176 VAL Chi-restraints excluded: chain m residue 51 ILE Chi-restraints excluded: chain h residue 23 THR Chi-restraints excluded: chain h residue 34 VAL Chi-restraints excluded: chain h residue 45 MET Chi-restraints excluded: chain h residue 46 THR Chi-restraints excluded: chain k residue 13 ILE Chi-restraints excluded: chain k residue 54 LYS Chi-restraints excluded: chain k residue 80 MET Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain n residue 13 MET Chi-restraints excluded: chain i residue 73 MET Chi-restraints excluded: chain N residue 3 LYS Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 43 MET Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain 6 residue 36 TYR Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain 6 residue 41 THR Chi-restraints excluded: chain 6 residue 59 VAL Chi-restraints excluded: chain 6 residue 66 VAL Chi-restraints excluded: chain 6 residue 81 ASP Chi-restraints excluded: chain 6 residue 83 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 581 random chunks: chunk 346 optimal weight: 10.0000 chunk 223 optimal weight: 9.9990 chunk 334 optimal weight: 0.5980 chunk 168 optimal weight: 0.5980 chunk 110 optimal weight: 0.5980 chunk 108 optimal weight: 0.5980 chunk 356 optimal weight: 0.9990 chunk 381 optimal weight: 8.9990 chunk 276 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 440 optimal weight: 40.0000 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 949 GLN ** 1 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11002 ASN 11209 ASN 3 28 GLN 3 138 GLN 3 422 GLN ** 3 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 45 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4208 moved from start: 0.6564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 44620 Z= 0.183 Angle : 0.675 24.692 61146 Z= 0.323 Chirality : 0.054 1.988 6013 Planarity : 0.005 0.065 7428 Dihedral : 16.909 172.588 10910 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.29 % Favored : 95.69 % Rotamer: Outliers : 4.44 % Allowed : 30.00 % Favored : 65.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -0.31 (0.12), residues: 5499 helix: 1.28 (0.13), residues: 1854 sheet: -0.33 (0.16), residues: 1108 loop : -1.27 (0.12), residues: 2537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP 1 732 HIS 0.018 0.001 HIS 2 478 PHE 0.030 0.002 PHE 3 788 TYR 0.024 0.001 TYR 3 970 ARG 0.011 0.001 ARG 3 390 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10998 Ramachandran restraints generated. 5499 Oldfield, 0 Emsley, 5499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10998 Ramachandran restraints generated. 5499 Oldfield, 0 Emsley, 5499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 4942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 300 time to evaluate : 4.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 TYR cc_start: 0.4794 (m-80) cc_final: 0.4529 (m-10) REVERT: 1 623 TYR cc_start: 0.6081 (OUTLIER) cc_final: 0.4808 (t80) REVERT: 1 722 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7934 (mp0) REVERT: 1 910 MET cc_start: 0.3994 (mmp) cc_final: 0.3727 (mmp) REVERT: 1 928 TYR cc_start: 0.6810 (OUTLIER) cc_final: 0.5362 (m-80) REVERT: 1 979 TYR cc_start: 0.7692 (t80) cc_final: 0.7006 (t80) REVERT: 1 1209 ASN cc_start: 0.7439 (OUTLIER) cc_final: 0.7223 (m-40) REVERT: 2 476 GLU cc_start: 0.6716 (mt-10) cc_final: 0.6503 (mm-30) REVERT: 2 566 ILE cc_start: 0.4788 (OUTLIER) cc_final: 0.4502 (pp) REVERT: 3 222 ARG cc_start: 0.5942 (mtt90) cc_final: 0.5379 (mtm-85) REVERT: 3 229 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6520 (mt-10) REVERT: 3 274 ARG cc_start: 0.6478 (OUTLIER) cc_final: 0.6175 (mtt180) REVERT: 