Starting phenix.real_space_refine on Sun Feb 18 15:22:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wvj_21920/02_2024/6wvj_21920.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wvj_21920/02_2024/6wvj_21920.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wvj_21920/02_2024/6wvj_21920.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wvj_21920/02_2024/6wvj_21920.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wvj_21920/02_2024/6wvj_21920.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wvj_21920/02_2024/6wvj_21920.pdb" } resolution = 3.36 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 ------------------------------------------------------------------------------- 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= -0.026 sd= 0.774 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 36 5.49 5 Mg 1 5.21 5 S 80 5.16 5 C 13981 2.51 5 N 3916 2.21 5 O 4351 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 26": "OE1" <-> "OE2" Residue "A GLU 69": "OE1" <-> "OE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A ASP 74": "OD1" <-> "OD2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 98": "OE1" <-> "OE2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A ASP 152": "OD1" <-> "OD2" Residue "A ASP 157": "OD1" <-> "OD2" Residue "A ASP 158": "OD1" <-> "OD2" Residue "A TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 219": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 26": "OE1" <-> "OE2" Residue "B ASP 59": "OD1" <-> "OD2" Residue "B ASP 74": "OD1" <-> "OD2" Residue "B TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B GLU 98": "OE1" <-> "OE2" Residue "B ASP 100": "OD1" <-> "OD2" Residue "B ASP 111": "OD1" <-> "OD2" Residue "B ASP 152": "OD1" <-> "OD2" Residue "B ASP 158": "OD1" <-> "OD2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "B ASP 197": "OD1" <-> "OD2" Residue "B GLU 208": "OE1" <-> "OE2" Residue "B PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 12": "NH1" <-> "NH2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C ASP 51": "OD1" <-> "OD2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C ASP 57": "OD1" <-> "OD2" Residue "C GLU 73": "OE1" <-> "OE2" Residue "C TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 80": "OE1" <-> "OE2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "C GLU 105": "OE1" <-> "OE2" Residue "C ASP 110": "OD1" <-> "OD2" Residue "C ASP 115": "OD1" <-> "OD2" Residue "C ASP 121": "OD1" <-> "OD2" Residue "C PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 178": "OD1" <-> "OD2" Residue "C ASP 185": "OD1" <-> "OD2" Residue "C ARG 197": "NH1" <-> "NH2" Residue "C GLU 213": "OE1" <-> "OE2" Residue "C TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 222": "OD1" <-> "OD2" Residue "C ASP 230": "OD1" <-> "OD2" Residue "C TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 241": "NH1" <-> "NH2" Residue "C PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 284": "NH1" <-> "NH2" Residue "C GLU 370": "OE1" <-> "OE2" Residue "C GLU 371": "OE1" <-> "OE2" Residue "C ASP 397": "OD1" <-> "OD2" Residue "C ASP 399": "OD1" <-> "OD2" Residue "C ASP 402": "OD1" <-> "OD2" Residue "C GLU 428": "OE1" <-> "OE2" Residue "C ARG 429": "NH1" <-> "NH2" Residue "C ARG 434": "NH1" <-> "NH2" Residue "C ASP 439": "OD1" <-> "OD2" Residue "C GLU 460": "OE1" <-> "OE2" Residue "C ASP 472": "OD1" <-> "OD2" Residue "C GLU 479": "OE1" <-> "OE2" Residue "C ARG 496": "NH1" <-> "NH2" Residue "C ARG 498": "NH1" <-> "NH2" Residue "C ARG 504": "NH1" <-> "NH2" Residue "C ASP 505": "OD1" <-> "OD2" Residue "C TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 518": "OE1" <-> "OE2" Residue "C TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 539": "NH1" <-> "NH2" Residue "C PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 544": "OE1" <-> "OE2" Residue "C TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 549": "NH1" <-> "NH2" Residue "C GLU 568": "OE1" <-> "OE2" Residue "C GLU 569": "OE1" <-> "OE2" Residue "C ASP 589": "OD1" <-> "OD2" Residue "C GLU 599": "OE1" <-> "OE2" Residue "C ASP 632": "OD1" <-> "OD2" Residue "C PHE 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 663": "OE1" <-> "OE2" Residue "C GLU 683": "OE1" <-> "OE2" Residue "C GLU 686": "OE1" <-> "OE2" Residue "C ARG 693": "NH1" <-> "NH2" Residue "C ARG 694": "NH1" <-> "NH2" Residue "C GLU 696": "OE1" <-> "OE2" Residue "C ASP 708": "OD1" <-> "OD2" Residue "C TYR 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 717": "NH1" <-> "NH2" Residue "C TYR 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 734": "OD1" <-> "OD2" Residue "C GLU 735": "OE1" <-> "OE2" Residue "C GLU 740": "OE1" <-> "OE2" Residue "C ASP 744": "OD1" <-> "OD2" Residue "C GLU 779": "OE1" <-> "OE2" Residue "C ASP 785": "OD1" <-> "OD2" Residue "C TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 793": "OE1" <-> "OE2" Residue "C GLU 796": "OE1" <-> "OE2" Residue "C GLU 798": "OE1" <-> "OE2" Residue "C ASP 801": "OD1" <-> "OD2" Residue "C ARG 811": "NH1" <-> "NH2" Residue "C ASP 812": "OD1" <-> "OD2" Residue "C ASP 819": "OD1" <-> "OD2" Residue "C ASP 826": "OD1" <-> "OD2" Residue "C ARG 827": "NH1" <-> "NH2" Residue "C ASP 838": "OD1" <-> "OD2" Residue "C ASP 840": "OD1" <-> "OD2" Residue "C ASP 889": "OD1" <-> "OD2" Residue "C PHE 893": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 895": "NH1" <-> "NH2" Residue "C GLU 896": "OE1" <-> "OE2" Residue "C ASP 897": "OD1" <-> "OD2" Residue "C ASP 899": "OD1" <-> "OD2" Residue "C GLU 921": "OE1" <-> "OE2" Residue "C GLU 942": "OE1" <-> "OE2" Residue "C TYR 946": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 954": "OD1" <-> "OD2" Residue "C PHE 992": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 993": "OD1" <-> "OD2" Residue "C GLU 997": "OE1" <-> "OE2" Residue "C GLU 998": "OE1" <-> "OE2" Residue "C GLU 1002": "OE1" <-> "OE2" Residue "C ASP 1012": "OD1" <-> "OD2" Residue "C TYR 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1024": "OE1" <-> "OE2" Residue "C ASP 1046": "OD1" <-> "OD2" Residue "C PHE 1070": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1086": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1094": "OE1" <-> "OE2" Residue "C ASP 1101": "OD1" <-> "OD2" Residue "C GLU 1111": "OE1" <-> "OE2" Residue "C GLU 1121": "OE1" <-> "OE2" Residue "C GLU 1126": "OE1" <-> "OE2" Residue "C GLU 1134": "OE1" <-> "OE2" Residue "C ASP 1141": "OD1" <-> "OD2" Residue "C ASP 1148": "OD1" <-> "OD2" Residue "C GLU 1151": "OE1" <-> "OE2" Residue "D PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D ASP 44": "OD1" <-> "OD2" Residue "D PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 57": "OD1" <-> "OD2" Residue "D TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 76": "OD1" <-> "OD2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D ARG 84": "NH1" <-> "NH2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "D GLU 96": "OE1" <-> "OE2" Residue "D GLU 127": "OE1" <-> "OE2" Residue "D TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 138": "OD1" <-> "OD2" Residue "D GLU 152": "OE1" <-> "OE2" Residue "D GLU 173": "OE1" <-> "OE2" Residue "D ASP 189": "OD1" <-> "OD2" Residue "D GLU 193": "OE1" <-> "OE2" Residue "D GLU 214": "OE1" <-> "OE2" Residue "D ASP 229": "OD1" <-> "OD2" Residue "D ARG 239": "NH1" <-> "NH2" Residue "D ARG 259": "NH1" <-> "NH2" Residue "D ASP 293": "OD1" <-> "OD2" Residue "D ARG 301": "NH1" <-> "NH2" Residue "D ASP 337": "OD1" <-> "OD2" Residue "D TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 360": "OE1" <-> "OE2" Residue "D PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 373": "OE1" <-> "OE2" Residue "D GLU 376": "OE1" <-> "OE2" Residue "D PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 427": "OE1" <-> "OE2" Residue "D PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 464": "OE1" <-> "OE2" Residue "D ASP 484": "OD1" <-> "OD2" Residue "D TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 505": "OE1" <-> "OE2" Residue "D ASP 520": "OD1" <-> "OD2" Residue "D GLU 521": "OE1" <-> "OE2" Residue "D TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 554": "NH1" <-> "NH2" Residue "D GLU 569": "OE1" <-> "OE2" Residue "D GLU 580": "OE1" <-> "OE2" Residue "D GLU 587": "OE1" <-> "OE2" Residue "D PHE 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 641": "OD1" <-> "OD2" Residue "D ARG 642": "NH1" <-> "NH2" Residue "D ASP 662": "OD1" <-> "OD2" Residue "D GLU 671": "OE1" <-> "OE2" Residue "D ASP 681": "OD1" <-> "OD2" Residue "D GLU 694": "OE1" <-> "OE2" Residue "D ASP 721": "OD1" <-> "OD2" Residue "D GLU 760": "OE1" <-> "OE2" Residue "D GLU 769": "OE1" <-> "OE2" Residue "D PHE 777": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 796": "OD1" <-> "OD2" Residue "D TYR 799": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 815": "OE1" <-> "OE2" Residue "D ASP 817": "OD1" <-> "OD2" Residue "D GLU 834": "OE1" <-> "OE2" Residue "D GLU 841": "OE1" <-> "OE2" Residue "D PHE 847": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 870": "OE1" <-> "OE2" Residue "D ASP 871": "OD1" <-> "OD2" Residue "D TYR 903": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 929": "OE1" <-> "OE2" Residue "D ARG 937": "NH1" <-> "NH2" Residue "D ASP 948": "OD1" <-> "OD2" Residue "D GLU 958": "OE1" <-> "OE2" Residue "D GLU 961": "OE1" <-> "OE2" Residue "D GLU 973": "OE1" <-> "OE2" Residue "D ASP 975": "OD1" <-> "OD2" Residue "D GLU 1026": "OE1" <-> "OE2" Residue "D ASP 1030": "OD1" <-> "OD2" Residue "D GLU 1033": "OE1" <-> "OE2" Residue "D ASP 1039": "OD1" <-> "OD2" Residue "D GLU 1045": "OE1" <-> "OE2" Residue "D TYR 1046": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1061": "OE1" <-> "OE2" Residue "D ASP 1064": "OD1" <-> "OD2" Residue "D ARG 1076": "NH1" <-> "NH2" Residue "D ASP 1095": "OD1" <-> "OD2" Residue "D GLU 1101": "OE1" <-> "OE2" Residue "D ASP 1131": "OD1" <-> "OD2" Residue "D GLU 1141": "OE1" <-> "OE2" Residue "D ARG 1144": "NH1" <-> "NH2" Residue "D GLU 1163": "OE1" <-> "OE2" Residue "D ARG 1181": "NH1" <-> "NH2" Residue "F ARG 26": "NH1" <-> "NH2" Residue "F ASP 35": "OD1" <-> "OD2" Residue "F GLU 53": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22367 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1688 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 214} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1663 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 214} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 8688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1117, 8688 Classifications: {'peptide': 1117} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 1062} Chain breaks: 2 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 8, 'ARG:plan': 6, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 90 Chain: "D" Number of atoms: 9085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1176, 9085 Classifications: {'peptide': 1176} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 52, 'TRANS': 1123} Chain breaks: 1 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 148 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 8, 'ARG:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 102 Chain: "F" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 478 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 59} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "T" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 385 Classifications: {'DNA': 19} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 18} Chain: "R" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 175 Classifications: {'RNA': 8} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 3} Link IDs: {'rna3p': 7} Chain: "N" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 202 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12462 SG CYS D 60 68.748 73.881 117.814 1.00 93.04 S ATOM 12478 SG CYS D 62 65.848 73.909 119.750 1.00100.22 S ATOM 12586 SG CYS D 75 68.454 71.660 120.817 1.00 90.54 S ATOM 12611 SG CYS D 78 65.998 70.895 118.159 1.00 94.90 S ATOM 18378 SG CYS D 818 110.171 42.222 72.853 1.00 67.88 S ATOM 18963 SG CYS D 892 106.801 43.756 72.517 1.00 60.22 S ATOM 19012 SG CYS D 899 109.827 45.738 71.906 1.00 57.65 S ATOM 19038 SG CYS D 902 108.878 43.298 69.631 1.00 56.16 S Time building chain proxies: 11.87, per 1000 atoms: 0.53 Number of scatterers: 22367 At special positions: 0 Unit cell: (150.36, 136.08, 132.