Starting phenix.real_space_refine on Tue Feb 20 05:39:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g18_4337/02_2024/6g18_4337.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g18_4337/02_2024/6g18_4337.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g18_4337/02_2024/6g18_4337.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g18_4337/02_2024/6g18_4337.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g18_4337/02_2024/6g18_4337.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g18_4337/02_2024/6g18_4337.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1657 5.49 5 S 213 5.16 5 C 46496 2.51 5 N 15333 2.21 5 O 20118 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F ASP 16": "OD1" <-> "OD2" Residue "F ASP 26": "OD1" <-> "OD2" Residue "F ASP 32": "OD1" <-> "OD2" Residue "F GLU 43": "OE1" <-> "OE2" Residue "F GLU 98": "OE1" <-> "OE2" Residue "F GLU 106": "OE1" <-> "OE2" Residue "M ASP 29": "OD1" <-> "OD2" Residue "M GLU 66": "OE1" <-> "OE2" Residue "M GLU 71": "OE1" <-> "OE2" Residue "M GLU 87": "OE1" <-> "OE2" Residue "P GLU 31": "OE1" <-> "OE2" Residue "P GLU 71": "OE1" <-> "OE2" Residue "P GLU 74": "OE1" <-> "OE2" Residue "P ASP 82": "OD1" <-> "OD2" Residue "P GLU 110": "OE1" <-> "OE2" Residue "Q PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 40": "OE1" <-> "OE2" Residue "Q GLU 61": "OE1" <-> "OE2" Residue "Q GLU 128": "OE1" <-> "OE2" Residue "R GLU 18": "OE1" <-> "OE2" Residue "R GLU 36": "OE1" <-> "OE2" Residue "R GLU 77": "OE1" <-> "OE2" Residue "R ARG 80": "NH1" <-> "NH2" Residue "R ASP 82": "OD1" <-> "OD2" Residue "R GLU 97": "OE1" <-> "OE2" Residue "R ASP 99": "OD1" <-> "OD2" Residue "S GLU 7": "OE1" <-> "OE2" Residue "S GLU 61": "OE1" <-> "OE2" Residue "S ASP 62": "OD1" <-> "OD2" Residue "T GLU 44": "OE1" <-> "OE2" Residue "T GLU 114": "OE1" <-> "OE2" Residue "T ASP 118": "OD1" <-> "OD2" Residue "Z GLU 61": "OE1" <-> "OE2" Residue "Z GLU 75": "OE1" <-> "OE2" Residue "c ASP 37": "OD1" <-> "OD2" Residue "c GLU 52": "OE1" <-> "OE2" Residue "c GLU 60": "OE1" <-> "OE2" Residue "c ARG 67": "NH1" <-> "NH2" Residue "f ARG 80": "NH1" <-> "NH2" Residue "f GLU 110": "OE1" <-> "OE2" Residue "g ASP 29": "OD1" <-> "OD2" Residue "g GLU 49": "OE1" <-> "OE2" Residue "g GLU 145": "OE1" <-> "OE2" Residue "g TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 223": "OE1" <-> "OE2" Residue "g TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 234": "OD1" <-> "OD2" Residue "g GLU 262": "OE1" <-> "OE2" Residue "g GLU 273": "OE1" <-> "OE2" Residue "g GLU 282": "OE1" <-> "OE2" Residue "g PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 6": "OD1" <-> "OD2" Residue "A GLU 12": "OE1" <-> "OE2" Residue "A ASP 44": "OD1" <-> "OD2" Residue "A GLU 56": "OE1" <-> "OE2" Residue "A GLU 69": "OE1" <-> "OE2" Residue "A PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 158": "OD1" <-> "OD2" Residue "B PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 68": "OE1" <-> "OE2" Residue "O ARG 104": "NH1" <-> "NH2" Residue "O ARG 150": "NH1" <-> "NH2" Residue "V PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 76": "NH1" <-> "NH2" Residue "x ARG 84": "NH1" <-> "NH2" Residue "x PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 114": "NH1" <-> "NH2" Residue "x ARG 119": "NH1" <-> "NH2" Residue "x PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 178": "NH1" <-> "NH2" Residue "x ARG 182": "NH1" <-> "NH2" Residue "x ARG 199": "NH1" <-> "NH2" Residue "x ARG 201": "NH1" <-> "NH2" Residue "x ARG 222": "NH1" <-> "NH2" Residue "x ARG 242": "NH1" <-> "NH2" Residue "x ARG 247": "NH1" <-> "NH2" Residue "y ARG 16": "NH1" <-> "NH2" Residue "y ARG 31": "NH1" <-> "NH2" Residue "y ARG 38": "NH1" <-> "NH2" Residue "y ARG 43": "NH1" <-> "NH2" Residue "y ARG 44": "NH1" <-> "NH2" Residue "y ARG 45": "NH1" <-> "NH2" Residue "y ARG 54": "NH1" <-> "NH2" Residue "y ARG 64": "NH1" <-> "NH2" Residue "y PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y GLU 222": "OE1" <-> "OE2" Residue "y ARG 264": "NH1" <-> "NH2" Residue "u ARG 73": "NH1" <-> "NH2" Residue "u ARG 93": "NH1" <-> "NH2" Residue "u ARG 128": "NH1" <-> "NH2" Residue "u ARG 132": "NH1" <-> "NH2" Residue "u ARG 139": "NH1" <-> "NH2" Residue "u PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 204": "NH1" <-> "NH2" Residue "u ARG 214": "NH1" <-> "NH2" Residue "u PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 249": "NH1" <-> "NH2" Residue "u TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 287": "NH1" <-> "NH2" Residue "u PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 492": "NH1" <-> "NH2" Residue "u ARG 499": "NH1" <-> "NH2" Residue "u PHE 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 537": "NH1" <-> "NH2" Residue "u TYR 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 571": "OE1" <-> "OE2" Residue "u ARG 599": "NH1" <-> "NH2" Residue "u GLU 612": "OE1" <-> "OE2" Residue "u ARG 624": "NH1" <-> "NH2" Residue "u ARG 642": "NH1" <-> "NH2" Residue "u PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 720": "NH1" <-> "NH2" Residue "u ARG 732": "NH1" <-> "NH2" Residue "u ARG 737": "NH1" <-> "NH2" Residue "w ARG 186": "NH1" <-> "NH2" Residue "w ARG 189": "NH1" <-> "NH2" Residue "w ARG 196": "NH1" <-> "NH2" Residue "w ARG 235": "NH1" <-> "NH2" Residue "w ARG 244": "NH1" <-> "NH2" Residue "w ARG 248": "NH1" <-> "NH2" Residue "w ARG 267": "NH1" <-> "NH2" Residue "w TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ARG 343": "NH1" <-> "NH2" Residue "w ARG 355": "NH1" <-> "NH2" Residue "w ARG 368": "NH1" <-> "NH2" Residue "v ASP 16": "OD1" <-> "OD2" Residue "v PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ARG 54": "NH1" <-> "NH2" Residue "v ARG 66": "NH1" <-> "NH2" Residue "v TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ARG 171": "NH1" <-> "NH2" Residue "v PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ARG 291": "NH1" <-> "NH2" Residue "v ARG 292": "NH1" <-> "NH2" Residue "t ASP 260": "OD1" <-> "OD2" Residue "t ARG 293": "NH1" <-> "NH2" Residue "t ASP 300": "OD1" <-> "OD2" Residue "t TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 418": "NH1" <-> "NH2" Residue "t ARG 430": "NH1" <-> "NH2" Residue "t ARG 442": "NH1" <-> "NH2" Residue "t PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 457": "NH1" <-> "NH2" Residue "t ARG 458": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 83819 Number of models: 1 Model: "" Number of chains: 37 Chain: "2" Number of atoms: 35407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1658, 35407 Inner-chain residues flagged as termini: ['pdbres=" C 21698 "'] Classifications: {'RNA': 1658} Modifications used: {'5*END': 1, 'rna2p_pur': 130, 'rna2p_pyr': 106, 'rna3p_pur': 752, 'rna3p_pyr': 670} Link IDs: {'rna2p': 235, 'rna3p': 1422} Chain breaks: 13 Chain: "F" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1495 Classifications: {'peptide': 189} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 183} Chain: "M" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 953 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "P" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 984 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "Q" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 969 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "R" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 990 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1083 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "T" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1122 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "Z" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 574 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "c" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 471 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 59} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "f" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 596 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "g" Number of atoms: 2433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2433 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "A" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1705 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain: "B" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1729 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "C" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1690 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "E" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2076 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 247} Chain: "G" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1862 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain: "H" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1501 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 9, 'TRANS': 176} Chain: "I" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1682 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain: "J" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1499 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "L" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1229 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain: "N" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "O" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1009 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "V" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 625 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "W" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "X" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "Y" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1014 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "b" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 640 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "e" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 438 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 51} Chain: "x" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1391 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 170} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "y" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2568 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 306} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "u" Number of atoms: 5062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 5062 Classifications: {'peptide': 629} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 586} Chain breaks: 4 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "w" Number of atoms: 2027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2027 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 13, 'TRANS': 235} Chain: "v" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2593 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 312} Chain breaks: 3 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "t" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1066 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 124} Chain breaks: 3 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 71954 SG CYS y 270 112.661 162.417 152.942 1.00 33.93 S ATOM 71974 SG CYS y 273 115.350 162.409 155.019 1.00 41.57 S ATOM 72071 SG CYS y 285 115.758 162.469 150.645 1.00 49.23 S ATOM 72093 SG CYS y 288 114.939 159.518 152.373 1.00 54.90 S Time building chain proxies: 32.52, per 1000 atoms: 0.39 Number of scatterers: 83819 At special positions: 0 Unit cell: (224.388, 247.152, 201.624, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 213 16.00 P 1657 15.00 O 20118 8.00 N 15333 7.00 C 46496 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: 30.67 Conformation dependent library (CDL) restraints added in 7.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN y 500 " pdb="ZN ZN y 500 " - pdb=" SG CYS y 273 " pdb="ZN ZN y 500 " - pdb=" SG CYS y 270 " pdb="ZN ZN y 500 " - pdb=" SG CYS y 285 " pdb="ZN ZN y 500 " - pdb=" SG CYS y 288 " Number of angles added : 6 11936 Ramachandran restraints generated. 5968 Oldfield, 0 Emsley, 5968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11328 Finding SS restraints... Secondary structure from input PDB file: 199 helices and 62 sheets defined 37.6% alpha, 17.3% beta 501 base pairs and 752 stacking pairs defined. Time for finding SS restraints: 26.49 Creating SS restraints... Processing helix chain 'F' and resid 18 through 22 Processing helix chain 'F' and resid 61 through 65 Processing helix chain 'F' and resid 67 through 75 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.540A pdb=" N ASN F 83 " --> pdb=" O GLY F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 105 removed outlier: 3.776A pdb=" N THR F 89 " --> pdb=" O LYS F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 120 Processing helix chain 'F' and resid 142 through 162 Processing helix chain 'F' and resid 168 through 183 Processing helix chain 'F' and resid 187 through 204 removed outlier: 4.086A pdb=" N ARG F 204 " --> pdb=" O ALA F 200 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 28 removed outlier: 4.034A pdb=" N LEU M 18 " --> pdb=" O VAL M 14 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLN M 19 " --> pdb=" O ASN M 15 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU M 20 " --> pdb=" O THR M 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 35 through 41 removed outlier: 3.646A pdb=" N ALA M 41 " --> pdb=" O GLU M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 58 through 72 removed outlier: 3.839A pdb=" N VAL M 62 " --> pdb=" O GLU M 58 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS M 72 " --> pdb=" O LEU M 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 81 through 90 removed outlier: 4.427A pdb=" N GLU M 87 " --> pdb=" O LYS M 83 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TRP M 88 " --> pdb=" O LYS M 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 119 through 132 Processing helix chain 'P' and resid 21 through 28 Processing helix chain 'P' and resid 29 through 34 removed outlier: 3.506A pdb=" N MET P 34 " --> pdb=" O TYR P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 48 Processing helix chain 'P' and resid 50 through 66 Processing helix chain 'P' and resid 86 through 90 removed outlier: 3.577A pdb=" N VAL P 90 " --> pdb=" O PRO P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 108 through 112 removed outlier: 3.882A pdb=" N ILE P 112 " --> pdb=" O PRO P 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 115 through 120 Processing helix chain 'Q' and resid 40 through 42 No H-bonds generated for 'chain 'Q' and resid 40 through 42' Processing helix chain 'Q' and resid 47 through 52 removed outlier: 4.022A pdb=" N LEU Q 51 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Processing helix chain 'Q' and resid 52 through 59 removed outlier: 3.616A pdb=" N LEU Q 58 " --> pdb=" O PRO Q 54 " (cutoff:3.500A) Processing helix chain 'Q' and resid 77 through 100 Processing helix chain 'Q' and resid 101 through 116 removed outlier: 3.771A pdb=" N LYS Q 105 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) Processing helix chain 'Q' and resid 117 through 120 Processing helix chain 'R' and resid 6 through 20 Processing helix chain 'R' and resid 27 through 39 Processing helix chain 'R' and resid 43 through 62 Processing helix chain 'R' and resid 73 through 83 Processing helix chain 'R' and resid 99 through 108 Processing helix chain 'S' and resid 25 through 30 Processing helix chain 'S' and resid 31 through 33 No H-bonds generated for 'chain 'S' and resid 31 through 33' Processing helix chain 'S' and resid 37 through 48 Processing helix chain 'S' and resid 60 through 73 removed outlier: 3.861A pdb=" N VAL S 64 " --> pdb=" O THR S 60 " (cutoff:3.500A) Processing helix chain 'S' and resid 74 through 78 Processing helix chain 'S' and resid 99 through 118 removed outlier: 3.757A pdb=" N LEU S 103 " --> pdb=" O LEU S 99 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP S 104 " --> pdb=" O ALA S 100 " (cutoff:3.500A) Processing helix chain 'S' and resid 119 through 128 Processing helix chain 'T' and resid 5 through 9 Processing helix chain 'T' and resid 10 through 26 removed outlier: 3.534A pdb=" N GLY T 26 " --> pdb=" O LEU T 22 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 67 removed outlier: 3.758A pdb=" N THR T 55 " --> pdb=" O ASN T 51 " (cutoff:3.500A) Processing helix chain 'T' and resid 71 through 79 Processing helix chain 'T' and resid 96 through 110 Processing helix chain 'T' and resid 124 through 144 removed outlier: 3.512A pdb=" N LYS T 144 " --> pdb=" O ALA T 140 " (cutoff:3.500A) Processing helix chain 'Z' and resid 51 through 60 Processing helix chain 'Z' and resid 61 through 65 removed outlier: 3.535A pdb=" N TYR Z 65 " --> pdb=" O VAL Z 62 " (cutoff:3.500A) Processing helix chain 'Z' and resid 69 through 77 Processing helix chain 'Z' and resid 80 through 94 Processing helix chain 'A' and resid 11 through 22 Processing helix chain 'A' and resid 34 through 36 No H-bonds generated for 'chain 'A' and resid 34 through 36' Processing helix chain 'A' and resid 50 through 67 Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'A' and resid 80 through 82 No H-bonds generated for 'chain 'A' and resid 80 through 82' Processing helix chain 'A' and resid 83 through 95 Processing helix chain 'A' and resid 131 through 141 Processing helix chain 'A' and resid 167 through 187 removed outlier: 3.667A pdb=" N GLY A 172 " --> pdb=" O ALA A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 206 through 216 removed outlier: 3.896A pdb=" N GLU A 211 " --> pdb=" O PRO A 207 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 26 Processing helix chain 'B' and resid 57 through 63 Processing helix chain 'B' and resid 72 through 74 No