3 534 ASN cc_start: 0.3108 (OUTLIER) cc_final: 0.2702 (p0) REVERT: 3 583 MET cc_start: -0.2166 (mmt) cc_final: -0.2813 (mtt) REVERT: 3 630 MET cc_start: 0.3082 (ppp) cc_final: 0.1465 (mmm) REVERT: 3 640 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7374 (pt) REVERT: 3 645 MET cc_start: -0.0220 (tmt) cc_final: -0.0764 (tpt) REVERT: 3 977 LEU cc_start: 0.5925 (OUTLIER) cc_final: 0.5566 (mt) REVERT: 3 998 HIS cc_start: 0.5154 (OUTLIER) cc_final: 0.4451 (t-90) REVERT: 3 1016 ARG cc_start: 0.3791 (OUTLIER) cc_final: 0.3418 (tpt170) REVERT: 5 25 ASP cc_start: 0.5301 (OUTLIER) cc_final: 0.4512 (t0) REVERT: E 158 GLU cc_start: 0.5230 (tm-30) cc_final: 0.4911 (tm-30) REVERT: E 160 MET cc_start: 0.3526 (OUTLIER) cc_final: 0.2474 (mpt) REVERT: E 232 MET cc_start: -0.1004 (tpt) cc_final: -0.1251 (tpt) REVERT: E 241 LYS cc_start: 0.7053 (OUTLIER) cc_final: 0.6332 (tppt) REVERT: E 242 PHE cc_start: 0.0590 (t80) cc_final: -0.0507 (t80) REVERT: m 20 MET cc_start: -0.0971 (tmm) cc_final: -0.1247 (tmm) REVERT: h 45 MET cc_start: 0.0585 (OUTLIER) cc_final: 0.0052 (tpt) REVERT: M 82 MET cc_start: 0.4254 (pp-130) cc_final: 0.3888 (pp-130) REVERT: n 13 MET cc_start: -0.0993 (OUTLIER) cc_final: -0.1518 (tpp) REVERT: n 69 MET cc_start: 0.1915 (ptm) cc_final: 0.0323 (pmm) REVERT: i 73 MET cc_start: 0.4111 (OUTLIER) cc_final: 0.3600 (ttm) outliers start: 136 outliers final: 73 residues processed: 414 average time/residue: 1.1922 time to fit residues: 642.6935 Evaluate side-chains 376 residues out of total 4942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 285 time to evaluate : 3.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 583 ILE Chi-restraints excluded: chain 1 residue 623 TYR Chi-restraints excluded: chain 1 residue 722 GLU Chi-restraints excluded: chain 1 residue 925 VAL Chi-restraints excluded: chain 1 residue 928 TYR Chi-restraints excluded: chain 1 residue 932 ILE Chi-restraints excluded: chain 1 residue 960 VAL Chi-restraints excluded: chain 1 residue 989 VAL Chi-restraints excluded: chain 1 residue 1004 ILE Chi-restraints excluded: chain 1 residue 1010 THR Chi-restraints excluded: chain 1 residue 1021 THR Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1063 LEU Chi-restraints excluded: chain 1 residue 1093 VAL Chi-restraints excluded: chain 1 residue 1097 LEU Chi-restraints excluded: chain 1 residue 1141 LEU Chi-restraints excluded: chain 1 residue 1169 VAL Chi-restraints excluded: chain 1 residue 1209 ASN Chi-restraints excluded: chain 1 residue 1291 ASP Chi-restraints excluded: chain 1 residue 1292 LYS Chi-restraints excluded: chain 1 residue 1294 THR Chi-restraints excluded: chain 2 residue 461 THR Chi-restraints excluded: chain 2 residue 477 MET Chi-restraints excluded: chain 2 residue 478 HIS Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 564 ILE Chi-restraints excluded: chain 2 residue 566 ILE Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 39 GLU Chi-restraints excluded: chain 3 residue 56 VAL Chi-restraints excluded: chain 3 residue 79 VAL Chi-restraints excluded: chain 3 residue 107 PHE Chi-restraints excluded: chain 3 residue 156 SER Chi-restraints excluded: chain 3 residue 165 THR Chi-restraints excluded: chain 3 residue 197 THR Chi-restraints excluded: chain 3 residue 229 GLU Chi-restraints excluded: chain 3 residue 274 ARG Chi-restraints excluded: chain 3 residue 314 THR Chi-restraints excluded: chain 3 residue 363 HIS Chi-restraints excluded: chain 3 residue 404 LEU Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 476 VAL Chi-restraints excluded: chain 3 residue 491 VAL Chi-restraints excluded: chain 3 residue 497 SER