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 80 16.00 P 36 15.00 Mg 1 11.99 O 4351 8.00 N 3916 7.00 C 13981 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.28 Conformation dependent library (CDL) restraints added in 4.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 78 " pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 902 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 899 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 818 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 892 " Number of angles added : 12 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5160 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 40 sheets defined 38.5% alpha, 17.2% beta 14 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 7.98 Creating SS restraints... Processing helix chain 'A' and resid 31 through 45 removed outlier: 3.737A pdb=" N THR A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER A 39 " --> pdb=" O THR A 35 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE A 43 " --> pdb=" O SER A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 83 Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 150 through 155 Processing helix chain 'A' and resid 205 through 226 removed outlier: 3.846A pdb=" N LEU A 217 " --> pdb=" O GLY A 213 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ILE A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N PHE A 224 " --> pdb=" O HIS A 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 47 Processing helix chain 'B' and resid 74 through 83 Processing helix chain 'B' and resid 150 through 155 removed outlier: 3.556A pdb=" N ASN B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 221 removed outlier: 3.878A pdb=" N HIS B 220 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 221 " --> pdb=" O LEU B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 226 Processing helix chain 'C' and resid 30 through 43 removed outlier: 4.177A pdb=" N THR C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 53 removed outlier: 3.583A pdb=" N GLN C 50 " --> pdb=" O ARG C 46 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP C 51 " --> pdb=" O GLU C 47 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE C 52 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 84 Processing helix chain 'C' and resid 191 through 198 removed outlier: 3.744A pdb=" N LEU C 195 " --> pdb=" O PRO C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 211 removed outlier: 4.403A pdb=" N ASP C 209 " --> pdb=" O GLN C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 224 removed outlier: 4.779A pdb=" N ASP C 222 " --> pdb=" O ARG C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 239 removed outlier: 3.789A pdb=" N ARG C 239 " --> pdb=" O GLU C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 259 removed outlier: 3.652A pdb=" N LEU C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 280 Processing helix chain 'C' and resid 281 through 286 Processing helix chain 'C' and resid 377 through 393 removed outlier: 3.711A pdb=" N ILE C 381 " --> pdb=" O THR C 377 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE C 382 " --> pdb=" O PRO C 378 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER C 383 " --> pdb=" O ALA C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 439 removed outlier: 3.502A pdb=" N GLN C 417 " --> pdb=" O GLY C 413 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE C 422 " --> pdb=" O ASN C 418 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY C 423 " --> pdb=" O GLN C 419 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET C 427 " --> pdb=" O GLY C 423 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU C 428 " --> pdb=" O LEU C 424 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ARG C 429 " --> pdb=" O SER C 425 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL C 430 " --> pdb=" O ARG C 426 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP C 439 " --> pdb=" O MET C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 448 Processing helix chain 'C' and resid 451 through 465 removed outlier: 3.848A pdb=" N ILE C 458 " --> pdb=" O VAL C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 483 Processing helix chain 'C' and resid 500 through 505 Processing helix chain 'C' and resid 507 through 511 removed outlier: 3.778A pdb=" N TYR C 511 " --> pdb=" O TYR C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 572 removed outlier: 3.721A pdb=" N TYR C 572 " --> pdb=" O GLU C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 586 removed outlier: 3.659A pdb=" N ALA C 586 " --> pdb=" O ASP C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 618 Processing helix chain 'C' and resid 633 through 645 removed outlier: 4.048A pdb=" N ARG C 645 " --> pdb=" O ALA C 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 670 Processing helix chain 'C' and resid 767 through 771 removed outlier: 4.053A pdb=" N ASN C 770 " --> pdb=" O ASP C 767 " (cutoff:3.500A) Processing helix chain 'C' and resid 779 through 784 Processing helix chain 'C' and resid 819 through 823 removed outlier: 3.556A pdb=" N ARG C 822 " --> pdb=" O ASP C 819 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ASN C 823 " --> pdb=" O ALA C 820 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 819 through 823' Processing helix chain 'C' and resid 896 through 898 No H-bonds generated for 'chain 'C' and resid 896 through 898' Processing helix chain 'C' and resid 960 through 965 removed outlier: 3.891A pdb=" N SER C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG C 965 " --> pdb=" O GLY C 961 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 960 through 965' Processing helix chain 'C' and resid 967 through 984 removed outlier: 4.179A pdb=" N VAL C 971 " --> pdb=" O ASN C 967 " (cutoff:3.500A) Processing helix chain 'C' and resid 996 through 1008 Processing helix chain 'C' and resid 1043 through 1048 Processing helix chain 'C' and resid 1066 through 1070 Processing helix chain 'C' and resid 1076 through 1087 Processing helix chain 'C' and resid 1088 through 1097 Processing helix chain 'C' and resid 1102 through 1116 removed outlier: 4.095A pdb=" N VAL C1107 " --> pdb=" O VAL C1103 " (cutoff:3.500A) Processing helix chain 'C' and resid 1125 through 1138 removed outlier: 3.647A pdb=" N LYS C1133 " --> pdb=" O LYS C1129 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 84 through 90 removed outlier: 3.631A pdb=" N ARG D 88 " --> pdb=" O ALA D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 112 through 118 Processing helix chain 'D' and resid 121 through 130 removed outlier: 4.216A pdb=" N GLU D 127 " --> pdb=" O ARG D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 163 removed outlier: 4.682A pdb=" N LYS D 161 " --> pdb=" O ALA D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 180 removed outlier: 4.219A pdb=" N LEU D 178 " --> pdb=" O ALA D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 195 Processing helix chain 'D' and resid 200 through 219 removed outlier: 3.707A pdb=" N ARG D 205 " --> pdb=" O GLN D 201 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL D 212 " --> pdb=" O LYS D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 225 Processing helix chain 'D' and resid 235 through 239 Processing helix chain 'D' and resid 252 through 275 removed outlier: 3.880A pdb=" N ASP D 256 " --> pdb=" O SER D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 297 removed outlier: 3.582A pdb=" N ASP D 297 " --> pdb=" O ASP D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 321 removed outlier: 3.913A pdb=" N LEU D 320 " --> pdb=" O LEU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 330 Processing helix chain 'D' and resid 359 through 366 removed outlier: 3.723A pdb=" N LEU D 363 " --> pdb=" O LYS D 359 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU D 364 " --> pdb=" O GLU D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 377 Processing helix chain 'D' and resid 382 through 392 Processing helix chain 'D' and resid 395 through 405 removed outlier: 3.849A pdb=" N ASP D 399 " --> pdb=" O PRO D 395 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU D 402 " --> pdb=" O TRP D 398 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER D 403 " --> pdb=" O ASP D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 421 No H-bonds generated for 'chain 'D' and resid 419 through 421' Processing helix chain 'D' and resid 439 through 441 No H-bonds generated for 'chain 'D' and resid 439 through 441' Processing helix chain 'D' and resid 442 through 447 Processing helix chain 'D' and resid 462 through 472 Processing helix chain 'D' and resid 493 through 504 Processing helix chain 'D' and resid 518 through 529 removed outlier: 3.662A pdb=" N ALA D 522 " --> pdb=" O ASN D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 544 No H-bonds generated for 'chain 'D' and resid 542 through 544' Processing helix chain 'D' and resid 563 through 568 Processing helix chain 'D' and resid 582 through 588 Processing helix chain 'D' and resid 601 through 609 Processing helix chain 'D' and resid 616 through 631 removed outlier: 3.704A pdb=" N LEU D 620 " --> pdb=" O LYS D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 633 through 655 removed outlier: 3.666A pdb=" N LYS D 653 " --> pdb=" O LYS D 649 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA D 654 " --> pdb=" O TYR D 650 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY D 655 " --> pdb=" O SER D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 659 through 663 Processing helix chain 'D' and resid 668 through 690 removed outlier: 3.706A pdb=" N LYS D 679 " --> pdb=" O GLU D 675 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN D 682 " --> pdb=" O SER D 678 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 720 removed outlier: 4.135A pdb=" N GLU D 699 " --> pdb=" O GLU D 695 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE D 702 " --> pdb=" O TYR D 698 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA D 707 " --> pdb=" O SER D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 732 Processing helix chain 'D' and resid 737 through 746 removed outlier: 4.036A pdb=" N GLN D 743 " --> pdb=" O SER D 739 " (cutoff:3.500A) Processing helix chain 'D' and resid 772 through 779 Processing helix chain 'D' and resid 780 through 808 removed outlier: 4.089A pdb=" N THR D 794 " --> pdb=" O THR D 790 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ALA D 795 " --> pdb=" O ALA D 791 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP D 796 " --> pdb=" O LEU D 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 838 through 844 removed outlier: 3.545A pdb=" N ILE D 844 " --> pdb=" O GLU D 840 " (cutoff:3.500A) Processing helix chain 'D' and resid 869 through 880 Processing helix chain 'D' and resid 888 through 892 Processing helix chain 'D' and resid 899 through 904 Processing helix chain 'D' and resid 918 through 929 Processing helix chain 'D' and resid 930 through 934 Processing helix chain 'D' and resid 952 through 961 removed outlier: 3.653A pdb=" N ILE D 956 " --> pdb=" O GLY D 952 " (cutoff:3.500A) Processing helix chain 'D' and resid 1030 through 1038 Processing helix chain 'D' and resid 1039 through 1059 removed outlier: 4.013A pdb=" N GLU D1045 " --> pdb=" O THR D1041 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR D1046 " --> pdb=" O THR D1042 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL D1054 " --> pdb=" O GLU D1050 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR D1055 " --> pdb=" O VAL D1051 " (cutoff:3.500A) Processing helix chain 'D' and resid 1063 through 1073 removed outlier: 3.927A pdb=" N VAL D1067 " --> pdb=" O GLY D1063 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET D1070 " --> pdb=" O HIS D1066 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN D1073 " --> pdb=" O VAL D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1096 through 1107 Processing helix chain 'D' and resid 1122 through 1128 removed outlier: 4.004A pdb=" N LEU D1128 " --> pdb=" O THR D1124 " (cutoff:3.500A) Processing helix chain 'D' and resid 1133 through 1138 Processing helix chain 'D' and resid 1141 through 1153 removed outlier: 3.514A pdb=" N ASP D1148 " --> pdb=" O ARG D1144 " (cutoff:3.500A) Processing helix chain 'D' and resid 1160 through 1168 removed outlier: 3.640A pdb=" N ASN D1164 " --> pdb=" O GLY D1160 " (cutoff:3.500A) Processing helix chain 'D' and resid 1173 through 1176 Processing helix chain 'D' and resid 1177 through 1182 Processing helix chain 'F' and resid 5 through 11 Processing helix chain 'F' and resid 15 through 34 Processing helix chain 'F' and resid 45 through 54 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 14 removed outlier: 6.807A pdb=" N LYS A 22 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ILE A 14 " --> pdb=" O PHE A 20 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N PHE A 20 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N PHE A 20 " --> pdb=" O THR A 200 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N THR A 200 " --> pdb=" O PHE A 20 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N LYS A 22 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N VAL A 198 " --> pdb=" O LYS A 22 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N VAL A 24 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LEU A 196 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N GLU A 26 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU A 194 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ALA A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL A 185 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR A 191 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG A 175 " --> pdb=" O TRP A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 102 removed outlier: 7.161A pdb=" N ARG A 137 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE A 58 " --> pdb=" O ARG A 137 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ARG A 139 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ILE A 56 " --> pdb=" O ARG A 139 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N THR A 141 " --> pdb=" O THR A 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89 Processing sheet with id=AA4, first strand: chain 'A' and resid 106 through 108 Processing sheet with id=AA5, first strand: chain 'A' and resid 148 through 149 Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 12 removed outlier: 6.606A pdb=" N ASP B 192 " --> pdb=" O PRO B 27 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N TYR B 191 " --> pdb=" O THR B 183 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 95 through 101 removed outlier: 7.176A pdb=" N ARG B 137 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ILE B 58 " --> pdb=" O ARG B 137 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG B 139 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE B 56 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR B 141 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN B 143 " --> pdb=" O ALA B 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 87 through 89 Processing sheet with id=AA9, first strand: chain 'B' and resid 105 through 108 Processing sheet with id=AB1, first strand: chain 'B' and resid 148 through 149 Processing sheet with id=AB2, first strand: chain 'C' and resid 4 through 8 removed outlier: 3.780A pdb=" N ARG C 12 " --> pdb=" O TYR C 8 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N ALA C 988 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ARG C 15 " --> pdb=" O ALA C 988 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 55 through 56 removed outlier: 3.707A pdb=" N ILE C 55 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU C 64 " --> pdb=" O ILE C 99 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE C 99 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N PHE C 66 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ARG C 97 " --> pdb=" O PHE C 66 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP C 68 " --> pdb=" O LYS C 95 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY C 114 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL C 94 " --> pdb=" O PHE C 112 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N PHE C 112 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N VAL C 96 " --> pdb=" O ASP C 110 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASP C 110 " --> pdb=" O VAL C 96 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU C 98 " --> pdb=" O ASP C 108 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASP C 108 " --> pdb=" O LEU C 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 125 through 127 Processing sheet with id=AB5, first strand: chain 'C' and resid 407 through 409 removed outlier: 3.940A pdb=" N SER C 136 " --> pdb=" O ARG C 485 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 144 through 147 removed outlier: 3.740A pdb=" N THR C 159 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 334 through 335 removed outlier: 3.762A pdb=" N VAL C 342 " --> pdb=" O GLY C 335 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 346 through 350 removed outlier: 3.536A pdb=" N ILE C 347 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE C 349 " --> pdb=" O ILE C 361 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 536 through 537 removed outlier: 5.754A pdb=" N ARG C 560 " --> pdb=" O ARG C 549 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 536 through 537 Processing sheet with id=AC2, first strand: chain 'C' and resid 674 through 675 removed outlier: 6.524A pdb=" N VAL C 674 " --> pdb=" O LEU C 742 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 707 through 711 removed outlier: 6.769A pdb=" N ASN C 689 " --> pdb=" O VAL C 685 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N VAL C 685 " --> pdb=" O ASN C 689 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TRP C 691 " --> pdb=" O GLU C 683 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 716 through 717 removed outlier: 3.664A pdb=" N VAL C 716 " --> pdb=" O TYR C 724 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 748 through 749 Processing sheet with id=AC6, first strand: chain 'C' and resid 757 through 763 removed outlier: 8.917A pdb=" N ILE C 955 " --> pdb=" O ASN C 758 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N MET C 760 " --> pdb=" O ILE C 955 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N LEU C 957 " --> pdb=" O MET C 760 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLY C 762 " --> pdb=" O LEU C 957 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE C 776 " --> pdb=" O MET C 956 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ILE C 775 " --> pdb=" O SER C 936 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE C 938 " --> pdb=" O ILE C 775 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N MET C 777 " --> pdb=" O ILE C 938 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 788 through 800 removed outlier: 6.491A pdb=" N SER C 789 " --> pdb=" O LYS C 916 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LYS C 916 " --> pdb=" O SER C 789 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N HIS C 791 " --> pdb=" O VAL C 914 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL C 914 " --> pdb=" O HIS C 791 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLU C 793 " --> pdb=" O TYR C 912 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N TYR C 912 " --> pdb=" O GLU C 793 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N TYR C 795 " --> pdb=" O ARG C 910 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ARG C 910 " --> pdb=" O TYR C 795 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N SER C 797 " --> pdb=" O LEU C 908 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LEU C 908 " --> pdb=" O SER C 797 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ALA C 799 " --> pdb=" O ASN C 906 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP C 889 " --> pdb=" O TYR C 912 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL C 914 " --> pdb=" O ILE C 887 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ILE C 887 " --> pdb=" O VAL C 914 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N LYS C 916 " --> pdb=" O GLY C 885 " (cutoff:3.500A) removed outlier: 9.358A pdb=" N GLY C 885 " --> pdb=" O LYS C 916 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 808 through 809 Processing sheet with id=AC9, first strand: chain 'C' and resid 1049 through 1051 removed outlier: 3.505A pdb=" N SER D 342 " --> pdb=" O MET D 455 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1074 through 1075 Processing sheet with id=AD2, first strand: chain 'D' and resid 9 through 11 Processing sheet with id=AD3, first strand: chain 'D' and resid 93 through 102 removed outlier: 3.515A pdb=" N LEU D 97 " --> pdb=" O ASP D 229 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ASP D 229 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 10.645A pdb=" N ALA D 99 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 10.548A pdb=" N ILE D 227 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 149 through 150 removed outlier: 7.047A pdb=" N GLN D 167 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 241 through 243 Processing sheet with id=AD6, first strand: chain 'D' and resid 515 through 516 removed outlier: 3.673A pdb=" N ALA D 540 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU D 557 " --> pdb=" O LEU D 596 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 752 through 753 removed outlier: 3.786A pdb=" N GLY D 756 " --> pdb=" O ASN D 753 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 812 through 813 removed outlier: 6.284A pdb=" N ILE D 812 " --> pdb=" O VAL D 898 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'D' and resid 824 through 826 Processing sheet with id=AE1, first strand: chain 'D' and resid 829 through 831 removed outlier: 6.685A pdb=" N LEU D 829 " --> pdb=" O ILE D 836 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU D 834 " --> pdb=" O GLU D 831 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 852 through 854 removed outlier: 7.194A pdb=" N VAL D 852 " --> pdb=" O LEU D 861 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLU D 859 " --> pdb=" O HIS D 854 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 978 through 981 Processing sheet with id=AE4, first strand: chain 'D' and resid 1093 through 1095 removed outlier: 7.217A pdb=" N THR D1115 " --> pdb=" O ILE D1081 " (cutoff:3.500A) 842 hydrogen bonds defined for protein. 2349 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 35 hydrogen bonds 62 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 9.82 Time building geometry restraints manager: 8.