H-bonds generated for 'chain 'B' and resid 72 through 74' Processing helix chain 'B' and resid 106 through 114 removed outlier: 3.514A pdb=" N VAL B 114 " --> pdb=" O MET B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 177 Processing helix chain 'B' and resid 180 through 189 removed outlier: 3.612A pdb=" N ASN B 186 " --> pdb=" O LYS B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 201 removed outlier: 3.655A pdb=" N LYS B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 233 Processing helix chain 'C' and resid 64 through 72 Processing helix chain 'C' and resid 78 through 84 removed outlier: 3.504A pdb=" N TYR C 82 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 98 removed outlier: 4.391A pdb=" N ILE C 94 " --> pdb=" O GLU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 161 Processing helix chain 'C' and resid 207 through 216 Processing helix chain 'C' and resid 232 through 250 removed outlier: 3.605A pdb=" N THR C 247 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N TYR C 248 " --> pdb=" O ILE C 244 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 256 removed outlier: 3.580A pdb=" N LEU C 255 " --> pdb=" O THR C 252 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TRP C 256 " --> pdb=" O PRO C 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 252 through 256' Processing helix chain 'C' and resid 264 through 269 Processing helix chain 'E' and resid 15 through 19 Processing helix chain 'E' and resid 37 through 41 removed outlier: 4.129A pdb=" N CYS E 41 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 50 Processing helix chain 'E' and resid 57 through 66 Processing helix chain 'E' and resid 117 through 119 No H-bonds generated for 'chain 'E' and resid 117 through 119' Processing helix chain 'E' and resid 247 through 262 Processing helix chain 'G' and resid 20 through 28 removed outlier: 3.554A pdb=" N LEU G 24 " --> pdb=" O ASP G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 145 Processing helix chain 'G' and resid 181 through 230 removed outlier: 3.604A pdb=" N LEU G 185 " --> pdb=" O THR G 181 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 34 Processing helix chain 'H' and resid 37 through 43 Processing helix chain 'H' and resid 65 through 67 No H-bonds generated for 'chain 'H' and resid 65 through 67' Processing helix chain 'H' and resid 68 through 75 Processing helix chain 'H' and resid 75 through 87 Processing helix chain 'H' and resid 117 through 121 removed outlier: 3.588A pdb=" N THR H 121 " --> pdb=" O ARG H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 134 removed outlier: 3.862A pdb=" N VAL H 134 " --> pdb=" O LEU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 169 through 181 Processing helix chain 'I' and resid 49 through 51 No H-bonds generated for 'chain 'I' and resid 49 through 51' Processing helix chain 'I' and resid 88 through 93 removed outlier: 3.824A pdb=" N ARG I 92 " --> pdb=" O ASN I 88 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR I 93 " --> pdb=" O GLU I 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 88 through 93' Processing helix chain 'I' and resid 106 through 118 Processing helix chain 'I' and resid 130 through 138 removed outlier: 3.709A pdb=" N LEU I 137 " --> pdb=" O GLU I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 154 removed outlier: 3.907A pdb=" N LYS I 154 " --> pdb=" O ASP I 150 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 169 Processing helix chain 'I' and resid 178 through 183 Processing helix chain 'I' and resid 191 through 206 removed outlier: 3.893A pdb=" N ALA I 204 " --> pdb=" O ARG I 200 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG I 205 " --> pdb=" O LYS I 201 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS I 206 " --> pdb=" O ILE I 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 21 through 36 Processing helix chain 'J' and resid 39 through 62 removed outlier: 4.088A pdb=" N VAL J 43 " --> pdb=" O ASN J 39 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR J 62 " --> pdb=" O ARG J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 84 removed outlier: 3.558A pdb=" N ILE J 84 " --> pdb=" O ARG J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 100 removed outlier: 3.575A pdb=" N ILE J 97 " --> pdb=" O LEU J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 107 removed outlier: 3.928A pdb=" N PHE J 105 " --> pdb=" O LYS J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 117 Processing helix chain 'J' and resid 122 through 132 Processing helix chain 'J' and resid 171 through 179 Processing helix chain 'L' and resid 23 through 30 removed outlier: 3.509A pdb=" N LYS L 30 " --> pdb=" O GLY L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 53 removed outlier: 3.581A pdb=" N ILE L 51 " --> pdb=" O PRO L 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 45 removed outlier: 4.363A pdb=" N LYS N 43 " --> pdb=" O LYS N 39 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY N 44 " --> pdb=" O LEU N 40 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 57 Processing helix chain 'N' and resid 62 through 67 Processing helix chain 'N' and resid 70 through 79 Processing helix chain 'N' and resid 85 through 105 Processing helix chain 'N' and resid 108 through 132 Processing helix chain 'O' and resid 70 through 88 Processing helix chain 'O' and resid 109 through 122 removed outlier: 3.685A pdb=" N GLN O 113 " --> pdb=" O GLY O 109 " (cutoff:3.500A) Processing helix chain 'V' and resid 56 through 62 removed outlier: 3.590A pdb=" N MET V 62 " --> pdb=" O ALA V 58 " (cutoff:3.500A) Processing helix chain 'V' and resid 64 through 76 Processing helix chain 'W' and resid 5 through 20 removed outlier: 3.631A pdb=" N ASP W 9 " --> pdb=" O ASN W 5 " (cutoff:3.500A) Processing helix chain 'W' and resid 31 through 44 Processing helix chain 'W' and resid 85 through 93 removed outlier: 3.620A pdb=" N TRP W 89 " --> pdb=" O ASP W 85 " (cutoff:3.500A) Processing helix chain 'W' and resid 113 through 120 Processing helix chain 'X' and resid 9 through 22 removed outlier: 3.879A pdb=" N TRP X 22 " --> pdb=" O ARG X 18 " (cutoff:3.500A) Processing helix chain 'X' and resid 24 through 32 Processing helix chain 'X' and resid 34 through 39 Processing helix chain 'X' and resid 130 through 136 Processing helix chain 'Y' and resid 36 through 48 Processing helix chain 'Y' and resid 78 through 86 Processing helix chain 'Y' and resid 87 through 93 removed outlier: 3.550A pdb=" N LEU Y 91 " --> pdb=" O PRO Y 87 " (cutoff:3.500A) Processing helix chain 'Y' and resid 103 through 117 removed outlier: 3.683A pdb=" N ARG Y 107 " --> pdb=" O SER Y 103 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS Y 116 " --> pdb=" O ASN Y 112 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL Y 117 " --> pdb=" O ARG Y 113 " (cutoff:3.500A) Processing helix chain 'Y' and resid 118 through 123 removed outlier: 3.657A pdb=" N ALA Y 121 " --> pdb=" O ARG Y 118 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS Y 122 " --> pdb=" O GLY Y 119 " (cutoff:3.500A) Processing helix chain 'b' and resid 11 through 18 Processing helix chain 'e' and resid 10 through 16 removed outlier: 3.764A pdb=" N GLY e 14 " --> pdb=" O GLY e 10 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR e 16 " --> pdb=" O VAL e 12 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 40 Processing helix chain 'x' and resid 84 through 91 Processing helix chain 'x' and resid 91 through 102 Proline residue: x 98 - end of helix removed outlier: 3.781A pdb=" N HIS x 102 " --> pdb=" O PRO x 98 " (cutoff:3.500A) Processing helix chain 'x' and resid 128 through 143 Processing helix chain 'x' and resid 145 through 150 Processing helix chain 'x' and resid 150 through 155 removed outlier: 3.690A pdb=" N ARG x 154 " --> pdb=" O LEU x 150 " (cutoff:3.500A) Processing helix chain 'x' and resid 166 through 168 No H-bonds generated for 'chain 'x' and resid 166 through 168' Processing helix chain 'x' and resid 173 through 185 Processing helix chain 'x' and resid 188 through 198 Processing helix chain 'x' and resid 214 through 230 removed outlier: 3.672A pdb=" N THR x 223 " --> pdb=" O LYS x 219 " (cutoff:3.500A) Processing helix chain 'x' and resid 233 through 248 removed outlier: 3.569A pdb=" N GLY x 239 " --> pdb=" O SER x 235 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA x 243 " --> pdb=" O GLY x 239 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG x 247 " --> pdb=" O ALA x 243 " (cutoff:3.500A) Processing helix chain 'y' and resid 10 through 16 removed outlier: 4.064A pdb=" N PHE y 14 " --> pdb=" O ASP y 10 " (cutoff:3.500A) Processing helix chain 'y' and resid 30 through 36 removed outlier: 3.943A pdb=" N VAL y 34 " --> pdb=" O ILE y 30 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR y 35 " --> pdb=" O ARG y 31 " (cutoff:3.500A) Processing helix chain 'y' and resid 39 through 47 Processing helix chain 'y' and resid 59 through 71 removed outlier: 4.138A pdb=" N PHE y 69 " --> pdb=" O LEU y 65 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS y 71 " --> pdb=" O THR y 67 " (cutoff:3.500A) Processing helix chain 'y' and resid 80 through 98 Processing helix chain 'y' and resid 99 through 103 removed outlier: 3.856A pdb=" N HIS y 102 " --> pdb=" O GLY y 99 " (cutoff:3.500A) Processing helix chain 'y' and resid 238 through 249 removed outlier: 3.601A pdb=" N VAL y 244 " --> pdb=" O ALA y 240 " (cutoff:3.500A) Processing helix chain 'y' and resid 380 through 385 removed outlier: 3.627A pdb=" N THR y 384 " --> pdb=" O SER y 380 " (cutoff:3.500A) Processing helix chain 'y' and resid 394 through 399 removed outlier: 3.654A pdb=" N ARG y 398 " --> pdb=" O ALA y 394 " (cutoff:3.500A) Processing helix chain 'u' and resid 49 through 73 removed outlier: 3.696A pdb=" N ALA u 57 " --> pdb=" O GLN u 53 " (cutoff:3.500A) Processing helix chain 'u' and resid 95 through 104 removed outlier: 4.093A pdb=" N ALA u 99 " --> pdb=" O SER u 95 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU u 102 " --> pdb=" O GLU u 98 " (cutoff:3.500A) Processing helix chain 'u' and resid 142 through 151 removed outlier: 3.675A pdb=" N ASP u 148 " --> pdb=" O HIS u 144 " (cutoff:3.500A) Processing helix chain 'u' and resid 167 through 181 removed outlier: 3.517A pdb=" N CYS u 173 " --> pdb=" O THR u 169 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA u 179 " --> pdb=" O SER u 175 " (cutoff:3.500A) Processing helix chain 'u' and resid 196 through 212 removed outlier: 3.762A pdb=" N ILE u 201 " --> pdb=" O LEU u 197 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ASP u 202 " --> pdb=" O LYS u 198 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG u 204 " --> pdb=" O GLN u 200 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS u 205 " --> pdb=" O ILE u 201 " (cutoff:3.500A) Processing helix chain 'u' and resid 225 through 238 Processing helix chain 'u' and resid 244 through 250 removed outlier: 3.513A pdb=" N ASP u 248 " --> pdb=" O LEU u 244 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG u 249 " --> pdb=" O ALA u 245 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG u 250 " --> pdb=" O PHE u 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 244 through 250' Processing helix chain 'u' and resid 398 through 403 removed outlier: 3.996A pdb=" N GLU u 403 " --> pdb=" O SER u 399 " (cutoff:3.500A) Processing helix chain 'u' and resid 465 through 480 Processing helix chain 'u' and resid 495 through 500 Processing helix chain 'u' and resid 523 through 526 Processing helix chain 'u' and resid 532 through 546 Processing helix chain 'u' and resid 567 through 576 Processing helix chain 'u' and resid 720 through 726 Processing helix chain 'w' and resid 180 through 193 removed outlier: 3.719A pdb=" N GLU w 190 " --> pdb=" O ARG w 186 " (cutoff:3.500A) Processing helix chain 'w' and resid 206 through 210 Processing helix chain 'w' and resid 212 through 221 removed outlier: 3.663A pdb=" N ILE w 216 " --> pdb=" O ASN w 212 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR w 218 " --> pdb=" O GLU w 214 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL w 219 " --> pdb=" O GLN w 215 " (cutoff:3.500A) Processing helix chain 'w' and resid 222 through 225 Processing helix chain 'w' and resid 226 through 240 removed outlier: 3.716A pdb=" N GLN w 232 " --> pdb=" O ALA w 228 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER w 239 " --> pdb=" O ARG w 235 " (cutoff:3.500A) Processing helix chain 'w' and resid 242 through 253 removed outlier: 3.550A pdb=" N PHE w 249 " --> pdb=" O MET w 245 " (cutoff:3.500A) Processing helix chain 'w' and resid 253 through 265 removed outlier: 3.526A pdb=" N ARG w 257 " --> pdb=" O VAL w 253 " (cutoff:3.500A) Processing helix chain 'w' and resid 269 through 279 removed outlier: 3.542A pdb=" N LEU w 276 " --> pdb=" O LEU w 272 " (cutoff:3.500A) Processing helix chain 'w' and resid 282 through 290 Processing helix chain 'w' and resid 290 through 298 removed outlier: 3.534A pdb=" N SER w 297 " --> pdb=" O PRO w 293 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLY w 298 " --> pdb=" O LEU w 294 " (cutoff:3.500A) Processing helix chain 'w' and resid 301 through 315 removed outlier: 3.977A pdb=" N ILE w 311 " --> pdb=" O ILE w 307 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE w 312 " --> pdb=" O VAL w 308 " (cutoff:3.500A) Processing helix chain 'w' and resid 318 through 332 removed outlier: 3.651A pdb=" N LYS w 328 " --> pdb=" O ALA w 324 " (cutoff:3.500A) Processing helix chain 'w' and resid 337 through 347 removed outlier: 3.962A pdb=" N PHE w 341 " --> pdb=" O ALA w 337 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU w 342 " --> pdb=" O ASN w 338 " (cutoff:3.500A) Processing helix chain 'w' and resid 353 through 365 removed outlier: 3.545A pdb=" N LEU w 357 " --> pdb=" O PRO w 353 " (cutoff:3.500A) Processing helix chain 'w' and resid 366 through 368 No H-bonds generated for 'chain 'w' and resid 366 through 368' Processing helix chain 'w' and resid 375 through 389 removed outlier: 3.720A pdb=" N HIS w 379 " --> pdb=" O PRO w 375 " (cutoff:3.500A) Processing helix chain 'w' and resid 394 through 408 removed outlier: 3.566A pdb=" N LEU w 402 " --> pdb=" O LYS w 398 " (cutoff:3.500A) Processing helix chain 'w' and resid 413 through 423 Processing helix chain 'v' and resid 14 through 28 removed outlier: 4.317A pdb=" N ARG v 18 " --> pdb=" O ARG v 14 " (cutoff:3.500A) Processing helix chain 'v' and resid 34 through 42 removed outlier: 3.737A pdb=" N ILE v 38 " --> pdb=" O PRO v 34 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA v 39 " --> pdb=" O GLY v 35 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N SER v 40 " --> pdb=" O SER v 36 " (cutoff:3.500A) Processing helix chain 'v' and resid 49 through 57 Processing helix chain 'v' and resid 76 through 91 removed outlier: 3.709A pdb=" N LEU v 83 " --> pdb=" O GLY v 79 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA v 84 " --> pdb=" O TYR v 80 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU v 85 " --> pdb=" O ASP v 81 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER v 90 " --> pdb=" O LYS v 86 " (cutoff:3.500A) Processing helix chain 'v' and resid 146 through 170 removed outlier: 3.515A pdb=" N SER v 154 " --> pdb=" O TRP v 150 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ARG v 155 " --> pdb=" O LEU v 151 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU v 156 " --> pdb=" O TYR v 152 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA v 158 " --> pdb=" O SER v 154 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET v 159 " --> pdb=" O ARG v 155 " (cutoff:3.500A) Processing helix chain 'v' and resid 197 through 199 No H-bonds generated for 'chain 'v' and resid 197 through 199' Processing helix chain 'v' and resid 204 through 222 removed outlier: 3.568A pdb=" N VAL v 208 " --> pdb=" O ASP v 204 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE v 216 " --> pdb=" O ALA v 212 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL v 217 " --> pdb=" O MET v 213 " (cutoff:3.500A) Processing helix chain 'v' and resid 257 through 277 removed outlier: 3.524A pdb=" N TYR v 261 " --> pdb=" O ASN v 257 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP v 265 " --> pdb=" O TYR v 261 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET v 274 " --> pdb=" O LYS v 270 " (cutoff:3.500A) Processing helix chain 'v' and resid 497 through 522 removed outlier: 3.556A pdb=" N ALA v 516 " --> pdb=" O GLN v 512 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG v 519 " --> pdb=" O SER v 515 " (cutoff:3.500A) Processing helix chain 'v' and resid 527 through 544 removed outlier: 3.701A pdb=" N GLU v 535 " --> pdb=" O LYS v 531 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN v 536 " --> pdb=" O GLN v 532 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET v 537 " --> pdb=" O ARG v 533 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN v 538 " --> pdb=" O ARG v 534 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN v 539 " --> pdb=" O GLU v 535 " (cutoff:3.500A) Processing helix chain 't' and resid 292 through 308 Processing helix chain 't' and resid 425 through 469 removed outlier: 3.588A pdb=" N ALA t 429 " --> pdb=" O GLU t 425 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG t 430 " --> pdb=" O ASP t 426 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL t 443 " --> pdb=" O LYS t 439 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG t 458 " --> pdb=" O LEU t 454 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU t 466 " --> pdb=" O GLU t 462 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS t 467 " --> pdb=" O LEU t 463 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS t 468 " --> pdb=" O LEU t 464 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 123 through 126 removed outlier: 8.103A pdb=" N ALA F 138 " --> pdb=" O ASN c 45 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N LYS c 47 " --> pdb=" O ALA F 138 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASP F 140 " --> pdb=" O LYS c 47 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N CYS c 27 " --> pdb=" O ARG c 20 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ARG c 20 " --> pdb=" O CYS c 27 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLN c 29 " --> pdb=" O LEU c 18 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS c 16 " --> pdb=" O ARG c 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 31 through 34 removed outlier: 4.020A pdb=" N CYS M 108 " --> pdb=" O GLY M 34 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 76 through 78 removed outlier: 6.443A pdb=" N VAL P 76 " --> pdb=" O GLY P 95 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N TYR P 97 " --> pdb=" O VAL P 76 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N THR P 78 " --> pdb=" O TYR P 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Q' and resid 9 through 16 removed outlier: 6.274A pdb=" N LEU Q 31 " --> pdb=" O ILE Q 68 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N VAL Q 70 " --> pdb=" O LEU Q 31 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N LYS Q 33 " --> pdb=" O VAL Q 70 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N VAL Q 72 " --> pdb=" O LYS Q 33 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'R' and resid 96 through 98 removed outlier: 6.389A pdb=" N ILE R 96 " --> pdb=" O GLN R 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'S' and resid 12 through 15 Processing sheet with id=AA7, first strand: chain 'T' and resid 81 through 83 Processing sheet with id=AA8, first strand: chain 'T' and resid 113 through 115 Processing sheet with id=AA9, first strand: chain 'Z' and resid 67 through 68 removed outlier: 6.741A pdb=" N ILE Z 108 " --> pdb=" O VAL Z 100 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'c' and resid 10 through 11 removed outlier: 3.649A pdb=" N LYS c 10 " --> pdb=" O LEU c 58 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'f' and resid 106 through 108 Processing sheet with id=AB3, first strand: chain 'f' and resid 132 through 134 Processing sheet with id=AB4, first strand: chain 'g' and resid 4 through 11 removed outlier: 7.341A pdb=" N VAL g 309 " --> pdb=" O ARG g 8 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N THR g 10 " --> pdb=" O VAL g 307 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL g 307 " --> pdb=" O THR g 10 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'g' and resid 18 through 23 removed outlier: 3.671A pdb=" N GLN g 20 " --> pdb=" O ALA g 34 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR g 39 " --> pdb=" O SER g 35 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE g 40 " --> pdb=" O ALA g 58 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ALA g 58 " --> pdb=" O ILE g 40 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N MET g 42 " --> pdb=" O GLN g 56 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'g' and resid 66 through 71 removed outlier: 3.767A pdb=" N THR g 86 " --> pdb=" O SER g 82 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG g 99 " --> pdb=" O LEU g 89 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ASP g 91 " --> pdb=" O THR g 97 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N THR g 97 " --> pdb=" O ASP g 91 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'g' and resid 108 through 113 removed outlier: 3.844A pdb=" N ILE g 129 " --> pdb=" O VAL g 142 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR g 140 " --> pdb=" O LEU g 131 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'g' and resid 151 through 155 removed outlier: 4.490A pdb=" N LEU g 173 " --> pdb=" O GLY g 169 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL g 174 " --> pdb=" O ASN g 187 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ASN g 187 " --> pdb=" O VAL g 174 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL g 176 " --> pdb=" O LYS g 185 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS g 183 " --> pdb=" O ASN g 178 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'g' and resid 195 through 200 removed outlier: 7.028A pdb=" N GLY g 210 " --> pdb=" O ASN g 196 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL g 198 " --> pdb=" O ALA g 208 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA g 208 " --> pdb=" O VAL g 198 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N VAL g 200 " --> pdb=" O LEU g 206 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU g 206 " --> pdb=" O VAL g 200 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N GLY g 211 " --> pdb=" O GLN g 215 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N GLN g 215 " --> pdb=" O GLY g 211 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ASP g 220 " --> pdb=" O HIS g 226 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N HIS g 226 " --> pdb=" O ASP g 220 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'g' and resid 238 through 241 removed outlier: 3.616A pdb=" N ALA g 238 " --> pdb=" O ALA g 251 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE g 256 " --> pdb=" O GLU g 269 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLU g 269 " --> pdb=" O ILE g 256 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE g 258 " --> pdb=" O VAL g 267 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 38 through 41 removed outlier: 6.838A pdb=" N ILE A 48 " --> pdb=" O TYR A 39 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 97 through 100 removed outlier: 6.355A pdb=" N VAL A 74 " --> pdb=" O THR A 97 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ILE A 99 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL A 76 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU A 122 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N LEU A 147 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N VAL A 124 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR A 144 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ILE A 161 " --> pdb=" O THR A 144 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA A 146 " --> pdb=" O ILE A 161 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 28 through 34 removed outlier: 4.140A pdb=" N GLY B 45 " --> pdb=" O VAL B 33 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 66 through 70 removed outlier: 6.866A pdb=" N LYS B 83 " --> pdb=" O MET B 103 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N MET B 103 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LYS B 85 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU B 97 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 13.020A pdb=" N ASN B 99 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 13.280A pdb=" N LYS B 219 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N HIS B 101 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N MET B 217 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LYS B 214 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU B 134 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 102 through 116 removed outlier: 5.283A pdb=" N ASP C 104 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLY C 131 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N VAL C 106 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG C 121 " --> pdb=" O LYS C 114 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 184 through 188 removed outlier: 6.851A pdb=" N VAL C 205 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ALA C 226 " --> pdb=" O VAL C 205 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 9 through 10 removed outlier: 4.390A pdb=" N LEU E 9 " --> pdb=" O ALA E 28 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 42 through 43 Processing sheet with id=AD1, first strand: chain 'E' and resid 75 through 76 removed outlier: 3.549A pdb=" N ASP E 88 " --> pdb=" O LEU E 101 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASN E 98 " --> pdb=" O ILE E 114 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N HIS E 112 " --> pdb=" O ARG E 100 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ILE E 102 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.903A pdb=" N ASP E 171 " --> pdb=" O GLN E 161 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ASP E 163 " --> pdb=" O ILE E 169 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ILE E 169 " --> pdb=" O ASP E 163 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 217 through 221 removed outlier: 7.358A pdb=" N VAL E 207 " --> pdb=" O ARG E 198 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ARG E 198 " --> pdb=" O VAL E 207 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N HIS E 209 " --> pdb=" O THR E 196 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ASN E 179 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU E 180 " --> pdb=" O ILE E 228 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 12 through 17 removed outlier: 6.490A pdb=" N ASN G 56 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LEU G 109 " --> pdb=" O GLY G 54 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLY G 54 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU G 111 " --> pdb=" O ILE G 52 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ILE G 52 " --> pdb=" O LEU G 111 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE G 113 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL G 50 " --> pdb=" O ILE G 113 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 72 through 77 Processing sheet with id=AD6, first strand: chain 'G' and resid 160 through 162 Processing sheet with id=AD7, first strand: chain 'H' and resid 47 through 52 removed outlier: 3.670A pdb=" N HIS H 91 " --> pdb=" O LYS H 58 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 184 through 188 removed outlier: 4.685A pdb=" N ASP H 184 " --> pdb=" O ARG H 152 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU H 153 " --> pdb=" O ILE H 144 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ILE H 144 " --> pdb=" O LEU H 153 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LYS H 155 " --> pdb=" O LYS H 142 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS H 142 " --> pdb=" O LYS H 155 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N HIS H 157 " --> pdb=" O VAL H 140 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 3 through 4 removed outlier: 3.753A pdb=" N ILE I 3 " --> pdb=" O GLY I 30 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 37 through 38 removed outlier: 6.357A pdb=" N ARG I 42 " --> pdb=" O LEU I 58 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 62 through 67 removed outlier: 7.443A pdb=" N ILE I 78 " --> pdb=" O ASP I 105 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ASP I 105 " --> pdb=" O ILE I 78 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE I 101 " --> pdb=" O VAL I 82 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N GLY I 187 " --> pdb=" O VAL I 62 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ASN I 64 " --> pdb=" O GLY I 187 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL I 189 " --> pdb=" O ASN I 64 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N SER I 66 " --> pdb=" O VAL I 189 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 136 through 137 Processing sheet with id=AE4, first strand: chain 'L' and resid 72 through 82 removed outlier: 16.569A pdb=" N LEU L 73 " --> pdb=" O LEU L 93 " (cutoff:3.500A) removed outlier: 15.311A pdb=" N LEU L 93 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N GLY L 75 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ASP L 91 " --> pdb=" O GLY L 75 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N VAL L 77 " --> pdb=" O ARG L 89 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ARG L 89 " --> pdb=" O VAL L 77 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS L 81 " --> pdb=" O THR L 85 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N THR L 85 " --> pdb=" O LYS L 81 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG L 101 " --> pdb=" O ILE L 96 " (cutoff:3.500A) removed outlier: 9.907A pdb=" N PHE L 140 " --> pdb=" O ASN L 108 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N SER L 110 " --> pdb=" O PHE L 140 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N VAL L 142 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N HIS L 112 " --> pdb=" O VAL L 142 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N LYS L 144 " --> pdb=" O HIS L 112 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR L 127 " --> pdb=" O LEU L 143 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N VAL L 145 " --> pdb=" O ILE L 125 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ILE L 125 " --> pdb=" O VAL L 145 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'O' and resid 52 through 57 removed outlier: 6.730A pdb=" N VAL O 44 " --> pdb=" O ILE O 53 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG O 55 " --> pdb=" O VAL O 42 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL O 42 " --> pdb=" O ARG O 55 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N THR O 57 " --> pdb=" O THR O 40 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N THR O 40 " --> pdb=" O THR O 57 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLY O 29 " --> pdb=" O HIS O 94 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N LYS O 96 " --> pdb=" O GLY O 29 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N CYS O 31 " --> pdb=" O LYS O 96 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ARG O 98 " --> pdb=" O CYS O 31 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE O 33 " --> pdb=" O ARG O 98 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N LEU O 93 " --> pdb=" O GLY O 127 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE O 129 " --> pdb=" O LEU O 93 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE O 95 " --> pdb=" O ILE O 129 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ASP O 131 " --> pdb=" O ILE O 95 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU O 97 " --> pdb=" O ASP O 131 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'V' and resid 32 through 39 removed outlier: 5.024A pdb=" N GLN V 49 " --> pdb=" O GLU V 38 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'W' and resid 71 through 74 removed outlier: 5.249A pdb=" N ILE W 125 " --> pdb=" O THR W 105 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N THR W 105 " --> pdb=" O ILE W 125 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'X' and resid 128 through 129 removed outlier: 6.597A pdb=" N LEU X 101 " --> pdb=" O VAL X 123 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N VAL X 125 " --> pdb=" O GLU X 99 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N GLU X 99 " --> pdb=" O VAL X 125 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ARG X 71 " --> pdb=" O LEU X 52 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N LYS X 54 " --> pdb=" O CYS X 69 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N CYS X 69 " --> pdb=" O LYS X 54 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N GLY X 56 " --> pdb=" O ARG X 67 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ARG X 67 " --> pdb=" O GLY X 56 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N PHE X 120 " --> pdb=" O THR X 82 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Y' and resid 6 through 15 removed outlier: 5.316A pdb=" N VAL Y 24 " --> pdb=" O ARG Y 10 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE Y 12 " --> pdb=" O GLN Y 22 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLN Y 22 " --> pdb=" O PHE Y 12 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N THR Y 14 " --> pdb=" O ARG Y 20 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG Y 20 " --> pdb=" O THR Y 14 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N LYS Y 68 " --> pdb=" O THR Y 62 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N THR Y 62 " --> pdb=" O LYS Y 68 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR Y 70 " --> pdb=" O PHE Y 60 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N PHE Y 60 " --> pdb=" O THR Y 70 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'b' and resid 43 through 47 Processing sheet with id=AF2, first strand: chain 'b' and resid 54 through 55 removed outlier: 7.052A pdb=" N VAL b 54 " --> pdb=" O LEU b 63 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'x' and resid 75 through 79 removed outlier: 8.613A pdb=" N HIS y 129 " --> pdb=" O ILE x 107 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N PHE x 109 " --> pdb=" O HIS y 129 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'x' and resid 159 through 164 Processing sheet with id=AF5, first strand: chain 'y' and resid 8 through 9 removed outlier: 7.923A pdb=" N VAL y 8 " --> pdb=" O LEU y 235 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'y' and resid 28 through 29 Processing sheet with id=AF7, first strand: chain 'y' and resid 111 through 112 removed outlier: 3.873A pdb=" N SER y 297 " --> pdb=" O HIS y 309 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'u' and resid 110 through 112 removed outlier: 3.754A pdb=" N CYS u 126 " --> pdb=" O HIS u 131 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLN u 84 " --> pdb=" O THR u 155 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N LEU u 157 " --> pdb=" O GLN u 84 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU u 86 " --> pdb=" O LEU u 157 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N LEU u 159 " --> pdb=" O LEU u 86 