Chi-restraints excluded: chain 3 residue 500 LEU Chi-restraints excluded: chain 3 residue 534 ASN Chi-restraints excluded: chain 3 residue 640 LEU Chi-restraints excluded: chain 3 residue 677 THR Chi-restraints excluded: chain 3 residue 718 ARG Chi-restraints excluded: chain 3 residue 747 SER Chi-restraints excluded: chain 3 residue 757 ILE Chi-restraints excluded: chain 3 residue 777 VAL Chi-restraints excluded: chain 3 residue 865 VAL Chi-restraints excluded: chain 3 residue 893 VAL Chi-restraints excluded: chain 3 residue 963 VAL Chi-restraints excluded: chain 3 residue 977 LEU Chi-restraints excluded: chain 3 residue 998 HIS Chi-restraints excluded: chain 3 residue 1016 ARG Chi-restraints excluded: chain 3 residue 1034 THR Chi-restraints excluded: chain 3 residue 1037 SER Chi-restraints excluded: chain 3 residue 1043 THR Chi-restraints excluded: chain 5 residue 25 ASP Chi-restraints excluded: chain 5 residue 26 THR Chi-restraints excluded: chain 5 residue 49 LEU Chi-restraints excluded: chain 5 residue 57 GLU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 400 HIS Chi-restraints excluded: chain C residue 469 GLU Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 241 LYS Chi-restraints excluded: chain O residue 19 ILE Chi-restraints excluded: chain O residue 45 ILE Chi-restraints excluded: chain O residue 48 PHE Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain m residue 51 ILE Chi-restraints excluded: chain h residue 34 VAL Chi-restraints excluded: chain h residue 45 MET Chi-restraints excluded: chain k residue 54 LYS Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain n residue 13 MET Chi-restraints excluded: chain i residue 73 MET Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 43 MET Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain 6 residue 36 TYR Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain 6 residue 41 THR Chi-restraints excluded: chain 6 residue 66 VAL Chi-restraints excluded: chain 6 residue 81 ASP Chi-restraints excluded: chain 6 residue 83 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 581 random chunks: chunk 509 optimal weight: 20.0000 chunk 536 optimal weight: 0.7980 chunk 489 optimal weight: 0.9980 chunk 521 optimal weight: 20.0000 chunk 314 optimal weight: 7.9990 chunk 227 optimal weight: 0.7980 chunk 409 optimal weight: 0.0270 chunk 160 optimal weight: 0.6980 chunk 471 optimal weight: 50.0000 chunk 493 optimal weight: 10.0000 chunk 520 optimal weight: 0.0370 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11209 ASN ** 3 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 983 ASN ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4168 moved from start: 0.6624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 44620 Z= 0.157 Angle : 0.650 24.802 61146 Z= 0.308 Chirality : 0.053 1.984 6013 Planarity : 0.005 0.061 7428 Dihedral : 16.799 171.984 10910 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.22 % Favored : 95.76 % Rotamer: Outliers : 3.20 % Allowed : 31.60 % Favored : 65.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -0.05 (0.12), residues: 5499 helix: 1.50 (0.13), residues: 1868 sheet: -0.13 (0.16), residues: 1109 loop : -1.16 (0.12), residues: 2522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 1 732 HIS 0.011 0.001 HIS 11210 PHE 0.026 0.001 PHE 3 788 TYR 0.017 0.001 TYR 6 71 ARG 0.010 0.000 ARG 3 10 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10998 Ramachandran restraints generated. 5499 Oldfield, 0 Emsley, 5499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10998 Ramachandran restraints generated. 