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7321 1.34 - 1.46: 3139 1.46 - 1.57: 12137 1.57 - 1.69: 70 1.69 - 1.81: 145 Bond restraints: 22812 Sorted by residual: bond pdb=" CZ ARG B 30 " pdb=" NH2 ARG B 30 " ideal model delta sigma weight residual 1.330 1.298 0.032 1.30e-02 5.92e+03 6.21e+00 bond pdb=" CZ ARG C 811 " pdb=" NH2 ARG C 811 " ideal model delta sigma weight residual 1.330 1.298 0.032 1.30e-02 5.92e+03 6.10e+00 bond pdb=" CZ ARG C 800 " pdb=" NH2 ARG C 800 " ideal model delta sigma weight residual 1.330 1.298 0.032 1.30e-02 5.92e+03 6.03e+00 bond pdb=" CZ ARG C 878 " pdb=" NH2 ARG C 878 " ideal model delta sigma weight residual 1.330 1.301 0.029 1.30e-02 5.92e+03 4.97e+00 bond pdb=" CZ ARG C 811 " pdb=" NH1 ARG C 811 " ideal model delta sigma weight residual 1.323 1.292 0.031 1.40e-02 5.10e+03 4.86e+00 ... (remaining 22807 not shown) Histogram of bond angle deviations from ideal: 99.26 - 106.21: 764 106.21 - 113.16: 12434 113.16 - 120.10: 8260 120.10 - 127.05: 9325 127.05 - 134.00: 271 Bond angle restraints: 31054 Sorted by residual: angle pdb=" CA GLU C 339 " pdb=" C GLU C 339 " pdb=" O GLU C 339 " ideal model delta sigma weight residual 117.94 121.81 -3.87 5.80e-01 2.97e+00 4.44e+01 angle pdb=" C GLN D1140 " pdb=" CA GLN D1140 " pdb=" CB GLN D1140 " ideal model delta sigma weight residual 116.63 109.31 7.32 1.16e+00 7.43e-01 3.98e+01 angle pdb=" N GLU B 26 " pdb=" CA GLU B 26 " pdb=" C GLU B 26 " ideal model delta sigma weight residual 108.22 112.48 -4.26 9.00e-01 1.23e+00 2.24e+01 angle pdb=" C ALA C1041 " pdb=" CA ALA C1041 " pdb=" CB ALA C1041 " ideal model delta sigma weight residual 116.54 111.22 5.32 1.15e+00 7.56e-01 2.14e+01 angle pdb=" C VAL B 25 " pdb=" CA VAL B 25 " pdb=" CB VAL B 25 " ideal model delta sigma weight residual 110.12 116.04 -5.92 1.36e+00 5.41e-01 1.90e+01 ... (remaining 31049 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 11814 17.96 - 35.92: 1518 35.92 - 53.87: 380 53.87 - 71.83: 95 71.83 - 89.79: 27 Dihedral angle restraints: 13834 sinusoidal: 5795 harmonic: 8039 Sorted by residual: dihedral pdb=" CA ASP B 192 " pdb=" C ASP B 192 " pdb=" N LYS B 193 " pdb=" CA LYS B 193 " ideal model delta harmonic sigma weight residual 180.00 154.08 25.92 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA ILE D 110 " pdb=" C ILE D 110 " pdb=" N PRO D 111 " pdb=" CA PRO D 111 " ideal model delta harmonic sigma weight residual 180.00 156.39 23.61 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA GLU C 105 " pdb=" C GLU C 105 " pdb=" N VAL C 106 " pdb=" CA VAL C 106 " ideal model delta harmonic sigma weight residual -180.00 -158.53 -21.47 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 13831 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2866 0.053 - 0.106: 614 0.106 - 0.159: 90 0.159 - 0.212: 10 0.212 - 0.265: 3 Chirality restraints: 3583 Sorted by residual: chirality pdb=" CA LYS C 845 " pdb=" N LYS C 845 " pdb=" C LYS C 845 " pdb=" CB LYS C 845 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CB ILE B 120 " pdb=" CA ILE B 120 " pdb=" CG1 ILE B 120 " pdb=" CG2 ILE B 120 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA ASP C 812 " pdb=" N ASP C 812 " pdb=" C ASP C 812 " pdb=" CB ASP C 812 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 3580 not shown) Planarity restraints: 3918 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 32 " -0.056 2.00e-02 2.50e+03 3.93e-02 3.08e+01 pdb=" CG TYR B 32 " -0.002 2.00e-02 2.50e+03 pdb=" CD1 TYR B 32 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR B 32 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR B 32 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR B 32 " 0.035 2.00e-02 2.50e+03 pdb=" CZ TYR B 32 " 0.019 2.00e-02 2.50e+03 pdb=" OH TYR B 32 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 191 " -0.032 2.00e-02 2.50e+03 1.84e-02 6.79e+00 pdb=" CG TYR B 191 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR B 191 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR B 191 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 191 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 191 " 0.019 2.00e-02 2.50e+03 pdb=" CZ TYR B 191 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 191 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG T 10 " -0.009 2.00e-02 2.50e+03 1.28e-02 4.89e+00 pdb=" N9 DG T 10 " 0.009 2.00e-02 2.50e+03 pdb=" C8 DG T 10 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DG T 10 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DG T 10 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG T 10 " 0.010 2.00e-02 2.50e+03 pdb=" O6 DG T 10 " -0.023 2.00e-02 2.50e+03 pdb=" N1 DG T 10 " 0.029 2.00e-02 2.50e+03 pdb=" C2 DG T 10 " -0.019 2.00e-02 2.50e+03 pdb=" N2 DG T 10 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DG T 10 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DG T 10 " 0.001 2.00e-02 2.50e+03 ... (remaining 3915 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 418 2.64 - 3.21: 21363 3.21 - 3.77: 33598 3.77 - 4.34: 47339 4.34 - 4.90: 78706 Nonbonded interactions: 181424 Sorted by model distance: nonbonded pdb=" OD1 ASP D 453 " pdb="MG MG D2001 " model vdw 2.079 2.170 nonbonded pdb=" OD1 ASP D 449 " pdb="MG MG D2001 " model vdw 2.082 2.170 nonbonded pdb=" OD1 ASP D 451 " pdb="MG MG D2001 " model vdw 2.083 2.170 nonbonded pdb=" O TRP C 766 " pdb=" OG1 THR D 652 " model vdw 2.118 2.440 nonbonded pdb=" O GLN C 419 " pdb=" OG SER C 457 " model vdw 2.152 2.440 ... (remaining 181419 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 5 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 62 or (resid 63 through 64 and (name \ N or name CA or name C or name O or name CB )) or resid 65 through 68 or (resid \ 69 and (name N or name CA or name C or name O or name CB )) or resid 70 through \ 87 or (resid 88 and (name N or name CA or name C or name O or name CB )) or res \ id 89 through 101 or (resid 102 and (name N or name CA or name C or name O or na \ me CB )) or resid 103 through 131 or (resid 132 through 134 and (name N or name \ CA or name C or name O or name CB )) or resid 135 through 156 or (resid 157 and \ (name N or name CA or name C or name O or name CB )) or resid 158 through 228)) selection = (chain 'B' and (resid 5 through 7 or (resid 8 and (name N or name CA or name C o \ r name O or name CB )) or resid 9 through 28 or (resid 29 and (name N or name CA \ or name C or name O or name CB )) or resid 30 through 58 or (resid 59 and (name \ N or name CA or name C or name O or name CB )) or resid 60 through 91 or (resid \ 92 through 93 and (name N or name CA or name C or name O or name CB )) or resid \ 94 through 228)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.710 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 69.510 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.070 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 22812 Z= 0.321 Angle : 0.746 8.567 31054 Z= 0.453 Chirality : 0.045 0.265 3583 Planarity : 0.004 0.047 3918 Dihedral : 17.450 89.788 8674 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.75 % Favored : 93.14 % Rotamer: Outliers : 5.36 % Allowed : 19.46 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.14), residues: 2786 helix: -1.63 (0.15), residues: 927 sheet: -1.57 (0.26), residues: 386 loop : -2.33 (0.14), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 199 HIS 0.006 0.001 HIS D 61 PHE 0.020 0.001 PHE A 20 TYR 0.075 0.002 TYR B 32 ARG 0.010 0.001 ARG D 84 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 375 time to evaluate : 2.897 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: A 197 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.7125 (m-30) REVERT: A 215 LYS cc_start: 0.7917 (ttpp) cc_final: 0.7701 (ttpp) REVERT: B 57 GLN cc_start: 0.7913 (tt0) cc_final: 0.7634 (tt0) REVERT: B 181 GLU cc_start: 0.8097 (mp0) cc_final: 0.7512 (pm20) REVERT: B 191 TYR cc_start: 0.7664 (m-80) cc_final: 0.7413 (m-80) REVERT: B 199 TRP cc_start: 0.7713 (m-90) cc_final: 0.7312 (m-90) REVERT: C 30 ILE cc_start: 0.9012 (pt) cc_final: 0.8739 (mt) REVERT: C 264 ARG cc_start: 0.8043 (mmm-85) cc_final: 0.7758 (mmm-85) REVERT: C 286 PHE cc_start: 0.7326 (OUTLIER) cc_final: 0.7086 (m-80) REVERT: C 486 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8491 (mt) REVERT: C 1115 LYS cc_start: 0.8331 (tmtt) cc_final: 0.8122 (tptt) REVERT: D 177 LYS cc_start: 0.8044 (mmtt) cc_final: 0.7510 (mmtt) REVERT: D 205 ARG cc_start: 0.8099 (ptp90) cc_final: 0.7791 (ptp90) REVERT: D 214 GLU cc_start: 0.6936 (mm-30) cc_final: 0.6671 (mm-30) REVERT: D 267 ARG cc_start: 0.6931 (ttp-170) cc_final: 0.6585 (ttp-170) REVERT: D 289 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7301 (tp40) REVERT: D 536 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7269 (mtp180) REVERT: D 593 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.7843 (ttp-170) REVERT: D 689 ARG cc_start: 0.7839 (mmp80) cc_final: 0.7509 (mmp80) outliers start: 124 outliers final: 86 residues processed: 485 average time/residue: 0.4046 time to fit residues: 286.2857 Evaluate side-chains 418 residues out of total 2411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 326 time to evaluate : 2.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain C residue 419 GLN Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 521 GLU Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 565 THR Chi-restraints excluded: chain C residue 568 GLU Chi-restraints excluded: chain C residue 589 ASP Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 678 HIS Chi-restraints excluded: chain C residue 686 GLU Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 730 VAL Chi-restraints excluded: chain C residue 749 GLU Chi-restraints excluded: chain C residue 873 ARG Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain D residue 9 TYR Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 289 GLN Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 399 ASP Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 536 ARG Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 593 ARG Chi-restraints excluded: chain D residue 639 MET Chi-restraints excluded: chain D residue 658 VAL Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 740 ASN Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 978 VAL Chi-restraints excluded: chain D residue 992 VAL Chi-restraints excluded: chain D residue 1080 VAL Chi-restraints excluded: chain D residue 1081 ILE Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain D residue 1175 THR Chi-restraints excluded: chain D residue 1177 MET Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain F residue 19 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 236 optimal weight: 9.9990 chunk 212 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 chunk 113 optimal weight: 20.0000 chunk 219 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 133 optimal weight: 20.0000 chunk 163 optimal weight: 10.0000 chunk 254 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN A 220 HIS B 57 GLN B 154 ASN ** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 689 ASN C 823 ASN ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 GLN D 458 HIS ** D 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1140 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22812 Z= 0.277 Angle : 0.617 10.033 31054 Z= 0.321 Chirality : 0.044 0.272 3583 Planarity : 0.004 0.053 3918 Dihedral : 11.648 73.411 3645 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.92 % Favored : 94.94 % Rotamer: Outliers : 5.10 % Allowed : 23.49 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.15), residues: 2786 helix: -0.67 (0.16), residues: 953 sheet: -1.19 (0.26), residues: 380 loop : -1.90 (0.15), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 199 HIS 0.004 0.001 HIS D1097 PHE 0.017 0.001 PHE C 470 TYR 0.015 0.001 TYR D 130 ARG 0.006 0.001 ARG C 539 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 336 time to evaluate : 2.563 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 14 ILE cc_start: 0.7512 (OUTLIER) cc_final: 0.7237 (tp) REVERT: B 44 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8731 (mp) REVERT: B 140 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8556 (mt) REVERT: B 191 TYR cc_start: 0.7535 (m-80) cc_final: 0.7327 (m-80) REVERT: C 264 ARG cc_start: 0.8093 (mmm-85) cc_final: 0.7801 (mmm-85) REVERT: C 485 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8689 (ptp-110) REVERT: C 595 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7234 (ptt-90) REVERT: D 36 TYR cc_start: 0.7805 (OUTLIER) cc_final: 0.7582 (m-80) REVERT: D 77 ARG cc_start: 0.7978 (mtm-85) cc_final: 0.7581 (ptt-90) REVERT: D 205 ARG cc_start: 0.8099 (ptp90) cc_final: 0.7783 (ptp90) REVERT: D 208 LYS cc_start: 0.8957 (mmtm) cc_final: 0.8663 (mmtm) REVERT: D 214 GLU cc_start: 0.6962 (mm-30) cc_final: 0.6712 (mm-30) REVERT: D 287 MET cc_start: 0.7953 (ttp) cc_final: 0.7699 (ttp) REVERT: D 289 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7138 (tp40) REVERT: D 593 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.7899 (ttp80) REVERT: D 689 ARG cc_start: 0.7842 (mmp80) cc_final: 0.7540 (mmp80) REVERT: D 864 GLU cc_start: 0.7795 (pt0) cc_final: 0.7525 (tt0) outliers start: 118 outliers final: 77 residues processed: 435 average time/residue: 0.4151 time to fit residues: 262.9342 Evaluate side-chains 404 residues out of total 2411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 319 time to evaluate : 3.