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL u 88 " --> pdb=" O LEU u 159 " (cutoff:3.500A) removed outlier: 9.684A pdb=" N LEU u 221 " --> pdb=" O TYR u 185 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU u 187 " --> pdb=" O LEU u 221 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'u' and resid 251 through 254 removed outlier: 4.196A pdb=" N ALA u 251 " --> pdb=" O SER u 583 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU u 289 " --> pdb=" O PHE u 297 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'u' and resid 257 through 264 removed outlier: 3.698A pdb=" N SER u 263 " --> pdb=" O VAL u 269 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N VAL u 269 " --> pdb=" O SER u 263 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY u 270 " --> pdb=" O GLU u 564 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLU u 564 " --> pdb=" O GLY u 270 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N SER u 563 " --> pdb=" O MET u 299 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N MET u 299 " --> pdb=" O SER u 563 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS u 346 " --> pdb=" O ILE u 302 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'u' and resid 528 through 530 removed outlier: 7.107A pdb=" N GLN u 529 " --> pdb=" O ILE t 367 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'u' and resid 623 through 625 removed outlier: 7.079A pdb=" N VAL u 665 " --> pdb=" O THR u 681 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N THR u 681 " --> pdb=" O VAL u 665 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU u 667 " --> pdb=" O ILE u 679 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'u' and resid 637 through 639 removed outlier: 6.217A pdb=" N HIS u 638 " --> pdb=" O ILE u 694 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ARG u 696 " --> pdb=" O HIS u 638 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL u 693 " --> pdb=" O VAL u 773 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ASN u 768 " --> pdb=" O GLU u 730 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLU u 730 " --> pdb=" O ASN u 768 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LYS u 752 " --> pdb=" O LYS u 742 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N HIS u 750 " --> pdb=" O PRO u 744 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS u 705 " --> pdb=" O VAL u 712 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ARG u 714 " --> pdb=" O PRO u 703 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'v' and resid 62 through 66 Processing sheet with id=AG6, first strand: chain 'v' and resid 96 through 103 removed outlier: 3.907A pdb=" N ILE v 111 " --> pdb=" O GLY v 98 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLN v 100 " --> pdb=" O ILE v 109 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE v 109 " --> pdb=" O GLN v 100 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N GLY v 102 " --> pdb=" O SER v 107 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N SER v 107 " --> pdb=" O GLY v 102 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASP v 180 " --> pdb=" O VAL v 187 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'v' and resid 194 through 195 Processing sheet with id=AG8, first strand: chain 'v' and resid 224 through 225 1933 hydrogen bonds defined for protein. 5511 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1254 hydrogen bonds 2048 hydrogen bond angles 0 basepair planarities 501 basepair parallelities 752 stacking parallelities Total time for adding SS restraints: 63.25 Time building geometry restraints manager: 33.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 11047 1.32 - 1.45: 32601 1.45 - 1.57: 41588 1.57 - 1.70: 3299 1.70 - 1.82: 333 Bond restraints: 88868 Sorted by residual: bond pdb=" CA PRO g 283 " pdb=" C PRO g 283 " ideal model delta sigma weight residual 1.514 1.539 -0.025 5.50e-03 3.31e+04 2.08e+01 bond pdb=" CA PRO N 136 " pdb=" C PRO N 136 " ideal model delta sigma weight residual 1.514 1.539 -0.025 5.50e-03 3.31e+04 1.99e+01 bond pdb=" CA PRO u 81 " pdb=" C PRO u 81 " ideal model delta sigma weight residual 1.517 1.555 -0.038 9.30e-03 1.16e+04 1.69e+01 bond pdb=" CA ILE w 292 " pdb=" CB ILE w 292 " ideal model delta sigma weight residual 1.534 1.560 -0.025 6.80e-03 2.16e+04 1.40e+01 bond pdb=" CA PRO u 661 " pdb=" C PRO u 661 " ideal model delta sigma weight residual 1.514 1.534 -0.019 5.50e-03 3.31e+04 1.24e+01 ... (remaining 88863 not shown) Histogram of bond angle deviations from ideal: 83.79 - 93.88: 2 93.88 - 103.97: 6536 103.97 - 114.06: 55590 114.06 - 124.15: 57020 124.15 - 134.23: 8765 Bond angle restraints: 127913 Sorted by residual: angle pdb=" N TYR t 357 " pdb=" CA TYR t 357 " pdb=" C TYR t 357 " ideal model delta sigma weight residual 108.76 83.79 24.97 1.69e+00 3.50e-01 2.18e+02 angle pdb=" O3' U 21494 " pdb=" C3' U 21494 " pdb=" C2' U 21494 " ideal model delta sigma weight residual 109.50 126.22 -16.72 1.50e+00 4.44e-01 1.24e+02 angle pdb=" C TYR t 357 " pdb=" CA TYR t 357 " pdb=" CB TYR t 357 " ideal model delta sigma weight residual 109.70 89.73 19.97 1.81e+00 3.05e-01 1.22e+02 angle pdb=" C4' G 21648 " pdb=" C3' G 21648 " pdb=" O3' G 21648 " ideal model delta sigma weight residual 109.40 123.64 -14.24 1.50e+00 4.44e-01 9.01e+01 angle pdb=" O3' G 2 547 " pdb=" C3' G 2 547 " pdb=" C2' G 2 547 " ideal model delta sigma weight residual 109.50 123.24 -13.74 1.50e+00 4.44e-01 8.39e+01 ... (remaining 127908 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 50752 35.81 - 71.62: 4932 71.62 - 107.43: 574 107.43 - 143.24: 20 143.24 - 179.05: 31 Dihedral angle restraints: 56309 sinusoidal: 38797 harmonic: 17512 Sorted by residual: dihedral pdb=" C TYR t 357 " pdb=" N TYR t 357 " pdb=" CA TYR t 357 " pdb=" CB TYR t 357 " ideal model delta harmonic sigma weight residual -122.60 -87.36 -35.24 0 2.50e+00 1.60e-01 1.99e+02 dihedral pdb=" O4' U 2 823 " pdb=" C1' U 2 823 " pdb=" N1 U 2 823 " pdb=" C2 U 2 823 " ideal model delta sinusoidal sigma weight residual 200.00 20.95 179.05 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C 21139 " pdb=" C1' C 21139 " pdb=" N1 C 21139 " pdb=" C2 C 21139 " ideal model delta sinusoidal sigma weight residual -160.00 17.97 -177.97 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 56306 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.168: 13631 0.168 - 0.336: 1941 0.336 - 0.504: 50 0.504 - 0.672: 12 0.672 - 0.840: 11 Chirality restraints: 15645 Sorted by residual: chirality pdb=" C3' G 21587 " pdb=" C4' G 21587 " pdb=" O3' G 21587 " pdb=" C2' G 21587 " both_signs ideal model delta sigma weight residual False -2.74 -1.90 -0.84 2.00e-01 2.50e+01 1.76e+01 chirality pdb=" C3' A 21601 " pdb=" C4' A 21601 " pdb=" O3' A 21601 " pdb=" C2' A 21601 " both_signs ideal model delta sigma weight residual False -2.74 -1.92 -0.82 2.00e-01 2.50e+01 1.68e+01 chirality pdb=" C3' C 21430 " pdb=" C4' C 21430 " pdb=" O3' C 21430 " pdb=" C2' C 21430 " both_signs ideal model delta sigma weight residual False -2.74 -1.93 -0.81 2.00e-01 2.50e+01 1.65e+01 ... (remaining 15642 not shown) Planarity restraints: 10091 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A 21144 " -0.023 2.00e-02 2.50e+03 3.92e-02 4.23e+01 pdb=" N9 A 21144 " 0.027 2.00e-02 2.50e+03 pdb=" C8 A 21144 " 0.025 2.00e-02 2.50e+03 pdb=" N7 A 21144 " 0.009 2.00e-02 2.50e+03 pdb=" C5 A 21144 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A 21144 " 0.002 2.00e-02 2.50e+03 pdb=" N6 A 21144 " -0.063 2.00e-02 2.50e+03 pdb=" N1 A 21144 " 0.096 2.00e-02 2.50e+03 pdb=" C2 A 21144 " -0.028 2.00e-02 2.50e+03 pdb=" N3 A 21144 " -0.027 2.00e-02 2.50e+03 pdb=" C4 A 21144 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 2 667 " 0.030 2.00e-02 2.50e+03 3.70e-02 3.07e+01 pdb=" N1 U 2 667 " -0.004 2.00e-02 2.50e+03 pdb=" C2 U 2 667 " 0.013 2.00e-02 2.50e+03 pdb=" O2 U 2 667 " 0.014 2.00e-02 2.50e+03 pdb=" N3 U 2 667 " -0.079 2.00e-02 2.50e+03 pdb=" C4 U 2 667 " -0.007 2.00e-02 2.50e+03 pdb=" O4 U 2 667 " 0.064 2.00e-02 2.50e+03 pdb=" C5 U 2 667 " -0.016 2.00e-02 2.50e+03 pdb=" C6 U 2 667 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 21671 " 0.010 2.00e-02 2.50e+03 2.97e-02 2.64e+01 pdb=" N9 G 21671 " 0.001 2.00e-02 2.50e+03 pdb=" C8 G 21671 " -0.005 2.00e-02 2.50e+03 pdb=" N7 G 21671 " -0.008 2.00e-02 2.50e+03 pdb=" C5 G 21671 " -0.006 2.00e-02 2.50e+03 pdb=" C6 G 21671 " -0.007 2.00e-02 2.50e+03 pdb=" O6 G 21671 " 0.044 2.00e-02 2.50e+03 pdb=" N1 G 21671 " -0.071 2.00e-02 2.50e+03 pdb=" C2 G 21671 " 0.057 2.00e-02 2.50e+03 pdb=" N2 G 21671 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G 21671 " -0.006 2.00e-02 2.50e+03 pdb=" C4 G 21671 " -0.006 2.00e-02 2.50e+03 ... (remaining 10088 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.13: 6 2.13 - 2.82: 18771 2.82 - 3.51: 109178 3.51 - 4.21: 243632 4.21 - 4.90: 338443 Nonbonded interactions: 710030 Sorted by model distance: nonbonded pdb=" N3 U 2 8 " pdb=" N6 A 21196 " model vdw 1.434 2.560 nonbonded pdb=" N6 A 2 830 " pdb=" N3 U 2 844 " model vdw 1.652 2.560 nonbonded pdb=" N1 A 2 872 " pdb=" O4 U 2 914 " model vdw 1.824 2.496 nonbonded pdb=" N6 A 2 872 " pdb=" N3 U 2 914 " model vdw 1.829 2.560 nonbonded pdb=" C2 U 2 8 " pdb=" N6 A 21196 " model vdw 1.979 3.340 ... (remaining 710025 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 12.300 Check model and map are aligned: 0.910 Set scattering table: 0.610 Process input model: 232.530 Find NCS groups from input model: 1.990 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 253.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 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 : 0.007 0.066 88868 Z= 0.450 Angle : 1.278 24.967 127913 Z= 0.849 Chirality : 0.103 0.840 15645 Planarity : 0.006 0.102 10091 Dihedral : 23.214 179.053 44981 Min Nonbonded Distance : 1.434 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.79 % Allowed : 5.85 % Favored : 93.36 % Rotamer: Outliers : 7.67 % Allowed : 11.52 % Favored : 80.81 % Cbeta Deviations : 0.53 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.09), residues: 5968 helix: -1.02 (0.10), residues: 2068 sheet: -1.07 (0.15), residues: 969 loop : -1.90 (0.10), residues: 2931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP X 22 HIS 0.013 0.002 HIS J 124 PHE 0.025 0.003 PHE x 140 TYR 0.022 0.003 TYR Q 99 ARG 0.025 0.001 ARG P 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11936 Ramachandran restraints generated. 5968 Oldfield, 0 Emsley, 5968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11936 Ramachandran restraints generated. 5968 Oldfield, 0 Emsley, 5968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2322 residues out of total 5267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 401 poor density : 1921 time to evaluate : 5.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 32 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.8351 (t0) REVERT: F 44 LYS cc_start: 0.8821 (ttpt) cc_final: 0.8495 (tppt) REVERT: F 79 HIS cc_start: 0.6921 (OUTLIER) cc_final: 0.5640 (t70) REVERT: F 102 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8157 (mp) REVERT: F 106 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8548 (tt0) REVERT: F 113 VAL cc_start: 0.8623 (t) cc_final: 0.8347 (m) REVERT: F 136 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.8424 (ptp-170) REVERT: F 140 ASP cc_start: 0.8470 (m-30) cc_final: 0.8156 (m-30) REVERT: F 185 SER cc_start: 0.8804 (t) cc_final: 0.8472 (p) REVERT: M 33 ARG cc_start: 0.6191 (OUTLIER) cc_final: 0.5489 (ptp-170) REVERT: M 84 LYS cc_start: 0.7615 (tptt) cc_final: 0.7270 (ptmm) REVERT: M 89 VAL cc_start: 0.6338 (t) cc_final: 0.4707 (t) REVERT: M 96 ARG cc_start: 0.7926 (ptt-90) cc_final: 0.7584 (ptt-90) REVERT: M 125 GLU cc_start: 0.6603 (OUTLIER) cc_final: 0.6333 (tp30) REVERT: P 21 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.7688 (p0) REVERT: P 24 GLN cc_start: 0.8533 (mt0) cc_final: 0.8128 (mt0) REVERT: P 29 SER cc_start: 0.9059 (t) cc_final: 0.8857 (p) REVERT: P 31 GLU cc_start: 0.8555 (tt0) cc_final: 0.8216 (mm-30) REVERT: P 34 MET cc_start: 0.7200 (OUTLIER) cc_final: 0.6846 (mtm) REVERT: P 35 GLN cc_start: 0.8794 (tt0) cc_final: 0.8426 (tt0) REVERT: P 38 SER cc_start: 0.9335 (t) cc_final: 0.9029 (p) REVERT: P 51 ARG cc_start: 0.8610 (tpt90) cc_final: 0.8239 (ttm110) REVERT: P 62 LYS cc_start: 0.8711 (tttt) cc_final: 0.8482 (tttt) REVERT: P 84 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8974 (pt) REVERT: P 101 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8695 (t) REVERT: P 108 LYS cc_start: 0.8911 (mttt) cc_final: 0.8350 (mmmt) REVERT: P 124 LYS cc_start: 0.9000 (mttt) cc_final: 0.8616 (mtmt) REVERT: Q 27 ARG cc_start: 0.7880 (ptt90) cc_final: 0.7406 (ttp80) REVERT: Q 29 ASN cc_start: 0.7937 (m-40) cc_final: 0.7651 (t0) REVERT: Q 43 GLU cc_start: 0.6624 (OUTLIER) cc_final: 0.6150 (tt0) REVERT: Q 80 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.8053 (tt0) REVERT: Q 85 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7764 (ptt180) REVERT: Q 125 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7672 (ptt-90) REVERT: R 7 LYS cc_start: 0.8160 (mtmt) cc_final: 0.7880 (tppt) REVERT: R 11 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.7928 (mttm) REVERT: R 20 TYR cc_start: 0.8246 (m-80) cc_final: 0.7887 (m-80) REVERT: R 21 TYR cc_start: 0.9232 (t80) cc_final: 0.8998 (t80) REVERT: R 23 ARG cc_start: 0.8279 (mpt-90) cc_final: 0.7946 (mtt-85) REVERT: R 74 GLN cc_start: 0.7855 (mm-40) cc_final: 0.7624 (mt0) REVERT: R 85 VAL cc_start: 0.9105 (OUTLIER) cc_final: 0.8878 (t) REVERT: R 89 SER cc_start: 0.8544 (OUTLIER) cc_final: 0.8335 (p) REVERT: R 92 ASP cc_start: 0.8527 (t70) cc_final: 0.8153 (t0) REVERT: R 104 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8300 (tp30) REVERT: R 107 LYS cc_start: 0.9080 (tttt) cc_final: 0.8581 (mtpp) REVERT: R 118 GLN cc_start: 0.7938 (tt0) cc_final: 0.7737 (tt0) REVERT: S 21 ASP cc_start: 0.8304 (t0) cc_final: 0.7829 (p0) REVERT: S 23 ARG cc_start: 0.8395 (ptt-90) cc_final: 0.7776 (ptm-80) REVERT: S 38 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7684 (mtm-85) REVERT: S 43 VAL cc_start: 0.8888 (OUTLIER) cc_final: 0.8631 (p) REVERT: S 78 LYS cc_start: 0.9076 (tttt) cc_final: 0.8814 (mptt) REVERT: S 81 ASP cc_start: 0.8662 (m-30) cc_final: 0.8426 (m-30) REVERT: S 96 SER cc_start: 0.8977 (t) cc_final: 0.8632 (t) REVERT: S 99 LEU cc_start: 0.8064 (mm) cc_final: 0.7434 (mt) REVERT: S 101 ASN cc_start: 0.8320 (m-40) cc_final: 0.7943 (p0) REVERT: S 105 ASN cc_start: 0.8810 (t0) cc_final: 0.8412 (m-40) REVERT: S 109 GLU cc_start: 0.9203 (tt0) cc_final: 0.8754 (mm-30) REVERT: S 112 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8202 (tt0) REVERT: T 24 LYS cc_start: 0.8857 (mmtt) cc_final: 0.8535 (ptmm) REVERT: T 33 TRP cc_start: 0.7708 (p90) cc_final: 0.7343 (p-90) REVERT: T 39 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8961 (mt) REVERT: T 49 ASP cc_start: 0.8172 (t0) cc_final: 0.7850 (t0) REVERT: T 65 TYR cc_start: 0.8693 (t80) cc_final: 0.8256 (t80) REVERT: T 82 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7794 (ttt-90) REVERT: T 88 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8545 (mmm) REVERT: T 122 LYS cc_start: 0.8232 (pttt) cc_final: 0.7975 (ptmt) REVERT: T 126 GLN cc_start: 0.8200 (tt0) cc_final: 0.7792 (tm-30) REVERT: T 129 ARG cc_start: 0.8036 (mtt90) cc_final: 0.7722 (mtp-110) REVERT: Z 47 LEU cc_start: 0.6582 (mp) cc_final: 0.6336 (mp) REVERT: Z 80 ARG cc_start: 0.8138 (mtt90) cc_final: 0.7865 (mmt90) REVERT: Z 101 SER cc_start: 0.8165 (t) cc_final: 0.7602 (p) REVERT: Z 104 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8264 (ptm-80) REVERT: Z 106 GLN cc_start: 0.9063 (tp40) cc_final: 0.8265 (tp40) REVERT: c 26 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8292 (pt0) REVERT: c 50 VAL cc_start: 0.9364 (t) cc_final: 0.9108 (m) REVERT: c 58 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8769 (mt) REVERT: f 100 LEU cc_start: 0.5470 (OUTLIER) cc_final: 0.5157 (mp) REVERT: f 108 VAL cc_start: 0.2528 (OUTLIER) cc_final: 0.1699 (p) REVERT: f 130 VAL cc_start: 0.6519 (t) cc_final: 0.5857 (t) REVERT: g 5 MET cc_start: 0.6819 (mmt) cc_final: 0.6452 (mmm) REVERT: g 6 THR cc_start: 0.8063 (OUTLIER) cc_final: 0.7862 (m) REVERT: g 31 ILE cc_start: 0.7597 (OUTLIER) cc_final: 0.6946 (mm) REVERT: g 42 MET cc_start: 0.8295 (ttt) cc_final: 0.8019 (ttp) REVERT: g 47 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.8037 (mtt90) REVERT: g 91 ASP cc_start: 0.8601 (t0) cc_final: 0.8370 (t0) REVERT: g 118 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7691 (mtp-110) REVERT: g 132 TRP cc_start: 0.7854 (m100) cc_final: 0.7158 (m100) REVERT: g 167 SER cc_start: 0.8302 (OUTLIER) cc_final: 0.7988 (p) REVERT: g 182 CYS cc_start: 0.8660 (t) cc_final: 0.8142 (t) REVERT: g 197 THR cc_start: 0.8294 (OUTLIER) cc_final: 0.8054 (p) REVERT: g 243 PRO cc_start: 0.7152 (Cg_endo) cc_final: 0.6905 (Cg_exo) REVERT: g 270 LEU cc_start: 0.8145 (mt) cc_final: 0.7581 (mp) REVERT: g 297 THR cc_start: 0.7342 (OUTLIER) cc_final: 0.6857 (p) REVERT: A 12 GLU cc_start: 0.8945 (tt0) cc_final: 0.8631 (mm-30) REVERT: A 34 MET cc_start: 0.8893 (mmm) cc_final: 0.8518 (mmp) REVERT: A 41 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8451 (ttt180) REVERT: A 117 ARG cc_start: 0.9022 (ptp-170) cc_final: 0.8611 (ttm110) REVERT: A 134 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8822 (mt) REVERT: A 155 ARG cc_start: 0.9155 (OUTLIER) cc_final: 0.8832 (mtt180) REVERT: A 209 GLU cc_start: 0.8706 (tt0) cc_final: 0.8414 (mm-30) REVERT: A 213 GLU cc_start: 0.8678 (mm-30) cc_final: 0.7866 (tm-30) REVERT: B 57 ILE cc_start: 0.7828 (OUTLIER) cc_final: 0.7504 (mm) REVERT: B 73 ASP cc_start: 0.8483 (m-30) cc_final: 