5499 Oldfield, 0 Emsley, 5499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 4942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 294 time to evaluate : 4.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 TYR cc_start: 0.4939 (m-80) cc_final: 0.4693 (m-10) REVERT: 1 910 MET cc_start: 0.4162 (mmp) cc_final: 0.3932 (mmp) REVERT: 1 1000 ILE cc_start: 0.6163 (OUTLIER) cc_final: 0.5918 (tp) REVERT: 2 477 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.7054 (pmm) REVERT: 3 222 ARG cc_start: 0.5696 (mtt90) cc_final: 0.5184 (mtm-85) REVERT: 3 274 ARG cc_start: 0.6386 (OUTLIER) cc_final: 0.5315 (mtm180) REVERT: 3 534 ASN cc_start: 0.2749 (OUTLIER) cc_final: 0.2299 (p0) REVERT: 3 583 MET cc_start: -0.2377 (mmt) cc_final: -0.2870 (ttm) REVERT: 3 630 MET cc_start: 0.3168 (ppp) cc_final: 0.1501 (mmm) REVERT: 3 640 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7308 (pt) REVERT: 3 645 MET cc_start: -0.0151 (tmt) cc_final: -0.0662 (tpt) REVERT: 3 998 HIS cc_start: 0.5002 (OUTLIER) cc_final: 0.4455 (t-90) REVERT: 3 1016 ARG cc_start: 0.4072 (OUTLIER) cc_final: 0.3755 (tpt170) REVERT: E 158 GLU cc_start: 0.5228 (tm-30) cc_final: 0.5020 (tm-30) REVERT: E 160 MET cc_start: 0.3317 (OUTLIER) cc_final: 0.2304 (mpt) REVERT: E 232 MET cc_start: -0.1070 (tpt) cc_final: -0.1365 (tpt) REVERT: E 241 LYS cc_start: 0.6814 (OUTLIER) cc_final: 0.6210 (tppt) REVERT: m 20 MET cc_start: -0.0755 (tmm) cc_final: -0.1102 (tmm) REVERT: h 45 MET cc_start: 0.0547 (OUTLIER) cc_final: 0.0057 (tpt) REVERT: M 82 MET cc_start: 0.4301 (pp-130) cc_final: 0.4054 (pp-130) REVERT: n 13 MET cc_start: -0.1001 (OUTLIER) cc_final: -0.1507 (tpp) REVERT: n 69 MET cc_start: 0.1951 (ptm) cc_final: 0.0350 (pmm) REVERT: i 73 MET cc_start: 0.4089 (OUTLIER) cc_final: 0.3670 (ttm) outliers start: 98 outliers final: 62 residues processed: 370 average time/residue: 1.1347 time to fit residues: 550.8116 Evaluate side-chains 353 residues out of total 4942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 279 time to evaluate : 4.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain 1 residue 583 ILE Chi-restraints excluded: chain 1 residue 925 VAL Chi-restraints excluded: chain 1 residue 928 TYR Chi-restraints excluded: chain 1 residue 1000 ILE Chi-restraints excluded: chain 1 residue 1004 ILE Chi-restraints excluded: chain 1 residue 1010 THR Chi-restraints excluded: chain 1 residue 1021 THR Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1063 LEU Chi-restraints excluded: chain 1 residue 1097 LEU Chi-restraints excluded: chain 1 residue 1141 LEU Chi-restraints excluded: chain 1 residue 1169 VAL Chi-restraints excluded: chain 1 residue 1170 THR Chi-restraints excluded: chain 1 residue 1291 ASP Chi-restraints excluded: chain 1 residue 1294 THR Chi-restraints excluded: chain 2 residue 461 THR Chi-restraints excluded: chain 2 residue 477 MET Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 511 LEU Chi-restraints excluded: chain 2 residue 564 ILE Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 56 VAL Chi-restraints excluded: chain 3 residue 107 PHE Chi-restraints excluded: chain 3 residue 156 SER Chi-restraints excluded: chain 3 residue 197 THR Chi-restraints excluded: chain 3 residue 274 ARG Chi-restraints excluded: chain 3 residue 404 LEU Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 476 VAL Chi-restraints excluded: chain 3 residue 491 VAL Chi-restraints excluded: chain 3 residue 497 SER Chi-restraints excluded: chain 3 residue 534 ASN Chi-restraints excluded: chain 3 residue 640 LEU Chi-restraints excluded: chain 3 residue 677 THR Chi-restraints excluded: chain 3 residue 718 ARG Chi-restraints excluded: chain 3 residue 747 SER Chi-restraints excluded: chain 3 residue 757 ILE Chi-restraints excluded: chain 3 residue 777 VAL Chi-restraints excluded: chain 3 residue 893 VAL Chi-restraints excluded: chain 3 residue 963 VAL Chi-restraints excluded: chain 3 residue 998 HIS Chi-restraints excluded: chain 3 residue 1016 ARG Chi-restraints excluded: chain 3 residue 1034 THR Chi-restraints excluded: chain 3 residue 1043 THR Chi-restraints excluded: chain 5 residue 49 LEU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 469 GLU Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 241 LYS Chi-restraints excluded: chain O residue 19 ILE Chi-restraints excluded: chain O residue 45 ILE Chi-restraints excluded: chain O residue 48 PHE Chi-restraints excluded: chain O residue 50 ASP Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain O residue 176 VAL Chi-restraints excluded: chain m residue 51 ILE Chi-restraints excluded: chain h residue 23 THR Chi-restraints excluded: chain h residue 45 MET Chi-restraints excluded: chain k residue 54 LYS Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain n residue 13 MET Chi-restraints excluded: chain i residue 73 MET Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 43 MET Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain 6 residue 36 TYR Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain 6 residue 41 THR Chi-restraints excluded: chain 6 residue 66 VAL Chi-restraints excluded: chain 6 residue 81 ASP Chi-restraints excluded: chain 6 residue 83 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 581 random chunks: chunk 342 optimal weight: 4.9990 chunk 551 optimal weight: 10.0000 chunk 336 optimal weight: 8.9990 chunk 261 optimal weight: 40.0000 chunk 383 optimal weight: 30.0000 chunk 578 optimal weight: 0.8980 chunk 532 optimal weight: 30.0000 chunk 460 optimal weight: 40.0000 chunk 47 optimal weight: 0.9990 chunk 356 optimal weight: 0.7980 chunk 282 optimal weight: 0.6980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 526 HIS ** 3 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4250 moved from start: 0.6790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 44620 Z= 0.280 Angle : 0.721 25.096 61146 Z= 0.347 Chirality : 0.056 1.996 6013 Planarity : 0.005 0.059 7428 Dihedral : 16.847 171.870 10910 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.26 % Favored : 94.71 % Rotamer: Outliers : 3.59 % Allowed : 31.34 % Favored : 65.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -0.14 (0.12), residues: 5499 helix: 1.44 (0.13), residues: 1847 sheet: -0.19 (0.16), residues: 1115 loop : -1.21 (0.12), residues: 2537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP 3 903 HIS 0.008 0.001 HIS 11256 PHE 0.036 0.002 PHE 3 788 TYR 0.034 0.002 TYR 3 970 ARG 0.010 0.001 ARG 1 549 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10998 Ramachandran restraints generated. 5499 Oldfield, 0 Emsley, 5499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10998 Ramachandran restraints generated. 5499 Oldfield, 0 Emsley, 5499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 4942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 278 time to evaluate : 4.