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 441 ASN Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 485 ARG Chi-restraints excluded: chain C residue 568 GLU Chi-restraints excluded: chain C residue 589 ASP Chi-restraints excluded: chain C residue 595 ARG Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 749 GLU Chi-restraints excluded: chain C residue 815 ASN Chi-restraints excluded: chain C residue 873 ARG Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 949 ASP Chi-restraints excluded: chain C residue 967 ASN Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain C residue 1095 ILE Chi-restraints excluded: chain D residue 9 TYR Chi-restraints excluded: chain D residue 36 TYR Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 289 GLN Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 593 ARG Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 740 ASN Chi-restraints excluded: chain D residue 744 LEU Chi-restraints excluded: chain D residue 766 SER Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 861 LEU Chi-restraints excluded: chain D residue 960 PHE Chi-restraints excluded: chain D residue 992 VAL Chi-restraints excluded: chain D residue 1002 TYR Chi-restraints excluded: chain D residue 1028 SER Chi-restraints excluded: chain D residue 1081 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1108 LEU Chi-restraints excluded: chain D residue 1175 THR Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain F residue 16 LYS Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 54 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 141 optimal weight: 7.9990 chunk 78 optimal weight: 0.1980 chunk 211 optimal weight: 4.9990 chunk 173 optimal weight: 6.9990 chunk 70 optimal weight: 20.0000 chunk 254 optimal weight: 9.9990 chunk 275 optimal weight: 8.9990 chunk 226 optimal weight: 4.9990 chunk 252 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 chunk 204 optimal weight: 9.9990 overall best weight: 5.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN B 57 GLN ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22812 Z= 0.251 Angle : 0.584 10.871 31054 Z= 0.302 Chirality : 0.043 0.283 3583 Planarity : 0.004 0.053 3918 Dihedral : 11.114 73.611 3569 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.46 % Favored : 94.44 % Rotamer: Outliers : 6.31 % Allowed : 23.75 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.15), residues: 2786 helix: -0.12 (0.17), residues: 943 sheet: -0.96 (0.26), residues: 391 loop : -1.61 (0.15), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 199 HIS 0.005 0.001 HIS D1097 PHE 0.016 0.001 PHE C 470 TYR 0.014 0.001 TYR D 130 ARG 0.007 0.000 ARG D 757 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 344 time to evaluate : 2.551 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: A 203 SER cc_start: 0.9418 (OUTLIER) cc_final: 0.8513 (p) REVERT: B 14 ILE cc_start: 0.7502 (OUTLIER) cc_final: 0.7256 (tp) REVERT: B 26 GLU cc_start: 0.7920 (pm20) cc_final: 0.7688 (pm20) REVERT: B 57 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7682 (tm-30) REVERT: B 140 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8563 (mt) REVERT: B 181 GLU cc_start: 0.7878 (mp0) cc_final: 0.7292 (pm20) REVERT: B 199 TRP cc_start: 0.7662 (m-90) cc_final: 0.7322 (m-90) REVERT: C 30 ILE cc_start: 0.8842 (pt) cc_final: 0.8621 (mt) REVERT: C 209 ASP cc_start: 0.7522 (OUTLIER) cc_final: 0.7259 (p0) REVERT: C 264 ARG cc_start: 0.8091 (mmm-85) cc_final: 0.7800 (mmm-85) REVERT: C 286 PHE cc_start: 0.7258 (OUTLIER) cc_final: 0.7012 (m-80) REVERT: C 485 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8711 (ptp-110) REVERT: C 595 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7198 (ptt-90) REVERT: D 77 ARG cc_start: 0.8070 (mtm-85) cc_final: 0.7477 (ptt-90) REVERT: D 205 ARG cc_start: 0.8092 (ptp90) cc_final: 0.7753 (ptp90) REVERT: D 208 LYS cc_start: 0.8998 (mmtm) cc_final: 0.8673 (mmtm) REVERT: D 214 GLU cc_start: 0.7004 (mm-30) cc_final: 0.6723 (mm-30) REVERT: D 289 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7123 (tp40) REVERT: D 593 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.7830 (ttp80) REVERT: D 689 ARG cc_start: 0.7845 (mmp80) cc_final: 0.7588 (mmp80) outliers start: 146 outliers final: 92 residues processed: 463 average time/residue: 0.4092 time to fit residues: 276.7541 Evaluate side-chains 429 residues out of total 2411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 327 time to evaluate : 2.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 57 GLN Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain C residue 49 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 441 ASN Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 485 ARG Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 565 THR Chi-restraints excluded: chain C residue 568 GLU Chi-restraints excluded: chain C residue 589 ASP Chi-restraints excluded: chain C residue 595 ARG Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain C residue 616 LYS Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 678 HIS Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 749 GLU Chi-restraints excluded: chain C residue 801 ASP Chi-restraints excluded: chain C residue 815 ASN Chi-restraints excluded: chain C residue 873 ARG Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 949 ASP Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain C residue 1095 ILE Chi-restraints excluded: chain D residue 9 TYR Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 283 ASN Chi-restraints excluded: chain D residue 289 GLN Chi-restraints excluded: chain D residue 326 ARG Chi-restraints excluded: chain D residue 359 LYS Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 593 ARG Chi-restraints excluded: chain D residue 658 VAL Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain D residue 740 ASN Chi-restraints excluded: chain D residue 744 LEU Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 766 SER Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 898 VAL Chi-restraints excluded: chain D residue 960 PHE Chi-restraints excluded: chain D residue 992 VAL Chi-restraints excluded: chain D residue 1002 TYR Chi-restraints excluded: chain D residue 1028 SER Chi-restraints excluded: chain D residue 1081 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1108 LEU Chi-restraints excluded: chain D residue 1123 ILE Chi-restraints excluded: chain D residue 1175 THR Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain F residue 16 LYS Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 54 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 251 optimal weight: 6.9990 chunk 191 optimal weight: 7.9990 chunk 132 optimal weight: 20.0000 chunk 28 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 chunk 255 optimal weight: 10.0000 chunk 270 optimal weight: 8.9990 chunk 133 optimal weight: 9.9990 chunk 242 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 865 ASN ** D 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 22812 Z= 0.315 Angle : 0.606 10.466 31054 Z= 0.314 Chirality : 0.044 0.215 3583 Planarity : 0.004 0.051 3918 Dihedral : 11.070 73.739 3559 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.06 % Favored : 94.83 % Rotamer: Outliers : 7.05 % Allowed : 24.18 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.15), residues: 2786 helix: 0.02 (0.17), residues: 944 sheet: -0.90 (0.26), residues: 391 loop : -1.53 (0.16), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 199 HIS 0.005 0.001 HIS D1097 PHE 0.018 0.001 PHE C 470 TYR 0.014 0.001 TYR F 46 ARG 0.007 0.000 ARG D 735 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 339 time to evaluate : 2.666 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: A 203 SER cc_start: 0.9392 (OUTLIER) cc_final: 0.8499 (p) REVERT: B 8 LYS cc_start: 0.7648 (pptt) cc_final: 0.7115 (pptt) REVERT: B 14 ILE cc_start: 0.7499 (OUTLIER) cc_final: 0.7252 (tp) REVERT: B 26 GLU cc_start: 0.8379 (pm20) cc_final: 0.7758 (pm20) REVERT: B 44 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8718 (mp) REVERT: B 57 GLN cc_start: 0.8103 (tm-30) cc_final: 0.7791 (tm-30) REVERT: B 137 ARG cc_start: 0.7489 (ttp80) cc_final: 0.7274 (tmt170) REVERT: B 140 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8632 (mt) REVERT: B 181 GLU cc_start: 0.7849 (mp0) cc_final: 0.7251 (pm20) REVERT: B 199 TRP cc_start: 0.7662 (m-90) cc_final: 0.7419 (m-90) REVERT: C 30 ILE cc_start: 0.8909 (pt) cc_final: 0.8565 (mt) REVERT: C 209 ASP cc_start: 0.7515 (OUTLIER) cc_final: 0.7290 (p0) REVERT: C 264 ARG cc_start: 0.8099 (mmm-85) cc_final: 0.7846 (mmm-85) REVERT: C 339 GLU cc_start: 0.0984 (OUTLIER) cc_final: 0.0175 (mt-10) REVERT: C 485 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8689 (ptp-110) REVERT: C 595 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7219 (ptt-90) REVERT: D 180 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.8040 (pm20) REVERT: D 205 ARG cc_start: 0.8098 (ptp90) cc_final: 0.7738 (ptp90) REVERT: D 208 LYS cc_start: 0.9019 (mmtm) cc_final: 0.8734 (mmtm) REVERT: D 214 GLU cc_start: 0.7017 (mm-30) cc_final: 0.6753 (mm-30) REVERT: D 289 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7218 (tp40) REVERT: D 593 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.7893 (ttp80) REVERT: D 689 ARG cc_start: 0.7891 (mmp80) cc_final: 0.7643 (mmp80) REVERT: D 883 GLU cc_start: 0.6514 (pm20) cc_final: 0.6285 (pm20) outliers start: 163 outliers final: 122 residues processed: 476 average time/residue: 0.4065 time to fit residues: 283.2281 Evaluate side-chains 457 residues out of total 2411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 324 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 49 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain C residue 441 ASN Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 485 ARG Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 565 THR Chi-restraints excluded: chain C residue 568 GLU Chi-restraints excluded: chain C residue 589 ASP Chi-restraints excluded: chain C residue 595 ARG Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain C residue 616 LYS Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 678 HIS Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 749 GLU Chi-restraints excluded: chain C residue 801 ASP Chi-restraints excluded: chain C residue 810 THR Chi-restraints excluded: chain C residue 815 ASN Chi-restraints excluded: chain C residue 873 ARG Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 949 ASP Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1031 SER Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain C residue 1095 ILE Chi-restraints excluded: chain C residue 1108 LYS Chi-restraints excluded: chain D residue 9 TYR Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 283 ASN Chi-restraints excluded: chain D residue 289 GLN Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 359 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 593 ARG Chi-restraints excluded: chain D residue 658 VAL Chi-restraints excluded: chain D residue 661 SER Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain D residue 719 SER Chi-restraints excluded: chain D residue 740 ASN Chi-restraints excluded: chain D residue 744 LEU Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 766 SER Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 827 LYS Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 866 GLU Chi-restraints excluded: chain D residue 898 VAL Chi-restraints excluded: chain D residue 950 THR Chi-restraints excluded: chain D residue 960 PHE Chi-restraints excluded: chain D residue 992 VAL Chi-restraints excluded: chain D residue 1002 TYR Chi-restraints excluded: chain D residue 1003 THR Chi-restraints excluded: chain D residue 1028 SER Chi-restraints excluded: chain D residue 1080 VAL Chi-restraints excluded: chain D residue 1081 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1095 ASP Chi-restraints excluded: chain D residue 1108 LEU Chi-restraints excluded: chain D residue 1135 SER Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain D residue 1175 THR Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain F residue 16 LYS Chi-restraints excluded: chain F residue 54 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 225 optimal weight: 10.0000 chunk 153 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 201 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 230 optimal weight: 7.9990 chunk 187 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 138 optimal weight: 0.8980 chunk 242 optimal weight: 10.0000 chunk 68 optimal weight: 20.