0.8038 (t0) REVERT: B 92 GLN cc_start: 0.8323 (mm-40) cc_final: 0.8099 (mm-40) REVERT: B 110 MET cc_start: 0.9056 (tpp) cc_final: 0.8826 (mmp) REVERT: B 150 ILE cc_start: 0.9330 (mm) cc_final: 0.9114 (mm) REVERT: B 162 ARG cc_start: 0.8765 (mtp-110) cc_final: 0.8496 (mtm-85) REVERT: B 175 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8672 (mm-30) REVERT: B 203 SER cc_start: 0.9145 (p) cc_final: 0.8783 (t) REVERT: C 68 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8058 (mtp180) REVERT: C 77 SER cc_start: 0.9305 (t) cc_final: 0.9039 (p) REVERT: C 121 ARG cc_start: 0.6826 (ptt90) cc_final: 0.6282 (mtm-85) REVERT: C 156 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8885 (mp) REVERT: C 216 MET cc_start: 0.8860 (mtm) cc_final: 0.8555 (mtp) REVERT: C 227 ARG cc_start: 0.9101 (ttt-90) cc_final: 0.8763 (mmm160) REVERT: E 22 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8529 (tttp) REVERT: E 87 MET cc_start: 0.9141 (mmm) cc_final: 0.8902 (mmm) REVERT: E 91 SER cc_start: 0.8701 (t) cc_final: 0.8298 (p) REVERT: E 158 ASP cc_start: 0.8738 (m-30) cc_final: 0.8356 (m-30) REVERT: E 164 LEU cc_start: 0.8254 (mt) cc_final: 0.7935 (mt) REVERT: E 182 MET cc_start: 0.8374 (ttm) cc_final: 0.8035 (ttt) REVERT: E 197 ASN cc_start: 0.8669 (t0) cc_final: 0.8066 (p0) REVERT: E 198 ARG cc_start: 0.8767 (tmm-80) cc_final: 0.8480 (ttt90) REVERT: E 205 PHE cc_start: 0.8870 (m-80) cc_final: 0.8560 (m-80) REVERT: E 224 ASN cc_start: 0.8742 (m-40) cc_final: 0.8462 (m110) REVERT: E 237 SER cc_start: 0.9176 (t) cc_final: 0.8795 (p) REVERT: E 248 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8563 (mt) REVERT: G 1 MET cc_start: 0.7770 (mmm) cc_final: 0.7412 (tpp) REVERT: G 17 GLU cc_start: 0.8902 (tt0) cc_final: 0.8443 (tm-30) REVERT: G 32 MET cc_start: 0.8606 (mtp) cc_final: 0.8257 (mtm) REVERT: G 43 GLU cc_start: 0.8307 (mt-10) cc_final: 0.7948 (pt0) REVERT: G 57 ASP cc_start: 0.7889 (p0) cc_final: 0.7638 (p0) REVERT: G 70 HIS cc_start: 0.7928 (m170) cc_final: 0.7540 (m170) REVERT: G 149 LYS cc_start: 0.7590 (tttt) cc_final: 0.7371 (mmtt) REVERT: G 151 ASP cc_start: 0.7442 (m-30) cc_final: 0.7067 (m-30) REVERT: G 154 ARG cc_start: 0.8253 (mtt180) cc_final: 0.7607 (mtp-110) REVERT: G 163 ASN cc_start: 0.7310 (p0) cc_final: 0.6904 (t0) REVERT: G 171 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8764 (p) REVERT: G 226 GLU cc_start: 0.8139 (tt0) cc_final: 0.7801 (mt-10) REVERT: H 10 LYS cc_start: 0.9054 (mttt) cc_final: 0.8662 (ptmt) REVERT: H 51 ILE cc_start: 0.7796 (pt) cc_final: 0.7488 (pt) REVERT: H 58 LYS cc_start: 0.8507 (mttt) cc_final: 0.8202 (ptmt) REVERT: H 99 ARG cc_start: 0.8406 (mmt90) cc_final: 0.7996 (ttt180) REVERT: H 144 ILE cc_start: 0.9427 (mp) cc_final: 0.9136 (mt) REVERT: H 163 GLN cc_start: 0.8497 (tt0) cc_final: 0.8120 (tt0) REVERT: I 3 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.8969 (mp) REVERT: I 17 LYS cc_start: 0.8551 (pttm) cc_final: 0.8319 (ptmm) REVERT: I 73 THR cc_start: 0.8696 (m) cc_final: 0.8350 (p) REVERT: I 92 ARG cc_start: 0.8402 (mtm180) cc_final: 0.8164 (ttm110) REVERT: I 116 HIS cc_start: 0.8785 (t70) cc_final: 0.8063 (t-170) REVERT: I 139 LYS cc_start: 0.7531 (tmtp) cc_final: 0.7302 (ptmm) REVERT: I 141 ARG cc_start: 0.8011 (mtt180) cc_final: 0.7428 (ptm160) REVERT: I 142 SER cc_start: 0.7987 (m) cc_final: 0.7582 (m) REVERT: I 151 GLU cc_start: 0.9016 (tt0) cc_final: 0.8726 (mt-10) REVERT: I 158 ILE cc_start: 0.8472 (mt) cc_final: 0.8120 (mm) REVERT: I 159 SER cc_start: 0.8287 (m) cc_final: 0.7685 (t) REVERT: I 163 GLU cc_start: 0.7533 (tm-30) cc_final: 0.7158 (mm-30) REVERT: I 167 GLN cc_start: 0.7882 (mm-40) cc_final: 0.7265 (mm110) REVERT: I 191 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7447 (mt-10) REVERT: J 24 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7776 (ttp80) REVERT: J 34 GLU cc_start: 0.8261 (mt-10) cc_final: 0.8018 (mt-10) REVERT: J 88 ASP cc_start: 0.8512 (m-30) cc_final: 0.7944 (t0) REVERT: J 135 ILE cc_start: 0.9294 (mm) cc_final: 0.9047 (mm) REVERT: J 146 SER cc_start: 0.9424 (m) cc_final: 0.9176 (t) REVERT: J 177 ASN cc_start: 0.8481 (m-40) cc_final: 0.8273 (m110) REVERT: L 8 ARG cc_start: 0.9015 (ttm-80) cc_final: 0.8778 (mtp180) REVERT: L 16 ILE cc_start: 0.8918 (mm) cc_final: 0.8583 (mt) REVERT: L 39 ASN cc_start: 0.8014 (t0) cc_final: 0.7590 (p0) REVERT: L 48 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.7900 (tppt) REVERT: L 63 THR cc_start: 0.9175 (p) cc_final: 0.8775 (t) REVERT: L 72 ILE cc_start: 0.9106 (mp) cc_final: 0.8873 (mm) REVERT: L 93 LEU cc_start: 0.9020 (mt) cc_final: 0.8668 (mt) REVERT: L 97 ARG cc_start: 0.8672 (mtp-110) cc_final: 0.8452 (ttp80) REVERT: L 130 GLU cc_start: 0.8598 (tt0) cc_final: 0.8396 (tt0) REVERT: N 9 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8363 (mttm) REVERT: N 27 LYS cc_start: 0.8527 (pttt) cc_final: 0.8106 (mmtt) REVERT: N 56 ASP cc_start: 0.8785 (m-30) cc_final: 0.8537 (m-30) REVERT: N 100 LYS cc_start: 0.8530 (tttt) cc_final: 0.8139 (ttpp) REVERT: N 142 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7655 (mm-30) REVERT: O 86 LYS cc_start: 0.9308 (tppp) cc_final: 0.9071 (mmmt) REVERT: O 87 GLU cc_start: 0.8650 (tp30) cc_final: 0.8247 (mt-10) REVERT: O 96 LYS cc_start: 0.8921 (mttt) cc_final: 0.8698 (mttp) REVERT: O 143 LYS cc_start: 0.8633 (tmmt) cc_final: 0.8241 (tppt) REVERT: O 147 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8164 (ttp-110) REVERT: V 4 ASP cc_start: 0.8452 (t70) cc_final: 0.8218 (p0) REVERT: V 13 VAL cc_start: 0.9339 (t) cc_final: 0.9089 (m) REVERT: V 61 ARG cc_start: 0.9131 (mtm110) cc_final: 0.8928 (ttp80) REVERT: W 9 ASP cc_start: 0.8793 (m-30) cc_final: 0.8590 (m-30) REVERT: W 31 SER cc_start: 0.9149 (t) cc_final: 0.8754 (m) REVERT: W 36 ARG cc_start: 0.8397 (mmt90) cc_final: 0.8100 (mmm160) REVERT: W 54 ASP cc_start: 0.8704 (t70) cc_final: 0.8414 (t0) REVERT: W 76 SER cc_start: 0.9427 (t) cc_final: 0.9117 (p) REVERT: W 78 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8972 (mtt-85) REVERT: W 84 LYS cc_start: 0.8906 (mttt) cc_final: 0.8485 (pttm) REVERT: W 85 ASP cc_start: 0.8822 (m-30) cc_final: 0.8388 (m-30) REVERT: W 90 GLN cc_start: 0.8917 (pt0) cc_final: 0.8518 (pt0) REVERT: W 91 ASN cc_start: 0.9097 (t0) cc_final: 0.8735 (t0) REVERT: W 104 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8663 (pp) REVERT: X 50 ILE cc_start: 0.9115 (mt) cc_final: 0.8745 (pt) REVERT: X 64 SER cc_start: 0.8888 (m) cc_final: 0.8553 (t) REVERT: X 69 CYS cc_start: 0.8929 (m) cc_final: 0.8640 (m) REVERT: X 127 ASN cc_start: 0.8967 (m-40) cc_final: 0.8625 (t0) REVERT: Y 18 LEU cc_start: 0.8997 (mt) cc_final: 0.8728 (mp) REVERT: Y 19 GLN cc_start: 0.9022 (mp10) cc_final: 0.8814 (mp10) REVERT: Y 20 ARG cc_start: 0.8504 (ptt180) cc_final: 0.8175 (ptm-80) REVERT: Y 42 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8759 (mt-10) REVERT: Y 61 ARG cc_start: 0.8937 (tpt170) cc_final: 0.8539 (mmm-85) REVERT: Y 68 LYS cc_start: 0.8973 (mttt) cc_final: 0.8608 (mppt) REVERT: Y 69 THR cc_start: 0.9242 (m) cc_final: 0.8579 (p) REVERT: Y 70 THR cc_start: 0.9230 (m) cc_final: 0.8912 (p) REVERT: Y 85 ASN cc_start: 0.8991 (m-40) cc_final: 0.8655 (m-40) REVERT: Y 86 GLU cc_start: 0.8744 (tp30) cc_final: 0.8455 (tp30) REVERT: b 8 LEU cc_start: 0.9004 (mt) cc_final: 0.8718 (mt) REVERT: b 16 LYS cc_start: 0.9196 (mttt) cc_final: 0.8858 (mmmt) REVERT: b 34 ASP cc_start: 0.8213 (t0) cc_final: 0.7130 (p0) REVERT: b 42 LYS cc_start: 0.8162 (tptt) cc_final: 0.7890 (mmtm) REVERT: b 72 ARG cc_start: 0.8810 (ptt180) cc_final: 0.8519 (ptm-80) REVERT: b 81 ARG cc_start: 0.8272 (ttt90) cc_final: 0.7913 (ttt90) REVERT: e 25 LYS cc_start: 0.8447 (pttt) cc_final: 0.7964 (mmtm) REVERT: e 36 MET cc_start: 0.8821 (ttp) cc_final: 0.8619 (ttm) REVERT: e 40 ARG cc_start: 0.8897 (ttt180) cc_final: 0.8553 (mtm110) REVERT: e 56 ASN cc_start: 0.8991 (t0) cc_final: 0.8775 (t0) REVERT: x 80 VAL cc_start: 0.9600 (p) cc_final: 0.9358 (m) REVERT: x 114 ARG cc_start: 0.7807 (mtt90) cc_final: 0.7535 (mtt90) REVERT: x 125 LYS cc_start: 0.9177 (tptt) cc_final: 0.8947 (ttpt) REVERT: x 145 GLN cc_start: 0.8769 (tt0) cc_final: 0.8404 (mm110) REVERT: x 147 GLU cc_start: 0.8769 (mp0) cc_final: 0.8393 (mp0) REVERT: x 157 ASP cc_start: 0.8591 (p0) cc_final: 0.8330 (p0) REVERT: x 172 LYS cc_start: 0.8856 (mptt) cc_final: 0.8552 (mtpp) REVERT: x 178 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8383 (mtt-85) REVERT: x 229 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8305 (mp) REVERT: x 240 ASN cc_start: 0.8822 (m-40) cc_final: 0.8558 (m-40) REVERT: y 10 ASP cc_start: 0.8660 (t70) cc_final: 0.8239 (t0) REVERT: y 64 ARG cc_start: 0.8440 (mtt180) cc_final: 0.8070 (mtm-85) REVERT: y 65 LEU cc_start: 0.8702 (tp) cc_final: 0.8463 (tp) REVERT: y 75 ASP cc_start: 0.8513 (m-30) cc_final: 0.8235 (m-30) REVERT: y 106 GLU cc_start: 0.8787 (mp0) cc_final: 0.8488 (mp0) REVERT: y 278 SER cc_start: 0.9087 (m) cc_final: 0.8457 (p) REVERT: y 280 MET cc_start: 0.8604 (mmm) cc_final: 0.8289 (tpt) REVERT: y 307 HIS cc_start: 0.8001 (p-80) cc_final: 0.7629 (p-80) REVERT: y 309 HIS cc_start: 0.8088 (m-70) cc_final: 0.7563 (m170) REVERT: y 342 GLU cc_start: 0.8777 (pm20) cc_final: 0.8347 (tp30) REVERT: y 345 ARG cc_start: 0.8553 (ttm170) cc_final: 0.8300 (ttt180) REVERT: y 365 ASP cc_start: 0.9137 (p0) cc_final: 0.8921 (p0) REVERT: y 367 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8149 (tp) REVERT: y 377 ASP cc_start: 0.8779 (t70) cc_final: 0.8555 (t0) REVERT: y 378 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8840 (pt) REVERT: u 74 GLN cc_start: 0.8494 (mt0) cc_final: 0.8184 (pt0) REVERT: u 178 PHE cc_start: 0.9112 (m-80) cc_final: 0.8671 (m-10) REVERT: u 180 GLN cc_start: 0.9368 (OUTLIER) cc_final: 0.9164 (tm-30) REVERT: u 213 LYS cc_start: 0.8794 (mttt) cc_final: 0.8404 (tptp) REVERT: u 217 HIS cc_start: 0.8955 (p90) cc_final: 0.8343 (p90) REVERT: u 219 LYS cc_start: 0.8546 (pttt) cc_final: 0.8202 (tttp) REVERT: u 225 THR cc_start: 0.7816 (OUTLIER) cc_final: 0.7457 (p) REVERT: u 228 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8150 (mt-10) REVERT: u 253 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8189 (mp) REVERT: u 299 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.7191 (ppp) REVERT: u 307 ASP cc_start: 0.8359 (t0) cc_final: 0.8116 (m-30) REVERT: u 403 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8184 (mm-30) REVERT: u 481 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8581 (mp0) REVERT: u 482 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7887 (pt0) REVERT: u 486 ASP cc_start: 0.7929 (t0) cc_final: 0.6719 (t0) REVERT: u 594 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8887 (mp) REVERT: u 596 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8434 (mtt) REVERT: u 715 TYR cc_start: 0.8861 (m-80) cc_final: 0.8590 (m-10) REVERT: u 738 ARG cc_start: 0.8070 (mmt180) cc_final: 0.7819 (ttm110) REVERT: u 766 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8301 (pp) REVERT: w 183 GLU cc_start: 0.8471 (tp30) cc_final: 0.8218 (tt0) REVERT: w 185 TYR cc_start: 0.8291 (m-80) cc_final: 0.8084 (m-10) REVERT: w 194 LYS cc_start: 0.8641 (mttt) cc_final: 0.8089 (tmtt) REVERT: w 218 TYR cc_start: 0.8443 (t80) cc_final: 0.7890 (t80) REVERT: w 223 GLU cc_start: 0.8068 (pt0) cc_final: 0.7465 (tp30) REVERT: w 225 TRP cc_start: 0.8053 (m-10) cc_final: 0.7327 (m-10) REVERT: w 230 MET cc_start: 0.8466 (mmm) cc_final: 0.8160 (mtp) REVERT: w 235 ARG cc_start: 0.8324 (ttp80) cc_final: 0.8064 (ttp80) REVERT: w 243 GLU cc_start: 0.7859 (tt0) cc_final: 0.7229 (tp30) REVERT: w 248 ARG cc_start: 0.6896 (mtt180) cc_final: 0.6639 (tpp-160) REVERT: w 251 ASN cc_start: 0.7511 (OUTLIER) cc_final: 0.7285 (m110) REVERT: w 301 THR cc_start: 0.4041 (p) cc_final: 0.3783 (m) REVERT: w 327 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7425 (tt) REVERT: w 328 LYS cc_start: 0.8533 (mttt) cc_final: 0.7689 (mmmt) REVERT: w 331 GLU cc_start: 0.6518 (mt-10) cc_final: 0.6155 (mt-10) REVERT: w 333 GLU cc_start: 0.7786 (mt-10) cc_final: 0.6900 (tm-30) REVERT: w 358 ASP cc_start: 0.8264 (m-30) cc_final: 0.7557 (t0) REVERT: w 396 ASP cc_start: 0.7865 (m-30) cc_final: 0.7410 (t0) REVERT: w 397 GLN cc_start: 0.8286 (pt0) cc_final: 0.7814 (pt0) REVERT: w 416 GLU cc_start: 0.8256 (mt-10) cc_final: 0.8036 (mt-10) REVERT: v 11 TYR cc_start: 0.7521 (m-80) cc_final: 0.6903 (m-80) REVERT: v 16 ASP cc_start: 0.6050 (m-30) cc_final: 0.5800 (p0) REVERT: v 30 HIS cc_start: 0.5891 (t70) cc_final: 0.5567 (t70) REVERT: v 74 ARG cc_start: 0.6403 (ptt90) cc_final: 0.6152 (ttp-170) REVERT: v 85 LEU cc_start: 0.8577 (mt) cc_final: 0.8321 (mt) REVERT: v 99 ASN cc_start: 0.4140 (m-40) cc_final: 0.3479 (m-40) REVERT: v 176 PRO cc_start: 0.7360 (Cg_exo) cc_final: 0.6778 (Cg_endo) REVERT: v 182 ASN cc_start: 0.7354 (m-40) cc_final: 0.7112 (t160) REVERT: v 183 ARG cc_start: 0.7709 (mtt90) cc_final: 0.7468 (mtm-85) REVERT: v 188 MET cc_start: 0.7558 (ptp) cc_final: 0.7344 (mtt) REVERT: v 213 MET cc_start: 0.8270 (mmm) cc_final: 0.6917 (ptm) REVERT: v 226 HIS cc_start: 0.6589 (t-90) cc_final: 0.6078 (t-90) REVERT: v 243 THR cc_start: 0.7094 (m) cc_final: 0.6689 (m) REVERT: v 244 MET cc_start: 0.6711 (mtm) cc_final: 0.5875 (mpp) REVERT: v 267 LYS cc_start: 0.8944 (mttt) cc_final: 0.8647 (ptmm) REVERT: v 268 CYS cc_start: 0.8073 (t) cc_final: 0.7710 (m) REVERT: v 297 ASP cc_start: 0.5853 (p0) cc_final: 0.5354 (p0) REVERT: t 250 MET cc_start: 0.4633 (OUTLIER) cc_final: 0.3290 (pmm) REVERT: t 251 ARG cc_start: 0.7524 (mtt180) cc_final: 0.7269 (mtp85) REVERT: t 299 ASN cc_start: 0.7858 (m-40) cc_final: 0.7350 (p0) REVERT: t 305 LYS cc_start: 0.7564 (OUTLIER) cc_final: 0.7179 (ttmm) REVERT: t 422 GLU cc_start: 0.7385 (mp0) cc_final: 0.7046 (pt0) REVERT: t 437 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7977 (tm-30) REVERT: t 440 GLU cc_start: 0.8414 (mt-10) cc_final: 0.7742 (tm-30) REVERT: t 455 GLU cc_start: 0.8336 (tm-30) cc_final: 0.7835 (tp30) REVERT: t 470 VAL cc_start: 0.8800 (t) cc_final: 0.8506 (t) REVERT: t 471 GLU cc_start: 0.7765 (tt0) cc_final: 0.7390 (pm20) outliers start: 401 outliers final: 60 residues processed: 2178 average time/residue: 0.8833 time to fit residues: 3115.3329 Evaluate side-chains 1305 residues out of total 5267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 1180 time to evaluate : 5.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 79 HIS Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain M residue 33 ARG Chi-restraints excluded: chain M residue 45 ARG Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 125 GLU Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain P residue 34 MET Chi-restraints excluded: chain P residue 81 ARG Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 101 THR Chi-restraints excluded: chain Q residue 43 GLU Chi-restraints excluded: chain Q residue 72 VAL Chi-restraints excluded: chain Q residue 80 GLN Chi-restraints excluded: chain Q residue 85 ARG Chi-restraints excluded: chain Q residue 118 THR Chi-restraints excluded: chain Q residue 125 ARG Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 11 LYS Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 89 SER Chi-restraints excluded: chain R residue 110 ASP Chi-restraints excluded: chain S residue 38 ARG Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 39 LEU Chi-restraints excluded: chain T residue 82 ARG Chi-restraints excluded: chain T residue 88 MET Chi-restraints excluded: chain Z residue 104 ARG Chi-restraints excluded: chain c residue 26 GLN Chi-restraints excluded: chain c residue 58 LEU Chi-restraints excluded: chain f residue 100 LEU Chi-restraints excluded: chain f residue 102 VAL Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 147 THR Chi-restraints excluded: chain g residue 6 THR Chi-restraints excluded: chain g residue 31 ILE Chi-restraints excluded: chain g residue 46 THR Chi-restraints excluded: chain g residue 47 ARG Chi-restraints excluded: chain g residue 64 HIS Chi-restraints excluded: chain g residue 118 ARG Chi-restraints excluded: chain g residue 167 SER Chi-restraints excluded: chain g residue 197 THR Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain g residue 200 VAL Chi-restraints excluded: chain g residue 231 ASP Chi-restraints excluded: chain g residue 240 CYS Chi-restraints excluded: chain g residue 297 THR Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain J residue 24 ARG Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 48 LYS Chi-restraints excluded: chain N residue 9 LYS Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain N residue 145 THR Chi-restraints excluded: chain O residue 147 ARG Chi-restraints excluded: chain V residue 43 THR Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain W residue 78 ARG Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain X residue 7 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain Y residue 40 ILE Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain e residue 12 VAL Chi-restraints excluded: chain x residue 86 THR Chi-restraints excluded: chain x residue 146 VAL Chi-restraints excluded: chain x residue 178 ARG Chi-restraints excluded: chain x residue 229 ILE Chi-restraints excluded: chain y residue 367 ILE Chi-restraints excluded: chain y residue 378 ILE Chi-restraints excluded: chain u residue 136 THR Chi-restraints excluded: chain u residue 180 GLN Chi-restraints excluded: chain u residue 207 LEU Chi-restraints excluded: chain u residue 222 LEU Chi-restraints excluded: chain u residue 225 THR Chi-restraints excluded: chain u residue 253 LEU Chi-restraints excluded: chain u residue 299 MET Chi-restraints excluded: chain u residue 594 LEU Chi-restraints excluded: chain u residue 596 MET Chi-restraints