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 928 TYR cc_start: 0.6849 (OUTLIER) cc_final: 0.5463 (m-80) REVERT: 1 966 GLN cc_start: 0.7492 (tp-100) cc_final: 0.7253 (mm-40) REVERT: 1 1287 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7436 (mp) REVERT: 2 477 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.7381 (pmm) REVERT: 3 10 ARG cc_start: 0.7783 (mtt-85) cc_final: 0.7531 (mtt90) REVERT: 3 222 ARG cc_start: 0.6053 (mtt90) cc_final: 0.5529 (mtm-85) REVERT: 3 274 ARG cc_start: 0.6596 (OUTLIER) cc_final: 0.5879 (mtm180) REVERT: 3 534 ASN cc_start: 0.2548 (OUTLIER) cc_final: 0.2175 (p0) REVERT: 3 583 MET cc_start: -0.2376 (mmt) cc_final: -0.3013 (mtt) REVERT: 3 640 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7405 (pt) REVERT: 3 645 MET cc_start: -0.0045 (tmt) cc_final: -0.0612 (tpt) REVERT: 3 734 LEU cc_start: 0.6574 (mt) cc_final: 0.6304 (mt) REVERT: 3 747 SER cc_start: 0.4025 (OUTLIER) cc_final: 0.3346 (m) REVERT: 3 977 LEU cc_start: 0.5938 (OUTLIER) cc_final: 0.5598 (mt) REVERT: 3 998 HIS cc_start: 0.5512 (OUTLIER) cc_final: 0.4818 (t-90) REVERT: 3 1016 ARG cc_start: 0.3892 (OUTLIER) cc_final: 0.3555 (tpt170) REVERT: E 160 MET cc_start: 0.3194 (OUTLIER) cc_final: 0.2310 (mpt) REVERT: E 232 MET cc_start: -0.0920 (tpt) cc_final: -0.1135 (tpt) REVERT: E 241 LYS cc_start: 0.6889 (OUTLIER) cc_final: 0.6206 (tppt) REVERT: m 20 MET cc_start: -0.0702 (tmm) cc_final: -0.1062 (tmm) REVERT: h 45 MET cc_start: 0.0537 (OUTLIER) cc_final: 0.0045 (tpt) REVERT: k 11 GLN cc_start: 0.1138 (OUTLIER) cc_final: 0.0067 (mm-40) REVERT: M 51 MET cc_start: 0.2856 (mmm) cc_final: 0.2020 (mmm) REVERT: M 82 MET cc_start: 0.4246 (pp-130) cc_final: 0.4032 (pp-130) REVERT: n 13 MET cc_start: -0.0810 (OUTLIER) cc_final: -0.1637 (tpp) REVERT: n 69 MET cc_start: 0.1885 (ptm) cc_final: 0.0292 (pmm) REVERT: i 73 MET cc_start: 0.4140 (OUTLIER) cc_final: 0.3693 (ttm) outliers start: 110 outliers final: 71 residues processed: 366 average time/residue: 1.0897 time to fit residues: 524.0258 Evaluate side-chains 364 residues out of total 4942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 277 time to evaluate : 3.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain 1 residue 583 ILE Chi-restraints excluded: chain 1 residue 837 THR Chi-restraints excluded: chain 1 residue 925 VAL Chi-restraints excluded: chain 1 residue 928 TYR Chi-restraints excluded: chain 1 residue 1004 ILE Chi-restraints excluded: chain 1 residue 1010 THR Chi-restraints excluded: chain 1 residue 1021 THR Chi-restraints excluded: chain 1 residue 1050 VAL Chi-restraints excluded: chain 1 residue 1063 LEU Chi-restraints excluded: chain 1 residue 1097 LEU Chi-restraints excluded: chain 1 residue 1141 LEU Chi-restraints excluded: chain 1 residue 1161 MET Chi-restraints excluded: chain 1 residue 1169 VAL Chi-restraints excluded: chain 1 residue 1170 THR Chi-restraints excluded: chain 1 residue 1287 ILE Chi-restraints excluded: chain 1 residue 1291 ASP Chi-restraints excluded: chain 1 residue 1294 THR Chi-restraints excluded: chain 2 residue 461 THR Chi-restraints excluded: chain 2 residue 477 MET Chi-restraints excluded: chain 2 residue 498 VAL Chi-restraints excluded: chain 2 residue 564 ILE Chi-restraints excluded: chain 3 residue 12 THR Chi-restraints excluded: chain 3 residue 56 VAL Chi-restraints excluded: chain 3 residue 64 SER Chi-restraints excluded: chain 3 residue 107 PHE Chi-restraints excluded: chain 3 residue 156 SER Chi-restraints excluded: chain 3 residue 165 THR Chi-restraints excluded: chain 3 residue 171 VAL Chi-restraints excluded: chain 3 residue 197 THR Chi-restraints excluded: chain 3 residue 274 ARG Chi-restraints excluded: chain 3 residue 404 LEU Chi-restraints excluded: chain 3 residue 429 ARG Chi-restraints excluded: chain 3 residue 476 VAL Chi-restraints excluded: chain 3 residue 491 VAL Chi-restraints excluded: chain 3 residue 497 SER Chi-restraints excluded: chain 3 residue 534 ASN Chi-restraints excluded: chain 3 residue 640 LEU Chi-restraints excluded: chain 3 residue 665 LEU Chi-restraints excluded: chain 3 residue 675 LEU Chi-restraints excluded: chain 3 residue 677 THR Chi-restraints