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22812 Z= 0.177 Angle : 0.556 10.823 31054 Z= 0.287 Chirality : 0.042 0.176 3583 Planarity : 0.004 0.050 3918 Dihedral : 10.860 73.522 3557 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.45 % Favored : 95.44 % Rotamer: Outliers : 4.93 % Allowed : 27.03 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.16), residues: 2786 helix: 0.32 (0.17), residues: 938 sheet: -0.68 (0.27), residues: 385 loop : -1.33 (0.16), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 199 HIS 0.004 0.000 HIS D1097 PHE 0.017 0.001 PHE C 58 TYR 0.013 0.001 TYR C 181 ARG 0.007 0.000 ARG A 139 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 357 time to evaluate : 2.591 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: A 203 SER cc_start: 0.9329 (OUTLIER) cc_final: 0.8573 (p) REVERT: B 8 LYS cc_start: 0.7479 (pptt) cc_final: 0.6947 (pptt) REVERT: B 14 ILE cc_start: 0.7484 (OUTLIER) cc_final: 0.7228 (tp) REVERT: B 26 GLU cc_start: 0.8260 (pm20) cc_final: 0.7690 (pm20) REVERT: B 30 ARG cc_start: 0.7800 (ttp80) cc_final: 0.7599 (mtp180) REVERT: B 44 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8681 (mp) REVERT: B 45 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8785 (mp) REVERT: B 57 GLN cc_start: 0.7942 (tm-30) cc_final: 0.7638 (tm-30) REVERT: B 90 TYR cc_start: 0.7344 (m-80) cc_final: 0.6701 (m-80) REVERT: B 119 GLU cc_start: 0.7302 (mp0) cc_final: 0.7042 (pm20) REVERT: B 130 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.7857 (mt) REVERT: B 137 ARG cc_start: 0.7568 (ttp80) cc_final: 0.7299 (tmt170) REVERT: B 140 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8563 (mt) REVERT: B 144 ARG cc_start: 0.8242 (ttp80) cc_final: 0.7925 (ttp-170) REVERT: B 181 GLU cc_start: 0.7796 (mp0) cc_final: 0.7190 (pm20) REVERT: B 199 TRP cc_start: 0.7618 (m-90) cc_final: 0.7345 (m-90) REVERT: C 30 ILE cc_start: 0.8877 (pt) cc_final: 0.8554 (mt) REVERT: C 209 ASP cc_start: 0.7443 (OUTLIER) cc_final: 0.7231 (p0) REVERT: C 264 ARG cc_start: 0.8131 (mmm-85) cc_final: 0.7904 (mmm-85) REVERT: C 286 PHE cc_start: 0.7152 (OUTLIER) cc_final: 0.6877 (m-80) REVERT: C 485 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8666 (ptp-110) REVERT: C 595 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7194 (ptt-90) REVERT: D 205 ARG cc_start: 0.8115 (ptp90) cc_final: 0.7759 (ptp90) REVERT: D 214 GLU cc_start: 0.6977 (mm-30) cc_final: 0.6721 (mm-30) REVERT: D 289 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.6770 (tt0) REVERT: D 331 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8638 (mt) REVERT: D 593 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.7843 (ttp80) REVERT: D 670 GLN cc_start: 0.7667 (mm-40) cc_final: 0.7310 (tp40) REVERT: F 19 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8939 (tt) outliers start: 114 outliers final: 76 residues processed: 452 average time/residue: 0.4263 time to fit residues: 283.4332 Evaluate side-chains 420 residues out of total 2411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 330 time to evaluate : 2.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain C residue 49 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 485 ARG Chi-restraints excluded: chain C residue 565 THR Chi-restraints excluded: chain C residue 568 GLU Chi-restraints excluded: chain C residue 589 ASP Chi-restraints excluded: chain C residue 595 ARG Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 749 GLU Chi-restraints excluded: chain C residue 801 ASP Chi-restraints excluded: chain C residue 815 ASN Chi-restraints excluded: chain C residue 873 ARG Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 949 ASP Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain C residue 1095 ILE Chi-restraints excluded: chain C residue 1098 VAL Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 289 GLN Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 593 ARG Chi-restraints excluded: chain D residue 661 SER Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 740 ASN Chi-restraints excluded: chain D residue 744 LEU Chi-restraints excluded: chain D residue 950 THR Chi-restraints excluded: chain D residue 960 PHE Chi-restraints excluded: chain D residue 992 VAL Chi-restraints excluded: chain D residue 1002 TYR Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1081 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1108 LEU Chi-restraints excluded: chain D residue 1123 ILE Chi-restraints excluded: chain D residue 1135 SER Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain F residue 16 LYS Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 54 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 91 optimal weight: 20.0000 chunk 243 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 158 optimal weight: 0.0060 chunk 66 optimal weight: 9.9990 chunk 270 optimal weight: 8.9990 chunk 224 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 overall best weight: 5.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN C 393 HIS ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22812 Z= 0.266 Angle : 0.591 10.410 31054 Z= 0.303 Chirality : 0.043 0.291 3583 Planarity : 0.004 0.068 3918 Dihedral : 10.795 73.637 3542 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.70 % Favored : 95.19 % Rotamer: Outliers : 6.66 % Allowed : 25.91 % Favored : 67.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.16), residues: 2786 helix: 0.36 (0.17), residues: 935 sheet: -0.58 (0.27), residues: 381 loop : -1.31 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 199 HIS 0.004 0.001 HIS D1097 PHE 0.017 0.001 PHE A 224 TYR 0.024 0.001 TYR D 162 ARG 0.016 0.001 ARG C 218 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 339 time to evaluate : 2.493 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 8 LYS cc_start: 0.7521 (pptt) cc_final: 0.7103 (pptt) REVERT: B 14 ILE cc_start: 0.7482 (OUTLIER) cc_final: 0.7245 (tp) REVERT: B 26 GLU cc_start: 0.8286 (pm20) cc_final: 0.7744 (pm20) REVERT: B 44 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8691 (mp) REVERT: B 45 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8691 (mp) REVERT: B 57 GLN cc_start: 0.7991 (tm-30) cc_final: 0.7609 (tm-30) REVERT: B 90 TYR cc_start: 0.7483 (m-80) cc_final: 0.6945 (m-80) REVERT: B 119 GLU cc_start: 0.7309 (mp0) cc_final: 0.7074 (mp0) REVERT: B 137 ARG cc_start: 0.7565 (ttp80) cc_final: 0.7316 (tmt170) REVERT: B 140 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8619 (mt) REVERT: B 181 GLU cc_start: 0.7787 (mp0) cc_final: 0.7180 (pm20) REVERT: B 199 TRP cc_start: 0.7629 (m-90) cc_final: 0.7423 (m-90) REVERT: C 30 ILE cc_start: 0.8928 (pt) cc_final: 0.8606 (mt) REVERT: C 48 MET cc_start: 0.7271 (tmm) cc_final: 0.7069 (tmm) REVERT: C 209 ASP cc_start: 0.7487 (OUTLIER) cc_final: 0.7256 (p0) REVERT: C 218 ARG cc_start: 0.6235 (OUTLIER) cc_final: 0.5341 (ptp90) REVERT: C 264 ARG cc_start: 0.8141 (mmm-85) cc_final: 0.7914 (mmm-85) REVERT: C 286 PHE cc_start: 0.7218 (OUTLIER) cc_final: 0.6979 (m-80) REVERT: C 339 GLU cc_start: 0.0956 (OUTLIER) cc_final: 0.0237 (mt-10) REVERT: C 485 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8695 (ptp-110) REVERT: C 489 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8192 (mt) REVERT: C 595 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7226 (ptt-90) REVERT: C 944 MET cc_start: 0.8670 (mmm) cc_final: 0.8461 (mmm) REVERT: C 978 MET cc_start: 0.9053 (tpt) cc_final: 0.8739 (tpt) REVERT: D 205 ARG cc_start: 0.8166 (ptp90) cc_final: 0.7832 (ptp90) REVERT: D 208 LYS cc_start: 0.8886 (mmtm) cc_final: 0.8567 (mmtm) REVERT: D 214 GLU cc_start: 0.6991 (mm-30) cc_final: 0.6742 (mm-30) REVERT: D 289 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7235 (tp40) REVERT: D 593 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.7743 (ttp80) REVERT: D 670 GLN cc_start: 0.7654 (mm-40) cc_final: 0.7388 (tp40) REVERT: D 963 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7519 (mtt90) REVERT: F 19 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9006 (tt) outliers start: 154 outliers final: 116 residues processed: 466 average time/residue: 0.4137 time to fit residues: 280.6872 Evaluate side-chains 461 residues out of total 2411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 330 time to evaluate : 2.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain C residue 49 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 485 ARG Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 565 THR Chi-restraints excluded: chain C residue 568 GLU Chi-restraints excluded: chain C residue 589 ASP Chi-restraints excluded: chain C residue 595 ARG Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 678 HIS Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 749 GLU Chi-restraints excluded: chain C residue 801 ASP Chi-restraints excluded: chain C residue 810 THR Chi-restraints excluded: chain C residue 815 ASN Chi-restraints excluded: chain C residue 873 ARG Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 936 SER Chi-restraints excluded: chain C residue 949 ASP Chi-restraints excluded: chain C residue 1031 SER Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain C residue 1095 ILE Chi-restraints excluded: chain C residue 1098 VAL Chi-restraints excluded: chain C residue 1108 LYS Chi-restraints excluded: chain D residue 9 TYR Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 289 GLN Chi-restraints excluded: chain D residue 359 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 473 MET Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 593 ARG Chi-restraints excluded: chain D residue 661 SER Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain D residue 719 SER Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 740 ASN Chi-restraints excluded: chain D residue 744 LEU Chi-restraints excluded: chain D residue 766 SER Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 827 LYS Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 866 GLU Chi-restraints excluded: chain D residue 898 VAL Chi-restraints excluded: chain D residue 950 THR Chi-restraints excluded: chain D residue 963 ARG Chi-restraints excluded: chain D residue 992 VAL Chi-restraints excluded: chain D