excluded: chain u residue 597 VAL Chi-restraints excluded: chain u residue 687 VAL Chi-restraints excluded: chain u residue 766 LEU Chi-restraints excluded: chain w residue 226 THR Chi-restraints excluded: chain w residue 251 ASN Chi-restraints excluded: chain w residue 327 LEU Chi-restraints excluded: chain w residue 395 THR Chi-restraints excluded: chain t residue 250 MET Chi-restraints excluded: chain t residue 305 LYS Chi-restraints excluded: chain t residue 362 ASN Chi-restraints excluded: chain t residue 363 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 757 random chunks: chunk 639 optimal weight: 4.9990 chunk 573 optimal weight: 4.9990 chunk 318 optimal weight: 4.9990 chunk 195 optimal weight: 2.9990 chunk 387 optimal weight: 4.9990 chunk 306 optimal weight: 6.9990 chunk 593 optimal weight: 0.8980 chunk 229 optimal weight: 3.9990 chunk 360 optimal weight: 0.8980 chunk 441 optimal weight: 0.9990 chunk 687 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 31 ASN F 83 ASN F 114 ASN Q 11 GLN Q 80 GLN Q 86 GLN R 29 HIS R 31 ASN R 74 GLN T 63 HIS T 105 GLN Z 106 GLN c 26 GLN f 135 HIS ** g 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 133 ASN ** g 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 226 HIS g 305 ASN ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 HIS C 272 HIS E 98 ASN E 179 ASN E 209 HIS H 76 GLN H 157 HIS I 87 ASN I 116 HIS I 168 GLN J 125 HIS L 106 HIS O 26 ASN O 38 ASN ** O 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 103 ASN V 49 GLN W 15 ASN W 70 ASN W 98 GLN X 46 HIS X 63 ASN Y 124 ASN b 29 ASN ** b 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 51 GLN e 22 GLN x 145 GLN ** x 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 232 ASN y 92 GLN y 129 HIS y 271 HIS y 290 ASN y 318 ASN y 344 GLN ** u 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 131 HIS u 144 HIS u 235 GLN u 256 HIS ** u 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 232 GLN w 251 ASN ** w 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 422 GLN v 46 HIS v 77 ASN v 118 GLN v 182 ASN v 230 ASN v 233 ASN v 255 HIS v 503 GLN t 362 ASN t 469 ASN Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 88868 Z= 0.236 Angle : 0.672 14.349 127913 Z= 0.343 Chirality : 0.040 0.336 15645 Planarity : 0.005 0.061 10091 Dihedral : 23.398 179.241 32819 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.94 % Favored : 95.93 % Rotamer: Outliers : 5.80 % Allowed : 18.52 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.10), residues: 5968 helix: 0.65 (0.11), residues: 2093 sheet: -0.87 (0.15), residues: 1024 loop : -1.54 (0.10), residues: 2851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP g 219 HIS 0.008 0.001 HIS v 255 PHE 0.020 0.002 PHE x 96 TYR 0.018 0.002 TYR M 114 ARG 0.018 0.001 ARG y 31 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11936 Ramachandran restraints generated. 5968 Oldfield, 0 Emsley, 5968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11936 Ramachandran restraints generated. 5968 Oldfield, 0 Emsley, 5968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1588 residues out of total 5267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 303 poor density : 1285 time to evaluate : 5.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 32 ASP cc_start: 0.8611 (OUTLIER) cc_final: 0.8389 (t0) REVERT: F 44 LYS cc_start: 0.8919 (ttpt) cc_final: 0.8585 (tppt) REVERT: F 75 SER cc_start: 0.9219 (t) cc_final: 0.9003 (m) REVERT: F 81 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8373 (ptt90) REVERT: F 88 MET cc_start: 0.7389 (ttm) cc_final: 0.6945 (tpp) REVERT: F 98 GLU cc_start: 0.8171 (tp30) cc_final: 0.7925 (tp30) REVERT: F 106 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8391 (tt0) REVERT: F 118 ASN cc_start: 0.9129 (m-40) cc_final: 0.8914 (m-40) REVERT: F 124 ASP cc_start: 0.8498 (t0) cc_final: 0.8199 (t0) REVERT: F 168 THR cc_start: 0.8953 (OUTLIER) cc_final: 0.8502 (m) REVERT: F 185 SER cc_start: 0.8710 (t) cc_final: 0.8308 (p) REVERT: F 204 ARG cc_start: 0.8136 (mmm160) cc_final: 0.7839 (mmm160) REVERT: M 15 ASN cc_start: 0.6623 (m-40) cc_final: 0.6280 (t0) REVERT: M 22 LEU cc_start: 0.6373 (mt) cc_final: 0.5922 (pp) REVERT: M 63 LYS cc_start: 0.7452 (mtmm) cc_final: 0.6951 (pttp) REVERT: M 91 LEU cc_start: 0.5136 (OUTLIER) cc_final: 0.4777 (mt) REVERT: M 96 ARG cc_start: 0.7390 (ptt-90) cc_final: 0.7024 (ptp90) REVERT: P 21 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.7638 (p0) REVERT: P 24 GLN cc_start: 0.8425 (mt0) cc_final: 0.8000 (mt0) REVERT: P 30 TYR cc_start: 0.7449 (OUTLIER) cc_final: 0.6970 (t80) REVERT: P 31 GLU cc_start: 0.8649 (tt0) cc_final: 0.8414 (mm-30) REVERT: P 32 GLN cc_start: 0.8998 (tt0) cc_final: 0.8663 (mm110) REVERT: P 51 ARG cc_start: 0.8859 (tpt90) cc_final: 0.8429 (ttm110) REVERT: P 81 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.6412 (mtp-110) REVERT: Q 27 ARG cc_start: 0.7912 (ptt90) cc_final: 0.7539 (ttp80) REVERT: Q 29 ASN cc_start: 0.8095 (m-40) cc_final: 0.7636 (t0) REVERT: Q 43 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6687 (tt0) REVERT: Q 66 VAL cc_start: 0.6932 (t) cc_final: 0.6572 (p) REVERT: Q 107 GLU cc_start: 0.8431 (tp30) cc_final: 0.8182 (pt0) REVERT: R 7 LYS cc_start: 0.8283 (mtmt) cc_final: 0.8076 (tppt) REVERT: R 11 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7859 (mttm) REVERT: R 18 GLU cc_start: 0.9111 (tt0) cc_final: 0.8616 (tp30) REVERT: R 20 TYR cc_start: 0.8500 (m-80) cc_final: 0.8170 (m-80) REVERT: R 21 TYR cc_start: 0.9153 (t80) cc_final: 0.8946 (t80) REVERT: R 23 ARG cc_start: 0.8324 (mpt-90) cc_final: 0.8064 (mtt-85) REVERT: R 37 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7725 (tp30) REVERT: R 73 LEU cc_start: 0.7803 (tp) cc_final: 0.7486 (tp) REVERT: R 77 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7375 (mp0) REVERT: R 92 ASP cc_start: 0.8746 (t70) cc_final: 0.8244 (t0) REVERT: R 97 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7652 (mp0) REVERT: R 107 LYS cc_start: 0.9218 (tttt) cc_final: 0.8784 (mtpp) REVERT: S 21 ASP cc_start: 0.8104 (t0) cc_final: 0.7840 (p0) REVERT: S 43 VAL cc_start: 0.8949 (OUTLIER) cc_final: 0.8747 (p) REVERT: S 78 LYS cc_start: 0.9064 (tttt) cc_final: 0.8801 (mptt) REVERT: S 96 SER cc_start: 0.8943 (t) cc_final: 0.8742 (t) REVERT: S 99 LEU cc_start: 0.7737 (mm) cc_final: 0.7357 (mt) REVERT: S 109 GLU cc_start: 0.9204 (tt0) cc_final: 0.8803 (tm-30) REVERT: S 112 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8150 (tt0) REVERT: T 24 LYS cc_start: 0.8900 (mmtt) cc_final: 0.8571 (ptmm) REVERT: T 88 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8569 (mpp) REVERT: T 122 LYS cc_start: 0.8126 (pttt) cc_final: 0.7803 (pptt) REVERT: T 126 GLN cc_start: 0.8591 (tt0) cc_final: 0.8120 (tm-30) REVERT: T 129 ARG cc_start: 0.8010 (mtt90) cc_final: 0.7600 (mtp-110) REVERT: Z 97 ILE cc_start: 0.8585 (mt) cc_final: 0.8384 (mm) REVERT: Z 101 SER cc_start: 0.8054 (t) cc_final: 0.7554 (p) REVERT: Z 106 GLN cc_start: 0.8900 (tp-100) cc_final: 0.8608 (tp40) REVERT: c 13 ARG cc_start: 0.8527 (mmm-85) cc_final: 0.8025 (mmm-85) REVERT: c 26 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8315 (pt0) REVERT: f 114 ILE cc_start: 0.2773 (OUTLIER) cc_final: 0.2454 (tp) REVERT: f 123 SER cc_start: 0.8274 (t) cc_final: 0.7760 (p) REVERT: f 132 MET cc_start: 0.6041 (mtt) cc_final: 0.5672 (mmt) REVERT: f 140 TYR cc_start: 0.6892 (t80) cc_final: 0.6504 (t80) REVERT: g 5 MET cc_start: 0.6929 (mmt) cc_final: 0.6722 (mmm) REVERT: g 47 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7772 (mtt90) REVERT: g 72 SER cc_start: 0.8186 (OUTLIER) cc_final: 0.7984 (p) REVERT: g 101 PHE cc_start: 0.8085 (m-80) cc_final: 0.7880 (m-80) REVERT: g 118 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.7969 (ttt90) REVERT: g 182 CYS cc_start: 0.8847 (t) cc_final: 0.8421 (p) REVERT: A 23 THR cc_start: 0.9239 (OUTLIER) cc_final: 0.8953 (m) REVERT: A 177 MET cc_start: 0.8519 (mtp) cc_final: 0.8309 (mtp) REVERT: A 200 ASP cc_start: 0.8710 (OUTLIER) cc_final: 0.8269 (m-30) REVERT: B 57 ILE cc_start: 0.7777 (OUTLIER) cc_final: 0.7548 (mm) REVERT: B 73 ASP cc_start: 0.8516 (m-30) cc_final: 0.8059 (t0) REVERT: B 113 MET cc_start: 0.8835 (mtm) cc_final: 0.8561 (ttm) REVERT: B 168 MET cc_start: 0.8615 (ttm) cc_final: 0.8410 (ttm) REVERT: B 175 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8731 (mm-30) REVERT: B 203 SER cc_start: 0.9242 (p) cc_final: 0.8881 (t) REVERT: C 61 MET cc_start: 0.8502 (tpp) cc_final: 0.7576 (pmm) REVERT: C 68 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.7969 (mtp180) REVERT: C 77 SER cc_start: 0.9234 (t) cc_final: 0.8993 (p) REVERT: C 123 ARG cc_start: 0.8148 (ptm160) cc_final: 0.7100 (mpt-90) REVERT: C 144 SER cc_start: 0.8525 (p) cc_final: 0.8275 (p) REVERT: C 145 LYS cc_start: 0.8384 (mttt) cc_final: 0.8063 (mttm) REVERT: C 267 GLN cc_start: 0.8788 (tm-30) cc_final: 0.8276 (tm-30) REVERT: E 22 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8270 (ttmm) REVERT: E 40 GLU cc_start: 0.8676 (pp20) cc_final: 0.8467 (pp20) REVERT: E 71 LYS cc_start: 0.8212 (mtpt) cc_final: 0.7654 (mtpp) REVERT: E 91 SER cc_start: 0.8931 (t) cc_final: 0.8681 (p) REVERT: E 151 ASP cc_start: 0.8799 (OUTLIER) cc_final: 0.8359 (t0) REVERT: E 182 MET cc_start: 0.8245 (ttm) cc_final: 0.8027 (ttt) REVERT: E 197 ASN cc_start: 0.8656 (t0) cc_final: 0.8341 (p0) REVERT: E 205 PHE cc_start: 0.8718 (m-80) cc_final: 0.8250 (m-80) REVERT: E 224 ASN cc_start: 0.8711 (m-40) cc_final: 0.8421 (m-40) REVERT: E 237 SER cc_start: 0.9147 (t) cc_final: 0.8823 (m) REVERT: E 242 LYS cc_start: 0.9041 (mmmt) cc_final: 0.8780 (mtpt) REVERT: E 248 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8723 (mt) REVERT: E 253 ASP cc_start: 0.8627 (t70) cc_final: 0.8110 (m-30) REVERT: G 1 MET cc_start: 0.7827 (mmm) cc_final: 0.7374 (tpp) REVERT: G 17 GLU cc_start: 0.8913 (tt0) cc_final: 0.8490 (tm-30) REVERT: G 29 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8356 (mm-30) REVERT: G 70 HIS cc_start: 0.7461 (m170) cc_final: 0.7058 (m170) REVERT: G 103 ASP cc_start: 0.8439 (t70) cc_final: 0.8230 (t70) REVERT: G 149 LYS cc_start: 0.7892 (tttt) cc_final: 0.7583 (mmtt) REVERT: G 154 ARG cc_start: 0.8194 (mtt180) cc_final: 0.7795 (mtm110) REVERT: G 163 ASN cc_start: 0.7280 (p0) cc_final: 0.6713 (t0) REVERT: G 204 GLU cc_start: 0.8396 (mm-30) cc_final: 0.7995 (mt-10) REVERT: G 226 GLU cc_start: 0.7907 (tt0) cc_final: 0.7703 (mt-10) REVERT: H 10 LYS cc_start: 0.9126 (mttt) cc_final: 0.8695 (ptmt) REVERT: H 50 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7469 (tm-30) REVERT: H 58 LYS cc_start: 0.8288 (mttt) cc_final: 0.7836 (pttm) REVERT: H 78 ARG cc_start: 0.8254 (mtp85) cc_final: 0.7745 (mtp85) REVERT: H 99 ARG cc_start: 0.8351 (mmt90) cc_final: 0.8037 (ttp80) REVERT: I 17 LYS cc_start: 0.8544 (pttm) cc_final: 0.8333 (ptmm) REVERT: I 116 HIS cc_start: 0.8778 (t-90) cc_final: 0.8046 (t-170) REVERT: I 139 LYS cc_start: 0.7644 (tmtp) cc_final: 0.7220 (ptmm) REVERT: I 141 ARG cc_start: 0.8120 (mtt180) cc_final: 0.7611 (ptm160) REVERT: I 151 GLU cc_start: 0.8974 (tt0) cc_final: 0.8641 (tm-30) REVERT: I 159 SER cc_start: 0.8116 (m) cc_final: 0.7791 (t) REVERT: I 163 GLU cc_start: 0.7674 (tm-30) cc_final: 0.7235 (tp30) REVERT: I 167 GLN cc_start: 0.7891 (mm-40) cc_final: 0.7531 (tp40) REVERT: J 34 GLU cc_start: 0.8355 (mt-10) cc_final: 0.8089 (mt-10) REVERT: J 88 ASP cc_start: 0.8473 (m-30) cc_final: 0.7919 (t0) REVERT: L 39 ASN cc_start: 0.7959 (t0) cc_final: 0.7676 (p0) REVERT: L 48 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7836 (tppt) REVERT: L 130 GLU cc_start: 0.8514 (tt0) cc_final: 0.8153 (tt0) REVERT: N 27 LYS cc_start: 0.8634 (pttt) cc_final: 0.8191 (mmtt) REVERT: N 49 GLN cc_start: 0.8905 (mm-40) cc_final: 0.8416 (mt0) REVERT: N 86 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7850 (tt0) REVERT: O 86 LYS cc_start: 0.9298 (tppp) cc_final: 0.9083 (mmmt) REVERT: O 87 GLU cc_start: 0.8494 (tp30) cc_final: 0.8164 (mt-10) REVERT: O 143 LYS cc_start: 0.8453 (tmmt) cc_final: 0.8073 (tppt) REVERT: O 147 ARG cc_start: 0.8909 (tpt90) cc_final: 0.8105 (mtm110) REVERT: V 4 ASP cc_start: 0.8550 (t70) cc_final: 0.8208 (p0) REVERT: V 64 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8216 (mt-10) REVERT: W 31 SER cc_start: 0.9052 (t) cc_final: 0.8731 (p) REVERT: W 36 ARG cc_start: 0.8427 (mmt90) cc_final: 0.8020 (mmm160) REVERT: W 49 GLU cc_start: 0.7926 (pt0) cc_final: 0.7604 (pt0) REVERT: W 54 ASP cc_start: 0.8634 (t70) cc_final: 0.8338 (t0) REVERT: W 76 SER cc_start: 0.9347 (t) cc_final: 0.9005 (p) REVERT: W 84 LYS cc_start: 0.8870 (mttt) cc_final: 0.8415 (pttm) REVERT: W 85 ASP cc_start: 0.8905 (m-30) cc_final: 0.8551 (m-30) REVERT: W 88 LYS cc_start: 0.8638 (ttmm) cc_final: 0.8085 (tttt) REVERT: W 90 GLN cc_start: 0.8837 (pt0) cc_final: 0.8474 (pt0) REVERT: W 104 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8562 (pp) REVERT: W 117 ARG cc_start: 0.8253 (tpp80) cc_final: 0.7822 (mtp85) REVERT: X 39 ASN cc_start: 0.9014 (t0) cc_final: 0.8770 (t0) REVERT: X 50 ILE cc_start: 0.9139 (mt) cc_final: 0.8810 (pt) REVERT: X 69 CYS cc_start: 0.8816 (m) cc_final: 0.8434 (m) REVERT: X 127 ASN cc_start: 0.8999 (m-40) cc_final: 0.8671 (t0) REVERT: Y 18 LEU cc_start: 0.9020 (mt) cc_final: 0.8729 (mp) REVERT: Y 19 GLN cc_start: 0.9203 (mp10) cc_final: 0.8743 (mp10) REVERT: Y 42 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8792 (mt-10) REVERT: Y 61 ARG cc_start: 0.9012 (tpt170) cc_final: 0.8632 (mmm-85) REVERT: Y 68 LYS cc_start: 0.9008 (mttt) cc_final: 0.8722 (mppt) REVERT: Y 70 THR cc_start: 0.9147 (m) cc_final: 0.8943 (p) REVERT: Y 85 ASN cc_start: 0.8790 (m-40) cc_final: 0.8467 (m-40) REVERT: b 16 LYS cc_start: 0.8985 (mttt) cc_final: 0.8783 (mmmt) REVERT: b 34 ASP cc_start: 0.8058 (t0) cc_final: 0.7058 (p0) REVERT: b 72 ARG cc_start: 0.8790 (ptt180) cc_final: 0.8376 (ptm-80) REVERT: e 25 LYS cc_start: 0.8409 (pttt) cc_final: 0.7984 (tppt) REVERT: e 40 ARG cc_start: 0.8836 (ttt180) cc_final: 0.8406 (mtm110) REVERT: x 80 VAL cc_start: 0.9552 (OUTLIER) cc_final: 0.9299 (m) REVERT: x 88 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.8861 (tt) REVERT: x 118 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8389 (mt) REVERT: x 145 GLN cc_start: 0.8651 (tt0) cc_final: 0.8435 (mm110) REVERT: x 147 GLU cc_start: 0.8723 (mp0) cc_final: 0.8501 (mp0) REVERT: x 157 ASP cc_start: 0.8427 (p0) cc_final: 0.8205 (p0) REVERT: x 167 ASP cc_start: 0.8631 (m-30) cc_final: 0.8299 (t0) REVERT: x 172 LYS cc_start: 0.8929 (mptt) cc_final: 0.8626 (mtpp) REVERT: x 240 ASN cc_start: 0.8951 (m-40) cc_final: 0.8645 (m-40) REVERT: y 64 ARG cc_start: 0.8549 (mtt180) cc_final: 0.8011 (mtm-85) REVERT: y 71 LYS cc_start: 0.8461 (pptt) cc_final: 0.8107 (mtmt) REVERT: y 75 ASP cc_start: 0.8387 (m-30) cc_final: 0.8054 (m-30) REVERT: y 109 LYS cc_start: 0.8174 (mmmm) cc_final: 0.7779 (ttpp) REVERT: y 129 HIS cc_start: 0.8337 (t70) cc_final: 0.8056 (t-90) REVERT: y 278 SER cc_start: 0.9140 (m) cc_final: 0.8633 (p) REVERT: y 280 MET cc_start: 0.8526 (mmm) cc_final: 0.8140 (tpt) REVERT: y 342 GLU cc_start: 0.8925 (pm20) cc_final: 0.8401 (tp30) REVERT: u 178 PHE cc_start: 0.9287 (m-80) cc_final: 0.8918 (m-10) REVERT: u 219 LYS cc_start: 0.8603 (pttt) cc_final: 0.8234 (tttp) REVERT: u 225 THR cc_start: 0.7856 (OUTLIER) cc_final: 0.7513 (p) REVERT: u 228 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8258 (mt-10) REVERT: u 481 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8506 (mm-30) REVERT: u 482 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7941 (tp30) REVERT: u 596 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8485 (mtt) REVERT: u 738 ARG cc_start: 0.8247 (mmt180) cc_final: 0.7974 (ttm110) REVERT: u 766 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8367 (pp) REVERT: w 194 LYS cc_start: 0.8700 (mttt) cc_final: 0.8022 (tmtt) REVERT: w 211 SER cc_start: 0.8177 (OUTLIER) cc_final: 0.7890 (m) REVERT: w 213 TRP cc_start: 0.8548 (p-90) cc_final: 0.8268 (p-90) REVERT: w 225 TRP cc_start: 0.8153 (m-10) cc_final: 0.7591 (m-10) REVERT: w 388 ARG cc_start: 0.5945 (tpm170) cc_final: 0.5687 (tpp-160) REVERT: w 389 TYR cc_start: 0.6626 (m-80) cc_final: 0.5216 (m-80) REVERT: w 397 GLN cc_start: 0.8230 (pt0) cc_final: 0.7578 (pm20) REVERT: v 11 TYR cc_start: 0.7334 (m-80) cc_final: 0.6727 (m-80) REVERT: v 25 MET cc_start: 0.8520 (mmm) cc_final: 0.8241 (mmm) REVERT: v 30 HIS cc_start: 0.5718 (t70) cc_final: 0.5200 (t-90) REVERT: v 123 LYS cc_start: 0.6795 (tttt) cc_final: 0.6587 (mtpp) REVERT: v 177 LYS cc_start: 0.8290 (tttt) cc_final: 0.7898 (mttm) REVERT: v 182 ASN cc_start: 0.7056 (m110) cc_final: 0.6818 (t0) REVERT: v 188 MET cc_start: 0.7305 (ptp) cc_final: 0.6888 (pmm) REVERT: v 213 MET cc_start: 0.8077 (mmm) cc_final: 0.7728 (mmm) REVERT: v 507 ARG cc_start: 0.7844 (mtt180) cc_final: 0.7506 (mtp85) REVERT: v 523 LYS cc_start: 0.6238 (mttt) cc_final: 0.5138 (tptt) REVERT: t 250 MET cc_start: 0.4999 (OUTLIER) cc_final: 0.4584 (pmm) REVERT: t 259 HIS cc_start: 0.6431 (p-80) cc_final: 0.5018 (t-90) REVERT: t 299 ASN cc_start: 0.7546 (m-40) cc_final: 0.7129 (p0) REVERT: t 313 ASN cc_start: 0.7439 (t0) cc_final: 0.7181 (t0) REVERT: t 432 GLN cc_start: 0.8269 (mm110) cc_final: 0.7997 (mm110) REVERT: t 444 GLU cc_start: 0.8132 (tt0) cc_final: 0.7822 (mt-10) REVERT: t 455 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7519 (tm-30) outliers start: 303 outliers final: 136 residues processed: 1475 average time/residue: 0.8559 time to fit residues: 2111.9154 Evaluate side-chains 1232 residues out of total 5267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 1061 time to evaluate : 5.