excluded: chain 3 residue 718 ARG Chi-restraints excluded: chain 3 residue 747 SER Chi-restraints excluded: chain 3 residue 757 ILE Chi-restraints excluded: chain 3 residue 777 VAL Chi-restraints excluded: chain 3 residue 865 VAL Chi-restraints excluded: chain 3 residue 893 VAL Chi-restraints excluded: chain 3 residue 963 VAL Chi-restraints excluded: chain 3 residue 977 LEU Chi-restraints excluded: chain 3 residue 998 HIS Chi-restraints excluded: chain 3 residue 1016 ARG Chi-restraints excluded: chain 3 residue 1034 THR Chi-restraints excluded: chain 3 residue 1043 THR Chi-restraints excluded: chain 3 residue 1116 SER Chi-restraints excluded: chain 3 residue 1200 THR Chi-restraints excluded: chain 5 residue 49 LEU Chi-restraints excluded: chain 5 residue 63 ARG Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 469 GLU Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 241 LYS Chi-restraints excluded: chain O residue 19 ILE Chi-restraints excluded: chain O residue 45 ILE Chi-restraints excluded: chain O residue 48 PHE Chi-restraints excluded: chain O residue 50 ASP Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain O residue 176 VAL Chi-restraints excluded: chain m residue 51 ILE Chi-restraints excluded: chain h residue 23 THR Chi-restraints excluded: chain h residue 34 VAL Chi-restraints excluded: chain h residue 45 MET Chi-restraints excluded: chain k residue 11 GLN Chi-restraints excluded: chain k residue 54 LYS Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain n residue 13 MET Chi-restraints excluded: chain i residue 70 VAL Chi-restraints excluded: chain i residue 73 MET Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 43 MET Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain 6 residue 36 TYR Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain 6 residue 41 THR Chi-restraints excluded: chain 6 residue 66 VAL Chi-restraints excluded: chain 6 residue 81 ASP Chi-restraints excluded: chain 6 residue 83 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 581 random chunks: chunk 366 optimal weight: 30.0000 chunk 490 optimal weight: 30.0000 chunk 141 optimal weight: 10.0000 chunk 424 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 461 optimal weight: 50.0000 chunk 193 optimal weight: 0.9990 chunk 474 optimal weight: 40.0000 chunk 58 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11194 HIS 3 219 HIS ** 3 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5193 r_free = 0.5193 target = 0.273871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.227107 restraints weight = 77083.097| |-----------------------------------------------------------------------------| r_work (start): 0.4692 rms_B_bonded: 3.53 r_work: 0.4056 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6101 moved from start: 0.7221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 44620 Z= 0.423 Angle : 0.825 24.910 61146 Z= 0.406 Chirality : 0.060 2.029 6013 Planarity : 0.006 0.069 7428 Dihedral : 17.007 172.396 10910 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.64 % Favored : 93.33 % Rotamer: Outliers : 4.18 % Allowed : 30.88 % Favored : 64.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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 (0.12), residues: 5499 helix: 1.03 (0.13), residues: 1841 sheet: -0.32 (0.16), residues: 1102 loop : -1.34 (0.12), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP 3 903 HIS 0.015 0.002 HIS 3 804 PHE 0.043 0.003 PHE 3 788 TYR 0.043 0.003 TYR 3 970 ARG 0.008 0.001 ARG 3 815 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14325.79 seconds wall clock time: 254 minutes 31.65 seconds (15271.65 seconds total)