residue 1002 TYR Chi-restraints excluded: chain D residue 1003 THR Chi-restraints excluded: chain D residue 1028 SER Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1064 ASP Chi-restraints excluded: chain D residue 1081 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1108 LEU Chi-restraints excluded: chain D residue 1135 SER Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain F residue 16 LYS Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 54 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 261 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 154 optimal weight: 7.9990 chunk 197 optimal weight: 8.9990 chunk 153 optimal weight: 3.9990 chunk 228 optimal weight: 10.0000 chunk 151 optimal weight: 10.0000 chunk 269 optimal weight: 7.9990 chunk 168 optimal weight: 20.0000 chunk 164 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22812 Z= 0.210 Angle : 0.578 11.424 31054 Z= 0.295 Chirality : 0.042 0.204 3583 Planarity : 0.004 0.047 3918 Dihedral : 10.719 73.583 3541 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.38 % Favored : 95.51 % Rotamer: Outliers : 6.14 % Allowed : 26.60 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.16), residues: 2786 helix: 0.45 (0.17), residues: 937 sheet: -0.52 (0.27), residues: 389 loop : -1.21 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 199 HIS 0.004 0.001 HIS D1097 PHE 0.013 0.001 PHE A 224 TYR 0.018 0.001 TYR D 162 ARG 0.011 0.001 ARG C 218 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 343 time to evaluate : 2.509 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 14 ILE cc_start: 0.7455 (OUTLIER) cc_final: 0.7218 (tp) REVERT: B 30 ARG cc_start: 0.7862 (ttp80) cc_final: 0.7610 (mtp-110) REVERT: B 44 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8694 (mp) REVERT: B 45 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8788 (mp) REVERT: B 73 GLU cc_start: 0.8205 (mp0) cc_final: 0.7952 (mt-10) REVERT: B 130 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.7855 (mt) REVERT: B 139 ARG cc_start: 0.6752 (ptm-80) cc_final: 0.6322 (ptm-80) REVERT: B 140 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8580 (mt) REVERT: B 144 ARG cc_start: 0.8238 (ttp80) cc_final: 0.7922 (ttp-170) REVERT: B 199 TRP cc_start: 0.7594 (m-90) cc_final: 0.7307 (m-90) REVERT: C 30 ILE cc_start: 0.8909 (pt) cc_final: 0.8587 (mt) REVERT: C 209 ASP cc_start: 0.7446 (OUTLIER) cc_final: 0.7214 (p0) REVERT: C 218 ARG cc_start: 0.6085 (OUTLIER) cc_final: 0.5164 (ptp90) REVERT: C 264 ARG cc_start: 0.8133 (mmm-85) cc_final: 0.7920 (mmm-85) REVERT: C 286 PHE cc_start: 0.7112 (OUTLIER) cc_final: 0.6882 (m-80) REVERT: C 485 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8681 (ptp-110) REVERT: C 489 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8161 (mt) REVERT: C 595 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7193 (ptt-90) REVERT: C 944 MET cc_start: 0.8678 (mmm) cc_final: 0.8461 (mmm) REVERT: D 205 ARG cc_start: 0.8172 (ptp90) cc_final: 0.7795 (ptp90) REVERT: D 208 LYS cc_start: 0.8909 (mmtm) cc_final: 0.8596 (mmtm) REVERT: D 214 GLU cc_start: 0.7019 (mm-30) cc_final: 0.6809 (mm-30) REVERT: D 289 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7071 (tp40) REVERT: D 593 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.7678 (ttp80) REVERT: D 670 GLN cc_start: 0.7624 (mm-40) cc_final: 0.7385 (tp40) REVERT: D 963 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7520 (mtt90) REVERT: F 19 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9020 (tt) outliers start: 142 outliers final: 106 residues processed: 460 average time/residue: 0.4000 time to fit residues: 269.3492 Evaluate side-chains 450 residues out of total 2411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 329 time to evaluate : 2.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain C residue 49 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 485 ARG Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 565 THR Chi-restraints excluded: chain C residue 568 GLU Chi-restraints excluded: chain C residue 589 ASP Chi-restraints excluded: chain C residue 595 ARG Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain C residue 616 LYS Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 749 GLU Chi-restraints excluded: chain C residue 801 ASP Chi-restraints excluded: chain C residue 810 THR Chi-restraints excluded: chain C residue 815 ASN Chi-restraints excluded: chain C residue 873 ARG Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 949 ASP Chi-restraints excluded: chain C residue 1031 SER Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain C residue 1095 ILE Chi-restraints excluded: chain C residue 1098 VAL Chi-restraints excluded: chain D residue 9 TYR Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 283 ASN Chi-restraints excluded: chain D residue 289 GLN Chi-restraints excluded: chain D residue 359 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 593 ARG Chi-restraints excluded: chain D residue 661 SER Chi-restraints excluded: chain D residue 719 SER Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 740 ASN Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 766 SER Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 861 LEU Chi-restraints excluded: chain D residue 950 THR Chi-restraints excluded: chain D residue 960 PHE Chi-restraints excluded: chain D residue 963 ARG Chi-restraints excluded: chain D residue 992 VAL Chi-restraints excluded: chain D residue 1002 TYR Chi-restraints excluded: chain D residue 1003 THR Chi-restraints excluded: chain D residue 1028 SER Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1064 ASP Chi-restraints excluded: chain D residue 1080 VAL Chi-restraints excluded: chain D residue 1081 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1108 LEU Chi-restraints excluded: chain D residue 1123 ILE Chi-restraints excluded: chain D residue 1135 SER Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain F residue 16 LYS Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 54 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 166 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 161 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 171 optimal weight: 40.0000 chunk 183 optimal weight: 5.9990 chunk 133 optimal weight: 20.0000 chunk 25 optimal weight: 8.9990 chunk 212 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C 642 ASN ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN D 743 GLN ** D 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22812 Z= 0.288 Angle : 0.615 12.789 31054 Z= 0.314 Chirality : 0.043 0.243 3583 Planarity : 0.004 0.071 3918 Dihedral : 10.755 73.684 3539 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.88 % Favored : 95.01 % Rotamer: Outliers : 6.36 % Allowed : 26.73 % Favored : 66.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.16), residues: 2786 helix: 0.39 (0.17), residues: 936 sheet: -0.51 (0.28), residues: 388 loop : -1.26 (0.16), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 199 HIS 0.004 0.001 HIS D1097 PHE 0.016 0.001 PHE C 470 TYR 0.017 0.001 TYR D 162 ARG 0.011 0.001 ARG D 735 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 334 time to evaluate : 2.587 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 14 ILE cc_start: 0.7474 (OUTLIER) cc_final: 0.7230 (tp) REVERT: B 44 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8690 (mp) REVERT: B 45 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8744 (mp) REVERT: B 90 TYR cc_start: 0.7400 (m-80) cc_final: 0.6790 (m-80) REVERT: B 119 GLU cc_start: 0.7138 (mp0) cc_final: 0.6934 (pm20) REVERT: B 140 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8607 (mt) REVERT: B 156 ARG cc_start: 0.7025 (mtm-85) cc_final: 0.6532 (mtm-85) REVERT: B 181 GLU cc_start: 0.7764 (mp0) cc_final: 0.7401 (pm20) REVERT: B 199 TRP cc_start: 0.7648 (m-90) cc_final: 0.7289 (m-90) REVERT: C 209 ASP cc_start: 0.7483 (OUTLIER) cc_final: 0.7248 (p0) REVERT: C 218 ARG cc_start: 0.5971 (OUTLIER) cc_final: 0.5293 (ptp-170) REVERT: C 264 ARG cc_start: 0.8137 (mmm-85) cc_final: 0.7919 (mmm-85) REVERT: C 339 GLU cc_start: 0.1011 (OUTLIER) cc_final: 0.0326 (mt-10) REVERT: C 485 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8659 (ptp-110) REVERT: C 489 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8203 (mt) REVERT: C 595 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.7204 (ptt-90) REVERT: C 944 MET cc_start: 0.8694 (mmm) cc_final: 0.8470 (mmm) REVERT: C 1140 MET cc_start: 0.8618 (mmp) cc_final: 0.8115 (mmp) REVERT: D 205 ARG cc_start: 0.8180 (ptp90) cc_final: 0.7821 (ptp90) REVERT: D 208 LYS cc_start: 0.8955 (mmtm) cc_final: 0.8624 (mmtm) REVERT: D 214 GLU cc_start: 0.7004 (mm-30) cc_final: 0.6801 (mm-30) REVERT: D 289 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7026 (tp40) REVERT: D 593 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.7584 (ttp80) REVERT: D 933 GLN cc_start: 0.7086 (mp-120) cc_final: 0.6866 (mp-120) REVERT: D 963 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7484 (mtt90) REVERT: F 19 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9060 (tt) outliers start: 147 outliers final: 116 residues processed: 453 average time/residue: 0.4146 time to fit residues: 274.8005 Evaluate side-chains 455 residues out of total 2411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 325 time to evaluate : 2.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain C residue 49 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 485 ARG Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 565 THR Chi-restraints excluded: chain C residue 568 GLU Chi-restraints excluded: chain C residue 589 ASP Chi-restraints excluded: chain C residue 595 ARG Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain C residue 616 LYS Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 749 GLU Chi-restraints excluded: chain C residue 801 ASP Chi-restraints excluded: chain C residue 810 THR Chi-restraints excluded: chain C residue 815 ASN Chi-restraints excluded: chain C residue 873 ARG Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 949 ASP Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1031 SER Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain C residue 1095 ILE Chi-restraints excluded: chain C residue 1098 VAL Chi-restraints excluded: chain C residue 1108 LYS Chi-restraints excluded: chain D residue 9 TYR Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 283 ASN Chi-restraints excluded: chain D residue 289 GLN Chi-restraints excluded: chain D residue 359 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 473 MET Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 593 ARG Chi-restraints excluded: chain D residue 661 SER Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain D residue 719 SER Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 740 ASN Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 766 SER Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 950 THR Chi-restraints excluded: chain D residue 963 ARG Chi-restraints excluded: chain D residue 992 VAL Chi-restraints excluded: chain D residue 1002 TYR Chi-restraints excluded: chain D residue 1003 THR Chi-restraints excluded: chain D residue 1028 SER Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1064 ASP Chi-restraints excluded: chain D residue 1080 VAL Chi-restraints excluded: chain D residue 1081 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1123 ILE Chi-restraints excluded: chain D residue 1135 SER Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 16 LYS Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 54 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 245 optimal weight: 10.0000 chunk 258 optimal weight: 8.9990 chunk 235 optimal weight: 6.9990 chunk 251 optimal weight: 20.0000 chunk 151 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 227 optimal weight: 4.9990 chunk 237 optimal weight: 9.9990 chunk 250 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 22812 Z= 0.312 Angle : 0.636 11.546 31054 Z= 0.325 Chirality : 0.044 0.196 3583 Planarity : 0.004 0.050 3918 Dihedral : 10.810 73.742 3536 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.99 % Favored : 94.90 % Rotamer: Outliers : 6.53 % Allowed : 26.95 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.16), residues: 2786 helix: 0.31 (0.17), residues: 942 sheet: -0.51 (0.28), residues: 388 loop : -1.27 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 199 HIS 0.006 0.001 HIS F 44 PHE 0.016 0.001 PHE C 470 TYR 0.017 0.001 TYR D 162 ARG 0.011 0.001 ARG D 735 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 330 time to evaluate : 2.374 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: A 203 SER cc_start: 0.9429 (OUTLIER) cc_final: 0.8712 (p) REVERT: B 14 ILE cc_start: 0.7479 (OUTLIER) cc_final: 0.7227 (tp) REVERT: B 44 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8693 (mp) REVERT: B 45 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8795 (mp) REVERT: B 57 GLN cc_start: 0.8000 (pt0) cc_final: 0.7700 (pt0) REVERT: B 90 TYR cc_start: 0.7455 (m-80) cc_final: 0.6691 (m-80) REVERT: B 140 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8629 (mt) REVERT: B 181 GLU cc_start: 0.7839 (mp0) cc_final: 0.7596 (pm20) REVERT: B 199 TRP cc_start: 0.7641 (m-90) cc_final: 0.7269 (m-90) REVERT: C 209 ASP cc_start: 0.7481 (OUTLIER) cc_final: 0.7246 (p0) REVERT: C 218 ARG cc_start: 0.5972 (OUTLIER) cc_final: 0.4897 (ptp-170) REVERT: C 264 ARG cc_start: 0.8148 (mmm-85) cc_final: 0.7931 (mmm-85) REVERT: C 339 GLU cc_start: 0.1022 (OUTLIER) cc_final: 0.0397 (mt-10) REVERT: C 489 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8186 (mt) REVERT: C 595 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7217 (ptt-90) REVERT: C 1140 MET cc_start: 0.8605 (mmp) cc_final: 0.8083 (mmp) REVERT: D 205 ARG cc_start: 0.8181 (ptp90) cc_final: 0.7796 (ptp90) REVERT: D 208 LYS cc_start: 0.8975 (mmtm) cc_final: 0.8647 (mmtm) REVERT: D 214 GLU cc_start: 0.6984 (mm-30) cc_final: 0.6771 (mm-30) REVERT: D 289 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7062 (tp40) REVERT: D 593 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.7780 (ttp80) REVERT: D 963 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7531 (mtt90) REVERT: F 19 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9049 (tt) outliers start: 151 outliers final: 127 residues processed: 454 average time/residue: 0.4025 time to fit residues: 267.8217 Evaluate side-chains 464 residues out of total 2411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 323 time to evaluate : 2.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 49 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 485 ARG Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 565 THR Chi-restraints excluded: chain C residue 568 GLU Chi-restraints excluded: chain C residue 589 ASP Chi-restraints excluded: chain C residue 595 ARG Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain C residue 616 LYS Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 678 HIS Chi-restraints excluded: chain C residue 686 GLU Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 749 GLU Chi-restraints excluded: chain C residue 815 ASN Chi-restraints excluded: chain C residue 873 ARG Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 949 ASP Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1031 SER Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain C residue 1095 ILE Chi-restraints excluded: chain C residue 1098 VAL Chi-restraints excluded: chain C residue 1108 LYS Chi-restraints excluded: chain D residue 9 TYR Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 283 ASN Chi-restraints excluded: chain D residue 289 GLN Chi-restraints excluded: chain D residue 359 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 473 MET Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 593 ARG Chi-restraints excluded: chain D residue 658 VAL Chi-restraints excluded: chain D residue 661 SER Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain D residue 719 SER Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 740 ASN Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 766 SER Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 861 LEU Chi-restraints excluded: chain D residue 950 THR Chi-restraints excluded: chain D residue 960 PHE Chi-restraints excluded: chain D residue 963 ARG Chi-restraints excluded: chain D residue 992 VAL Chi-restraints excluded: chain D residue 1002 TYR Chi-restraints excluded: chain D residue 1003 THR Chi-restraints excluded: chain D residue 1028 SER Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1064 ASP Chi-restraints excluded: chain D residue 1080 VAL Chi-restraints excluded: chain D residue 1081 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1108 LEU Chi-restraints excluded: chain D residue 1123 ILE Chi-restraints excluded: chain D residue 1135 SER Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 16 LYS Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 54 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 165 optimal weight: 8.9990 chunk 265 optimal weight: 9.9990 chunk 162 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 chunk 184 optimal weight: 6.9990 chunk 278 optimal weight: 20.0000 chunk 256 optimal weight: 20.0000 chunk 222 optimal weight: 8.9990 chunk 23 optimal weight: 20.0000 chunk 171 optimal weight: 4.9990 chunk 136 optimal weight: 0.0370 overall best weight: 5.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22812 Z= 0.265 Angle : 0.628 12.839 31054 Z= 0.320 Chirality : 0.043 0.160 3583 Planarity : 0.004 0.050 3918 Dihedral : 10.788 73.700 3536 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.74 % Favored : 95.15 % Rotamer: Outliers : 5.93 % Allowed : 27.85 % Favored : 66.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.16), residues: 2786 helix: 0.36 (0.17), residues: 937 sheet: -0.49 (0.28), residues: 391 loop : -1.25 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 199 HIS 0.004 0.001 HIS D1097 PHE 0.015 0.001 PHE C 470 TYR 0.016 0.001 TYR D 162 ARG 0.010 0.001 ARG D 700 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 330 time to evaluate : 2.393 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: A 203 SER cc_start: 0.9406 (OUTLIER) cc_final: 0.8701 (p) REVERT: B 14 ILE cc_start: 0.7487 (OUTLIER) cc_final: 0.7234 (tp) REVERT: B 44 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8702 (mp) REVERT: B 45 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8835 (mp) REVERT: B 181 GLU cc_start: 0.7841 (mp0) cc_final: 0.7251 (pm20) REVERT: B 199 TRP cc_start: 0.7629 (m-90) cc_final: 0.7278 (m-90) REVERT: C 209 ASP cc_start: 0.7463 (OUTLIER) cc_final: 0.7223 (p0) REVERT: C 218 ARG cc_start: 0.5901 (OUTLIER) cc_final: 0.5283 (ptp-170) REVERT: C 264 ARG cc_start: 0.8143 (mmm-85) cc_final: 0.7926 (mmm-85) REVERT: C 339 GLU cc_start: 0.0989 (OUTLIER) cc_final: 0.0372 (mt-10) REVERT: C 489 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8186 (mt) REVERT: C 595 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7225 (ptt-90) REVERT: C 944 MET cc_start: 0.8687 (mmm) cc_final: 0.8459 (mmm) REVERT: C 1140 MET cc_start: 0.8563 (mmp) cc_final: 0.8001 (mmp) REVERT: D 205 ARG cc_start: 0.8167 (ptp90) cc_final: 0.7723 (ptp90) REVERT: D 208 LYS cc_start: 0.8947 (mmtm) cc_final: 0.8614 (mmtm) REVERT: D 214 GLU cc_start: 0.6993 (mm-30) cc_final: 0.6779 (mm-30) REVERT: D 289 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.6893 (tp40) REVERT: D 593 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.7695 (ttp80) REVERT: D 933 GLN cc_start: 0.7042 (mp-120) cc_final: 0.6817 (mp-120) REVERT: D 963 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7498 (mtt90) outliers start: 137 outliers final: 123 residues processed: 446 average time/residue: 0.4086 time to fit residues: 268.6843 Evaluate side-chains 460 residues out of total 2411 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 325 time to evaluate : 2.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 49 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 209 ASP Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 485 ARG Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 565 THR Chi-restraints excluded: chain C residue 568 GLU Chi-restraints excluded: chain C residue 589 ASP Chi-restraints excluded: chain C residue 595 ARG Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain C residue 616 LYS Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 678 HIS Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 749 GLU Chi-restraints excluded: chain C residue 815 ASN Chi-restraints excluded: chain C residue 873 ARG Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 949 ASP Chi-restraints excluded: chain C residue 1031 SER Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain C residue 1095 ILE Chi-restraints excluded: chain C residue 1098 VAL Chi-restraints excluded: chain D residue 9 TYR Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 283 ASN Chi-restraints excluded: chain D residue 289 GLN Chi-restraints excluded: chain D residue 359 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 473 MET Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 593 ARG Chi-restraints excluded: chain D residue 661 SER Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain D residue 719 SER Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 740 ASN Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 766 SER Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 950 THR Chi-restraints excluded: chain D residue 960 PHE Chi-restraints excluded: chain D residue 963 ARG Chi-restraints excluded: chain D residue 992 VAL Chi-restraints excluded: chain D residue 1002 TYR Chi-restraints excluded: chain D residue 1003 THR Chi-restraints excluded: chain D residue 1028 SER Chi-restraints excluded: chain D residue 1064 ASP Chi-restraints excluded: chain D residue 1080 VAL Chi-restraints excluded: chain D residue 1081 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1108 LEU Chi-restraints excluded: chain D residue 1123 ILE Chi-restraints excluded: chain D residue 1135 SER Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 16 LYS Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 54 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 176 optimal weight: 2.9990 chunk 236 optimal weight: 20.0000 chunk 68 optimal weight: 30.0000 chunk 204 optimal weight: 8.9990 chunk 32 optimal weight: 30.0000 chunk 61 optimal weight: 5.9990 chunk 222 optimal weight: 20.0000 chunk 93 optimal weight: 0.0770 chunk 228 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 40 optimal weight: 20.0000 overall best weight: 5.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 126 HIS ** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.115372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.098082 restraints weight = 47665.527| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.55 r_work: 0.3177 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22812 Z= 0.273 Angle : 0.633 12.763 31054 Z= 0.323 Chirality : 0.043 0.162 3583 Planarity : 0.004 0.051 3918 Dihedral : 10.804 73.676 3536 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.95 % Favored : 94.94 % Rotamer: Outliers : 6.44 % Allowed : 27.47 % Favored : 66.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.16), residues: 2786 helix: 0.40 (0.17), residues: 937 sheet: -0.48 (0.28), residues: 391 loop : -1.24 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 199 HIS 0.004 0.001 HIS D1097 PHE 0.015 0.001 PHE C 470 TYR 0.017 0.001 TYR D 162 ARG 0.011 0.001 ARG D 735 =============================================================================== Job complete usr+sys time: 5390.54 seconds wall clock time: 98 minutes 6.15 seconds (5886.15 seconds total)