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 72 HIS Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain P residue 16 THR Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain P residue 30 TYR Chi-restraints excluded: chain P residue 81 ARG Chi-restraints excluded: chain P residue 82 ASP Chi-restraints excluded: chain Q residue 25 CYS Chi-restraints excluded: chain Q residue 43 GLU Chi-restraints excluded: chain Q residue 72 VAL Chi-restraints excluded: chain Q residue 123 ASP Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 11 LYS Chi-restraints excluded: chain R residue 70 SER Chi-restraints excluded: chain R residue 77 GLU Chi-restraints excluded: chain R residue 81 ARG Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain R residue 110 ASP Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 68 ILE Chi-restraints excluded: chain S residue 71 MET Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 88 MET Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain c residue 26 GLN Chi-restraints excluded: chain c residue 37 ASP Chi-restraints excluded: chain c residue 59 LEU Chi-restraints excluded: chain f residue 102 VAL Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 114 ILE Chi-restraints excluded: chain g residue 46 THR Chi-restraints excluded: chain g residue 47 ARG Chi-restraints excluded: chain g residue 72 SER Chi-restraints excluded: chain g residue 93 THR Chi-restraints excluded: chain g residue 118 ARG Chi-restraints excluded: chain g residue 148 SER Chi-restraints excluded: chain g residue 249 CYS Chi-restraints excluded: chain g residue 297 THR Chi-restraints excluded: chain A residue 11 LYS Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 129 ILE Chi-restraints excluded: chain H residue 165 ASN Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 48 LYS Chi-restraints excluded: chain L residue 60 CYS Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain O residue 40 THR Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 95 ILE Chi-restraints excluded: chain O residue 100 THR Chi-restraints excluded: chain V residue 42 VAL Chi-restraints excluded: chain V residue 47 ASN Chi-restraints excluded: chain V residue 70 LEU Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain X residue 7 LEU Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 63 ASN Chi-restraints excluded: chain X residue 110 HIS Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 40 ILE Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 55 ILE Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain b residue 37 CYS Chi-restraints excluded: chain b residue 78 SER Chi-restraints excluded: chain x residue 78 ILE Chi-restraints excluded: chain x residue 80 VAL Chi-restraints excluded: chain x residue 88 LEU Chi-restraints excluded: chain x residue 102 HIS Chi-restraints excluded: chain x residue 118 ILE Chi-restraints excluded: chain x residue 155 LEU Chi-restraints excluded: chain x residue 162 SER Chi-restraints excluded: chain y residue 34 VAL Chi-restraints excluded: chain y residue 69 PHE Chi-restraints excluded: chain y residue 235 LEU Chi-restraints excluded: chain y residue 251 HIS Chi-restraints excluded: chain y residue 281 SER Chi-restraints excluded: chain y residue 303 ASP Chi-restraints excluded: chain y residue 371 SER Chi-restraints excluded: chain y residue 379 SER Chi-restraints excluded: chain y residue 389 ASP Chi-restraints excluded: chain y residue 404 SER Chi-restraints excluded: chain u residue 73 ARG Chi-restraints excluded: chain u residue 103 LEU Chi-restraints excluded: chain u residue 136 THR Chi-restraints excluded: chain u residue 207 LEU Chi-restraints excluded: chain u residue 222 LEU Chi-restraints excluded: chain u residue 225 THR Chi-restraints excluded: chain u residue 226 GLN Chi-restraints excluded: chain u residue 235 GLN Chi-restraints excluded: chain u residue 297 PHE Chi-restraints excluded: chain u residue 348 ASP Chi-restraints excluded: chain u residue 511 THR Chi-restraints excluded: chain u residue 596 MET Chi-restraints excluded: chain u residue 597 VAL Chi-restraints excluded: chain u residue 687 VAL Chi-restraints excluded: chain u residue 761 SER Chi-restraints excluded: chain u residue 766 LEU Chi-restraints excluded: chain u residue 778 THR Chi-restraints excluded: chain w residue 211 SER Chi-restraints excluded: chain w residue 226 THR Chi-restraints excluded: chain w residue 236 ILE Chi-restraints excluded: chain w residue 403 GLU Chi-restraints excluded: chain v residue 237 ASP Chi-restraints excluded: chain v residue 260 TRP Chi-restraints excluded: chain v residue 503 GLN Chi-restraints excluded: chain t residue 250 MET Chi-restraints excluded: chain t residue 261 GLU Chi-restraints excluded: chain t residue 297 VAL Chi-restraints excluded: chain t residue 469 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 757 random chunks: chunk 382 optimal weight: 4.9990 chunk 213 optimal weight: 5.9990 chunk 572 optimal weight: 9.9990 chunk 468 optimal weight: 0.7980 chunk 189 optimal weight: 5.9990 chunk 688 optimal weight: 0.0030 chunk 743 optimal weight: 9.9990 chunk 613 optimal weight: 2.9990 chunk 682 optimal weight: 0.9990 chunk 234 optimal weight: 4.9990 chunk 552 optimal weight: 0.5980 overall best weight: 1.0794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 114 ASN P 35 GLN P 103 ASN Q 86 GLN R 74 GLN S 87 GLN ** g 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 119 GLN ** g 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 HIS G 65 GLN G 110 ASN ** G 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 GLN I 168 GLN J 177 ASN L 108 ASN ** O 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 GLN W 70 ASN Y 19 GLN Y 124 ASN ** b 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 65 GLN e 22 GLN e 37 GLN e 39 ASN ** e 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 115 ASN ** x 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 360 ASN ** u 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 284 ASN ** u 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 401 GLN ** w 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 201 HIS v 226 HIS v 508 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 88868 Z= 0.166 Angle : 0.585 13.981 127913 Z= 0.300 Chirality : 0.037 0.310 15645 Planarity : 0.004 0.068 10091 Dihedral : 23.219 179.546 32663 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.07 % Favored : 95.83 % Rotamer: Outliers : 5.22 % Allowed : 20.22 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.11), residues: 5968 helix: 1.18 (0.12), residues: 2075 sheet: -0.77 (0.15), residues: 1022 loop : -1.34 (0.11), residues: 2871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP g 310 HIS 0.007 0.001 HIS y 307 PHE 0.022 0.001 PHE x 96 TYR 0.020 0.001 TYR R 84 ARG 0.009 0.000 ARG Q 117 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11936 Ramachandran restraints generated. 5968 Oldfield, 0 Emsley, 5968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11936 Ramachandran restraints generated. 5968 Oldfield, 0 Emsley, 5968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1402 residues out of total 5267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 1129 time to evaluate : 5.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 32 ASP cc_start: 0.8599 (OUTLIER) cc_final: 0.8386 (t0) REVERT: F 44 LYS cc_start: 0.8884 (ttpt) cc_final: 0.8555 (tppt) REVERT: F 75 SER cc_start: 0.9208 (t) cc_final: 0.9004 (m) REVERT: F 79 HIS cc_start: 0.6202 (OUTLIER) cc_final: 0.5478 (t70) REVERT: F 81 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.8199 (ptt90) REVERT: F 98 GLU cc_start: 0.8275 (tp30) cc_final: 0.7893 (tp30) REVERT: F 106 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8442 (tt0) REVERT: F 124 ASP cc_start: 0.8544 (t0) cc_final: 0.8253 (t0) REVERT: F 168 THR cc_start: 0.8981 (OUTLIER) cc_final: 0.8476 (m) REVERT: F 185 SER cc_start: 0.8774 (t) cc_final: 0.8526 (p) REVERT: M 15 ASN cc_start: 0.6701 (m-40) cc_final: 0.6399 (t0) REVERT: M 63 LYS cc_start: 0.7624 (mtmm) cc_final: 0.7128 (pttp) REVERT: M 91 LEU cc_start: 0.4430 (OUTLIER) cc_final: 0.4122 (mt) REVERT: P 21 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.7622 (p0) REVERT: P 24 GLN cc_start: 0.8434 (mt0) cc_final: 0.8024 (mt0) REVERT: P 30 TYR cc_start: 0.7652 (OUTLIER) cc_final: 0.6941 (t80) REVERT: P 31 GLU cc_start: 0.8664 (tt0) cc_final: 0.8424 (mp0) REVERT: P 32 GLN cc_start: 0.9028 (tt0) cc_final: 0.8732 (mm110) REVERT: P 41 GLN cc_start: 0.8867 (mm-40) cc_final: 0.8607 (mp10) REVERT: P 51 ARG cc_start: 0.8890 (tpt90) cc_final: 0.8509 (ttm110) REVERT: P 112 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8050 (mt) REVERT: Q 27 ARG cc_start: 0.7830 (ptt90) cc_final: 0.7464 (ttp80) REVERT: Q 29 ASN cc_start: 0.7987 (m-40) cc_final: 0.7574 (t0) REVERT: Q 66 VAL cc_start: 0.6809 (t) cc_final: 0.6439 (p) REVERT: Q 107 GLU cc_start: 0.8350 (tp30) cc_final: 0.8036 (pt0) REVERT: Q 129 SER cc_start: 0.7168 (t) cc_final: 0.6710 (m) REVERT: R 7 LYS cc_start: 0.8394 (mtmt) cc_final: 0.8118 (tppt) REVERT: R 11 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7993 (mttm) REVERT: R 18 GLU cc_start: 0.9087 (tt0) cc_final: 0.8824 (pp20) REVERT: R 37 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7718 (tp30) REVERT: R 77 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7375 (mp0) REVERT: R 92 ASP cc_start: 0.8683 (t70) cc_final: 0.8258 (t0) REVERT: R 97 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7541 (mp0) REVERT: R 107 LYS cc_start: 0.9127 (tttt) cc_final: 0.8786 (mtpp) REVERT: S 77 TYR cc_start: 0.8882 (m-80) cc_final: 0.8479 (m-80) REVERT: S 78 LYS cc_start: 0.9036 (tttt) cc_final: 0.8826 (mptt) REVERT: S 85 ASN cc_start: 0.8083 (OUTLIER) cc_final: 0.7683 (m110) REVERT: S 97 GLN cc_start: 0.8925 (tp40) cc_final: 0.8385 (tp40) REVERT: S 109 GLU cc_start: 0.9204 (tt0) cc_final: 0.8736 (mm-30) REVERT: S 112 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8091 (tt0) REVERT: T 24 LYS cc_start: 0.8848 (mmtt) cc_final: 0.8489 (ptmm) REVERT: T 49 ASP cc_start: 0.8569 (t70) cc_final: 0.8292 (t70) REVERT: T 51 ASN cc_start: 0.9058 (OUTLIER) cc_final: 0.8831 (p0) REVERT: T 108 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8686 (mt-10) REVERT: T 122 LYS cc_start: 0.8075 (pttt) cc_final: 0.7797 (pptt) REVERT: T 126 GLN cc_start: 0.8591 (tt0) cc_final: 0.8149 (tm-30) REVERT: T 129 ARG cc_start: 0.8076 (mtt90) cc_final: 0.7665 (mtp-110) REVERT: Z 101 SER cc_start: 0.8149 (t) cc_final: 0.7614 (p) REVERT: Z 106 GLN cc_start: 0.8731 (tp-100) cc_final: 0.8379 (tp40) REVERT: c 13 ARG cc_start: 0.8667 (mmm-85) cc_final: 0.8446 (mmm-85) REVERT: c 26 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8329 (pt0) REVERT: f 114 ILE cc_start: 0.2989 (OUTLIER) cc_final: 0.2656 (tp) REVERT: f 123 SER cc_start: 0.8258 (t) cc_final: 0.7842 (p) REVERT: g 21 ILE cc_start: 0.8518 (mt) cc_final: 0.8284 (mm) REVERT: g 47 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7753 (mtt90) REVERT: g 101 PHE cc_start: 0.8001 (m-80) cc_final: 0.7796 (m-80) REVERT: g 118 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.8053 (mmm160) REVERT: g 182 CYS cc_start: 0.8827 (t) cc_final: 0.8500 (p) REVERT: A 25 LEU cc_start: 0.8972 (mt) cc_final: 0.8649 (mt) REVERT: A 32 PHE cc_start: 0.8707 (OUTLIER) cc_final: 0.8390 (t80) REVERT: A 111 GLN cc_start: 0.8761 (pm20) cc_final: 0.8544 (pm20) REVERT: A 209 GLU cc_start: 0.8400 (tt0) cc_final: 0.7896 (tp30) REVERT: B 57 ILE cc_start: 0.7551 (OUTLIER) cc_final: 0.7341 (mm) REVERT: B 73 ASP cc_start: 0.8514 (m-30) cc_final: 0.8075 (t0) REVERT: B 168 MET cc_start: 0.8498 (ttm) cc_final: 0.8252 (ttm) REVERT: B 175 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8700 (mm-30) REVERT: B 203 SER cc_start: 0.9266 (p) cc_final: 0.8915 (t) REVERT: C 61 MET cc_start: 0.8491 (tpp) cc_final: 0.7452 (pmm) REVERT: C 68 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.7900 (mtp180) REVERT: C 77 SER cc_start: 0.9206 (t) cc_final: 0.8927 (p) REVERT: C 122 THR cc_start: 0.8949 (m) cc_final: 0.8744 (t) REVERT: C 123 ARG cc_start: 0.8037 (ptm160) cc_final: 0.7120 (mpt-90) REVERT: C 144 SER cc_start: 0.8461 (p) cc_final: 0.8172 (p) REVERT: C 145 LYS cc_start: 0.8439 (mttt) cc_final: 0.8011 (mttm) REVERT: C 159 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8472 (mttp) REVERT: C 160 LEU cc_start: 0.8846 (mt) cc_final: 0.8538 (mp) REVERT: C 173 LYS cc_start: 0.8490 (mttp) cc_final: 0.8194 (mtpt) REVERT: C 267 GLN cc_start: 0.8740 (tm-30) cc_final: 0.8177 (tm-30) REVERT: E 22 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8354 (ttmm) REVERT: E 71 LYS cc_start: 0.8192 (mtpt) cc_final: 0.7834 (mtpt) REVERT: E 73 ASP cc_start: 0.8711 (m-30) cc_final: 0.8487 (m-30) REVERT: E 87 MET cc_start: 0.9183 (tpp) cc_final: 0.8669 (mmm) REVERT: E 158 ASP cc_start: 0.8741 (m-30) cc_final: 0.8051 (m-30) REVERT: E 197 ASN cc_start: 0.8743 (t0) cc_final: 0.8502 (p0) REVERT: E 237 SER cc_start: 0.9161 (t) cc_final: 0.8784 (m) REVERT: E 242 LYS cc_start: 0.9044 (mmmt) cc_final: 0.8783 (mtpt) REVERT: E 253 ASP cc_start: 0.8679 (t70) cc_final: 0.8142 (m-30) REVERT: G 1 MET cc_start: 0.7781 (mmm) cc_final: 0.7144 (tpp) REVERT: G 17 GLU cc_start: 0.8879 (tt0) cc_final: 0.8533 (tm-30) REVERT: G 29 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8446 (mm-30) REVERT: G 70 HIS cc_start: 0.7506 (m170) cc_final: 0.7169 (m170) REVERT: G 103 ASP cc_start: 0.8384 (t70) cc_final: 0.8024 (t70) REVERT: G 154 ARG cc_start: 0.8296 (mtt180) cc_final: 0.7772 (mtm110) REVERT: G 163 ASN cc_start: 0.7282 (p0) cc_final: 0.6691 (t0) REVERT: G 204 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8072 (mt-10) REVERT: G 219 GLU cc_start: 0.7193 (tm-30) cc_final: 0.6993 (tm-30) REVERT: G 226 GLU cc_start: 0.7931 (tt0) cc_final: 0.7690 (mt-10) REVERT: H 10 LYS cc_start: 0.9096 (mttt) cc_final: 0.8677 (ptmt) REVERT: H 17 ASP cc_start: 0.6942 (t70) cc_final: 0.6725 (t70) REVERT: H 28 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6818 (mm) REVERT: H 58 LYS cc_start: 0.8333 (mttt) cc_final: 0.7996 (pttt) REVERT: H 76 GLN cc_start: 0.8465 (tp40) cc_final: 0.7664 (tt0) REVERT: H 82 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8192 (mp0) REVERT: H 99 ARG cc_start: 0.8311 (mmt90) cc_final: 0.7997 (ttp80) REVERT: H 122 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8578 (tp) REVERT: H 159 ASP cc_start: 0.9230 (OUTLIER) cc_final: 0.8864 (m-30) REVERT: I 17 LYS cc_start: 0.8558 (pttm) cc_final: 0.8341 (ptmm) REVERT: I 73 THR cc_start: 0.8484 (m) cc_final: 0.8158 (p) REVERT: I 95 THR cc_start: 0.9488 (m) cc_final: 0.9133 (p) REVERT: I 105 ASP cc_start: 0.8557 (t0) cc_final: 0.8213 (p0) REVERT: I 139 LYS cc_start: 0.7709 (tmtp) cc_final: 0.7273 (ptmm) REVERT: I 141 ARG cc_start: 0.7998 (mtt180) cc_final: 0.7513 (ptm160) REVERT: I 159 SER cc_start: 0.7939 (m) cc_final: 0.7648 (t) REVERT: I 163 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7211 (tp30) REVERT: I 167 GLN cc_start: 0.7828 (mm-40) cc_final: 0.7437 (tp40) REVERT: J 88 ASP cc_start: 0.8391 (m-30) cc_final: 0.7839 (t0) REVERT: J 154 GLN cc_start: 0.8453 (tt0) cc_final: 0.8173 (tt0) REVERT: L 39 ASN cc_start: 0.8054 (t0) cc_final: 0.7768 (p0) REVERT: L 48 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7895 (tppt) REVERT: L 130 GLU cc_start: 0.8559 (tt0) cc_final: 0.8115 (tt0) REVERT: N 27 LYS cc_start: 0.8633 (pttt) cc_final: 0.8146 (mmtt) REVERT: N 49 GLN cc_start: 0.8893 (mm-40) cc_final: 0.8461 (mt0) REVERT: N 86 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7836 (tt0) REVERT: O 86 LYS cc_start: 0.9279 (tppp) cc_final: 0.9046 (mmmt) REVERT: O 87 GLU cc_start: 0.8336 (tp30) cc_final: 0.7912 (mt-10) REVERT: O 143 LYS cc_start: 0.8444 (tmmt) cc_final: 0.8015 (tppt) REVERT: O 147 ARG cc_start: 0.8894 (tpt90) cc_final: 0.8101 (mtm110) REVERT: V 4 ASP cc_start: 0.8441 (t70) cc_final: 0.8103 (p0) REVERT: V 32 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8199 (pt) REVERT: V 64 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8250 (mt-10) REVERT: W 31 SER cc_start: 0.9067 (t) cc_final: 0.8745 (p) REVERT: W 76 SER cc_start: 0.9410 (t) cc_final: 0.9059 (p) REVERT: W 88 LYS cc_start: 0.8697 (ttmm) cc_final: 0.8073 (tttt) REVERT: W 90 GLN cc_start: 0.8826 (pt0) cc_final: 0.8603 (pt0) REVERT: W 104 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8491 (pp) REVERT: W 117 ARG cc_start: 0.8238 (tpp80) cc_final: 0.8033 (mtp85) REVERT: X 50 ILE cc_start: 0.9137 (mt) cc_final: 0.8821 (pt) REVERT: X 69 CYS cc_start: 0.8673 (m) cc_final: 0.8271 (m) REVERT: X 127 ASN cc_start: 0.8935 (m-40) cc_final: 0.8657 (t0) REVERT: Y 18 LEU cc_start: 0.8955 (mt) cc_final: 0.8737 (mp) REVERT: Y 19 GLN cc_start: 0.9087 (mp-120) cc_final: 0.8831 (mp10) REVERT: Y 42 GLU cc_start: 0.9056 (mm-30) cc_final: 0.8762 (mt-10) REVERT: Y 53 ASP cc_start: 0.9163 (m-30) cc_final: 0.8835 (p0) REVERT: Y 61 ARG cc_start: 0.9006 (tpt170) cc_final: 0.8560 (mmm-85) REVERT: Y 68 LYS cc_start: 0.8882 (mttt) cc_final: 0.8676 (mppt) REVERT: Y 70 THR cc_start: 0.8983 (m) cc_final: 0.8747 (p) REVERT: Y 74 MET cc_start: 0.8435 (mtm) cc_final: 0.8223 (mtm) REVERT: Y 85 ASN cc_start: 0.8696 (m-40) cc_final: 0.8434 (m-40) REVERT: b 16 LYS cc_start: 0.9053 (mttt) cc_final: 0.8798 (mmmt) REVERT: b 34 ASP cc_start: 0.8005 (t0) cc_final: 0.7013 (p0) REVERT: b 72 ARG cc_start: 0.8834 (ptt180) cc_final: 0.8420 (ptm-80) REVERT: e 25 LYS cc_start: 0.8391 (pttt) cc_final: 0.7962 (mmtm) REVERT: e 40 ARG cc_start: 0.8813 (ttt180) cc_final: 0.8386 (mtm110) REVERT: x 80 VAL cc_start: 0.9554 (OUTLIER) cc_final: 0.9338 (m) REVERT: x 88 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8797 (tt) REVERT: x 145 GLN cc_start: 0.8692 (tt0) cc_final: 0.8372 (mm110) REVERT: x 172 LYS cc_start: 0.9022 (mptt) cc_final: 0.8721 (mtpp) REVERT: x 240 ASN cc_start: 0.8925 (m-40) cc_final: 0.8635 (m-40) REVERT: y 64 ARG cc_start: 0.8558 (mtt180) cc_final: 0.8042 (mtm-85) REVERT: y 75 ASP cc_start: 0.8326 (m-30) cc_final: 0.8017 (m-30) REVERT: y 109 LYS cc_start: 0.8162 (mmmm) cc_final: 0.7679 (ttpp) REVERT: y 278 SER cc_start: 0.9161 (m) cc_final: 0.8624 (p) REVERT: y 342 GLU cc_start: 0.8849 (pm20) cc_final: 0.8342 (tp30) REVERT: y 408 PHE cc_start: 0.9209 (m-80) cc_final: 0.8984 (m-10) REVERT: u 178 PHE cc_start: 0.9252 (m-80) cc_final: 0.8906 (m-10) REVERT: u 219 LYS cc_start: 0.8644 (pttt) cc_final: 0.8196 (tttp) REVERT: u 225 THR cc_start: 0.7750 (m) cc_final: 0.7493 (p) REVERT: u 228 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8153 (mt-10) REVERT: u 401 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8500 (tt0) REVERT: u 481 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8472 (mm-30) REVERT: u 482 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7936 (tp30) REVERT: u 532 ASN cc_start: 0.8706 (t0) cc_final: 0.7999 (t0) REVERT: u 738 ARG cc_start: 0.8207 (mmt180) cc_final: 0.7862 (ttm110) REVERT: u 741 ILE cc_start: 0.8869 (pp) cc_final: 0.8618 (pp) REVERT: u 766 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8276 (pp) REVERT: w 194 LYS cc_start: 0.8753 (mttt) cc_final: 0.8060 (tmtt) REVERT: w 211 SER cc_start: 0.8237 (OUTLIER) cc_final: 0.7952 (m) REVERT: w 213 TRP cc_start: 0.8544 (p-90) cc_final: 0.8282 (p-90) REVERT: w 221 GLU cc_start: 0.7123 (tt0) cc_final: 0.6914 (tt0) REVERT: w 225 TRP cc_start: 0.8044 (m-10) cc_final: 0.7623 (m-10) REVERT: w 267 ARG cc_start: 0.8166 (ptt90) cc_final: 0.7121 (ttt180) REVERT: w 273 TYR cc_start: 0.7862 (t80) cc_final: 0.7645 (t80) REVERT: w 388 ARG cc_start: 0.6113 (tpm170) cc_final: 0.5779 (tpp-160) REVERT: w 389 TYR cc_start: 0.6532 (m-80) cc_final: 0.5155 (m-80) REVERT: w 397 GLN cc_start: 0.7893 (pt0) cc_final: 0.7259 (pm20) REVERT: v 30 HIS cc_start: 0.5822 (t70) cc_final: 0.5559 (t70) REVERT: v 165 MET cc_start: 0.7521 (ptm) cc_final: 0.6718 (ptm) REVERT: v 183 ARG cc_start: 0.7465 (mtm-85) cc_final: 0.7209 (ttm-80) REVERT: v 188 MET cc_start: 0.7352 (ptp) cc_final: 0.7064 (mtt) REVERT: v 213 MET cc_start: 0.8010 (mmm) cc_final: 0.7647 (mmm) REVERT: v 274 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.7996 (mtt) REVERT: v 523 LYS cc_start: 0.6349 (mttt) cc_final: 0.5269 (tptt) REVERT: t 250 MET cc_start: 0.4599 (OUTLIER) cc_final: 0.4135 (pmm) REVERT: t 259 HIS cc_start: 0.6605 (p-80) cc_final: 0.5239 (t-90) REVERT: t 304 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7384 (tt0) REVERT: t 313 ASN cc_start: 0.7330 (t0) cc_final: 0.6993 (t0) REVERT: t 440 GLU cc_start: 0.8429 (mt-10) cc_final: 0.7974 (tm-30) REVERT: t 456 LYS cc_start: 0.8402 (tttp) cc_final: 0.8201 (ttpt) REVERT: t 462 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7736 (tm-30) outliers start: 273 outliers final: 147 residues processed: 1300 average time/residue: 0.7898 time to fit residues: 1737.1313 Evaluate side-chains 1199 residues out of total 5267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 1016 time to evaluate : 5.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 79 HIS Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 72 HIS Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 30 TYR Chi-restraints excluded: chain P residue 38 SER Chi-restraints excluded: chain P residue 82 ASP Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain Q residue 25 CYS Chi-restraints excluded: chain Q residue 43 GLU Chi-restraints excluded: chain Q residue 72 VAL Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 11 LYS Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain R residue 70 SER Chi-restraints excluded: chain R residue 77 GLU Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain R residue 110 ASP Chi-restraints excluded: chain R residue 116 ASN Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 68 ILE Chi-restraints excluded: chain S residue 85 ASN Chi-restraints excluded: chain S residue 87 GLN Chi-restraints excluded: chain S residue 106 LYS Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 44 GLU Chi-restraints excluded: chain T residue 51 ASN Chi-restraints excluded: chain Z residue 57 LYS Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain c residue 9 ILE Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 26 GLN Chi-restraints excluded: chain c residue 57 THR Chi-restraints excluded: chain c residue 59 LEU Chi-restraints excluded: chain f residue 102 VAL Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 114 ILE Chi-restraints excluded: chain f residue 147 THR Chi-restraints excluded: chain g residue 46 THR Chi-restraints excluded: chain g residue 47 ARG Chi-restraints excluded: chain g residue 64 HIS Chi-restraints excluded: chain g residue 118 ARG Chi-restraints excluded: chain g residue 240 CYS Chi-restraints excluded: chain g residue 249 CYS Chi-restraints excluded: chain g residue 264 LYS Chi-restraints excluded: chain g residue 303 THR Chi-restraints excluded: chain A residue 11 LYS Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 95 ASP Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 159 LYS Chi-restraints excluded: chain C residue 172 ASN Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 218 LYS Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 159 ASP Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 138 ASN Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 73 GLU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 48 LYS Chi-restraints excluded: chain L residue 60 CYS Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain N residue 9 LYS Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain N residue 143 SER Chi-restraints excluded: chain N residue 145 THR Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 42 VAL Chi-restraints excluded: chain V residue 70 LEU Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 121 THR Chi-restraints excluded: chain X residue 7 LEU Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 110 HIS Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 55 ILE Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain b residue 37 CYS Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 36 MET Chi-restraints excluded: chain e residue 37 GLN Chi-restraints excluded: chain x residue 80 VAL Chi-restraints excluded: chain x residue 88 LEU Chi-restraints excluded: chain x residue 102 HIS Chi-restraints excluded: chain x residue 118 ILE Chi-restraints excluded: chain x residue 152 LEU Chi-restraints excluded: chain x residue 160 LEU Chi-restraints excluded: chain x residue 218 ILE Chi-restraints excluded: chain y residue 235 LEU Chi-restraints excluded: chain y residue 251 HIS Chi-restraints excluded: chain y residue 303 ASP Chi-restraints excluded: chain y residue 371 SER Chi-restraints excluded: chain y residue 379 SER Chi-restraints excluded: chain y residue 389 ASP Chi-restraints excluded: chain u residue 73 ARG Chi-restraints excluded: chain u residue 103 LEU Chi-restraints excluded: chain u residue 136 THR Chi-restraints excluded: chain u residue 217 HIS Chi-restraints excluded: chain u residue 222 LEU Chi-restraints excluded: chain u residue 226 GLN Chi-restraints excluded: chain u residue 297 PHE Chi-restraints excluded: chain u residue 348 ASP Chi-restraints excluded: chain u residue 401 GLN Chi-restraints excluded: chain u residue 687 VAL Chi-restraints excluded: chain u residue 761 SER Chi-restraints excluded: chain u residue 766 LEU Chi-restraints excluded: chain u residue 778 THR Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 211 SER Chi-restraints excluded: chain w residue 226 THR Chi-restraints excluded: chain w residue 306 ILE Chi-restraints excluded: chain w residue 317 ILE Chi-restraints excluded: chain w residue 403 GLU Chi-restraints excluded: chain v residue 101 MET Chi-restraints excluded: chain v residue 260 TRP Chi-restraints excluded: chain v residue 274 MET Chi-restraints excluded: chain v residue 278 SER Chi-restraints excluded: chain t residue 250 MET Chi-restraints excluded: chain t residue 261 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 757 random chunks: chunk 680 optimal weight: 3.9990 chunk 517 optimal weight: 10.0000 chunk 357 optimal weight: 9.9990 chunk 76 optimal weight: 8.9990 chunk 328 optimal weight: 3.9990 chunk 462 optimal weight: 1.9990 chunk 691 optimal weight: 0.9980 chunk 731 optimal weight: 6.9990 chunk 361 optimal weight: 2.9990 chunk 655 optimal weight: 0.0470 chunk 197 optimal weight: 6.9990 overall best weight: 2.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 GLN P 35 GLN P 79 HIS ** P 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 74 GLN ** S 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 51 ASN ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 ASN G 65 GLN G 110 ASN ** G 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 GLN I 168 GLN J 140 GLN L 19 ASN N 58 HIS ** O 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 GLN W 70 ASN X 26 GLN X 63 ASN Y 19 GLN ** b 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 65 GLN e 22 GLN e 56 ASN x 210 HIS ** u 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 232 GLN ** w 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 99 ASN t 299 ASN t 465 ASN t 469 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 88868 Z= 0.227 Angle : 0.599 14.200 127913 Z= 0.305 Chirality : 0.038 0.352 15645 Planarity : 0.004 0.052 10091 Dihedral : 23.143 179.887 32639 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.14 % Favored : 95.74 % Rotamer: Outliers : 5.97 % Allowed : 20.57 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.11), residues: 5968 helix: 1.25 (0.12), residues: 2072 sheet: -0.77 (0.15), residues: 1029 loop : -1.26 (0.11), residues: 2867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 82 HIS 0.007 0.001 HIS y 307 PHE 0.029 0.002 PHE H 19 TYR 0.019 0.002 TYR E 149 ARG 0.033 0.001 ARG G 25 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11936 Ramachandran restraints generated. 5968 Oldfield, 0 Emsley, 5968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11936 Ramachandran restraints generated. 5968 Oldfield, 0 Emsley, 5968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1364 residues out of total 5267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 312 poor density : 1052 time to evaluate : 5.405 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: F 75 SER cc_start: 0.9226 (t) cc_final: 0.9016 (m) REVERT: F 77 MET cc_start: 0.8995 (ptt) cc_final: 0.8792 (ptt) REVERT: F 79 HIS cc_start: 0.6440 (OUTLIER) cc_final: 0.5993 (t70) REVERT: F 81 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8206 (ptt90) REVERT: F 98 GLU cc_start: 0.8346 (tp30) cc_final: 0.7896 (tp30) REVERT: F 106 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8368 (tt0) REVERT: F 124 ASP cc_start: 0.8633 (t0) cc_final: 0.8424 (t0) REVERT: F 168 THR cc_start: 0.8976 (OUTLIER) cc_final: 0.8672 (m) REVERT: F 185 SER cc_start: 0.8676 (t) cc_final: 0.8347 (p) REVERT: M 22 LEU cc_start: 0.6695 (mt) cc_final: 0.6214 (pp) REVERT: M 63 LYS cc_start: 0.7641 (mtmm) cc_final: 0.7155 (pttp) REVERT: M 91 LEU cc_start: 0.4747 (OUTLIER) cc_final: 0.3899 (mt) REVERT: M 96 ARG cc_start: 0.6746 (ptt-90) cc_final: 0.6187 (ptp90) REVERT: P 21 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.7648 (p0) REVERT: P 24 GLN cc_start: 0.8401 (mt0) cc_final: 0.8004 (mt0) REVERT: P 30 TYR cc_start: 0.7767 (OUTLIER) cc_final: 0.6788 (t80) REVERT: P 31 GLU cc_start: 0.8754 (tt0) cc_final: 0.8501 (mp0) REVERT: P 32 GLN cc_start: 0.9029 (tt0) cc_final: 0.8632 (mm110) REVERT: P 41 GLN cc_start: 0.8972 (mm-40) cc_final: 0.8600 (mp10) REVERT: P 50 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8038 (mmt180) REVERT: P 51 ARG cc_start: 0.8907 (ttt90) cc_final: 0.8551 (ttm110) REVERT: P 104 GLN cc_start: 0.9187 (mm-40) cc_final: 0.8918 (mm-40) REVERT: P 112 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8042 (mt) REVERT: Q 27 ARG cc_start: 0.7992 (ptt90) cc_final: 0.7696 (ttp80) REVERT: Q 29 ASN cc_start: 0.8009 (m-40) cc_final: 0.7576 (t0) REVERT: Q 66 VAL cc_start: 0.6981 (t) cc_final: 0.6610 (p) REVERT: Q 107 GLU cc_start: 0.8271 (tp30) cc_final: 0.7992 (pt0) REVERT: Q 114 GLN cc_start: 0.9161 (tp40) cc_final: 0.8536 (pt0) REVERT: Q 129 SER cc_start: 0.7190 (t) cc_final: 0.6750 (m) REVERT: R 7 LYS cc_start: 0.8382 (mtmt) cc_final: 0.8037 (tppt) REVERT: R 11 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7916 (mtpt) REVERT: R 21 TYR cc_start: 0.8951 (t80) cc_final: 0.8721 (t80) REVERT: R 22 THR cc_start: 0.8987 (m) cc_final: 0.8621 (t) REVERT: R 77 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7429 (mp0) REVERT: R 84 TYR cc_start: 0.8471 (t80) cc_final: 0.8172 (t80) REVERT: R 87 GLU cc_start: 0.8473 (pm20) cc_final: 0.8265 (tp30) REVERT: R 92 ASP cc_start: 0.8695 (t70) cc_final: 0.8304 (t0) REVERT: R 97 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7571 (mp0) REVERT: R 107 LYS cc_start: 0.9186 (tttt) cc_final: 0.8900 (mtpp) REVERT: S 63 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7372 (mt-10) REVERT: S 78 LYS cc_start: 0.9079 (tttt) cc_final: 0.8862 (mptt) REVERT: S 89 ASP cc_start: 0.8543 (m-30) cc_final: 0.8320 (m-30) REVERT: S 109 GLU cc_start: 0.9205 (tt0) cc_final: 0.8759 (mm-30) REVERT: S 112 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8113 (tt0) REVERT: T 13 GLU cc_start: 0.7752 (mp0) cc_final: 0.7506 (tp30) REVERT: T 24 LYS cc_start: 0.8851 (mmtt) cc_final: 0.8495 (ptmm) REVERT: T 122 LYS cc_start: 0.8123 (pttt) cc_final: 0.7829 (pptt) REVERT: T 126 GLN cc_start: 0.8532 (tt0) cc_final: 0.8129 (tm-30) REVERT: T 129 ARG cc_start: 0.8086 (mtt90) cc_final: 0.7705 (mtp-110) REVERT: Z 99 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8460 (tt) REVERT: Z 101 SER cc_start: 0.8288 (t) cc_final: 0.7699 (p) REVERT: c 13 ARG cc_start: 0.8535 (mmm-85) cc_final: 0.8331 (mmm-85) REVERT: c 26 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8329 (pt0) REVERT: f 114 ILE cc_start: 0.3067 (OUTLIER) cc_final: 0.2739 (tp) REVERT: f 118 ARG cc_start: 0.5147 (ttm-80) cc_final: 0.4850 (ttt90) REVERT: g 21 ILE cc_start: 0.8591 (mt) cc_final: 0.8318 (mm) REVERT: g 101 PHE cc_start: 0.7977 (m-80) cc_final: 0.7708 (m-80) REVERT: g 118 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8031 (mmm160) REVERT: A 32 PHE cc_start: 0.8810 (OUTLIER) cc_final: 0.8527 (t80) REVERT: A 111 GLN cc_start: 0.8762 (pm20) cc_final: 0.8551 (pm20) REVERT: A 151 ASP cc_start: 0.8848 (p0) cc_final: 0.8524 (p0) REVERT: A 166 LYS cc_start: 0.9003 (mttm) cc_final: 0.8656 (mtmm) REVERT: A 209 GLU cc_start: 0.8431 (tt0) cc_final: 0.7907 (tp30) REVERT: B 73 ASP cc_start: 0.8533 (m-30) cc_final: 0.8082 (t0) REVERT: B 168 MET cc_start: 0.8557 (ttm) cc_final: 0.8339 (ttm) REVERT: B 175 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8586 (mm-30) REVERT: B 203 SER cc_start: 0.9337 (p) cc_final: 0.8972 (t) REVERT: C 61 MET cc_start: 0.8415 (tpp) cc_final: 0.7397 (pmm) REVERT: C 68 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.7976 (mtp180) REVERT: C 77 SER cc_start: 0.9197 (t) cc_final: 0.8954 (p) REVERT: C 123 ARG cc_start: 0.8046 (ptm160) cc_final: 0.7117 (mpt-90) REVERT: C 144 SER cc_start: 0.8474 (p) cc_final: 0.8204 (p) REVERT: C 145 LYS cc_start: 0.8444 (mttt) cc_final: 0.8061 (mttm) REVERT: C 160 LEU cc_start: 0.8921 (mt) cc_final: 0.8609 (mp) REVERT: C 267 GLN cc_start: 0.8794 (tm-30) cc_final: 0.8200 (tm-30) REVERT: E 22 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8432 (ttmm) REVERT: E 71 LYS cc_start: 0.8078 (mtpt) cc_final: 0.7849 (mtpt) REVERT: E 87 MET cc_start: 0.9220 (tpp) cc_final: 0.8763 (mmm) REVERT: E 158 ASP cc_start: 0.8735 (m-30) cc_final: 0.8298 (m-30) REVERT: E 197 ASN cc_start: 0.8792 (t0) cc_final: 0.8567 (p0) REVERT: E 224 ASN cc_start: 0.8603 (m110) cc_final: 0.8293 (m-40) REVERT: E 237 SER cc_start: 0.9162 (t) cc_final: 0.8755 (m) REVERT: E 242 LYS cc_start: 0.9045 (mmmt) cc_final: 0.8800 (mptt) REVERT: E 253 ASP cc_start: 0.8718 (t70) cc_final: 0.8194 (m-30) REVERT: G 1 MET cc_start: 0.7914 (mmm) cc_final: 0.7458 (tpp) REVERT: G 17 GLU cc_start: 0.8893 (tt0) cc_final: 0.8354 (tm-30) REVERT: G 70 HIS cc_start: 0.7446 (m170) cc_final: 0.7156 (m170) REVERT: G 103 ASP cc_start: 0.8487 (t70) cc_final: 0.8066 (t70) REVERT: G 163 ASN cc_start: 0.7368 (p0) cc_final: 0.6640 (t0) REVERT: G 204 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8054 (mt-10) REVERT: G 219 GLU cc_start: 0.7225 (tm-30) cc_final: 0.6974 (tm-30) REVERT: G 226 GLU cc_start: 0.7950 (tt0) cc_final: 0.7685 (mt-10) REVERT: H 10 LYS cc_start: 0.9122 (mttt) cc_final: 0.8730 (ptmt) REVERT: H 50 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7510 (tm-30) REVERT: H 51 ILE cc_start: 0.7558 (pt) cc_final: 0.7356 (mt) REVERT: H 58 LYS cc_start: 0.8430 (mttt) cc_final: 0.8094 (pttt) REVERT: H 76 GLN cc_start: 0.8376 (tp40) cc_final: 0.7580 (tt0) REVERT: H 99 ARG cc_start: 0.8361 (mmt90) cc_final: 0.7995 (ttp80) REVERT: H 122 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8625 (tp) REVERT: H 148 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8828 (mt) REVERT: H 159 ASP cc_start: 0.9206 (OUTLIER) cc_final: 0.8903 (m-30) REVERT: I 73 THR cc_start: 0.8566 (m) cc_final: 0.8228 (p) REVERT: I 95 THR cc_start: 0.9508 (m) cc_final: 0.9044 (p) REVERT: I 139 LYS cc_start: 0.7743 (tmtp) cc_final: 0.7160 (ptmm) REVERT: I 159 SER cc_start: 0.7931 (m) cc_final: 0.7621 (t) REVERT: I 163 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7300 (tp30) REVERT: I 167 GLN cc_start: 0.7849 (mm-40) cc_final: 0.7416 (tp40) REVERT: J 88 ASP cc_start: 0.8443 (m-30) cc_final: 0.7828 (t0) REVERT: J 107 GLU cc_start: 0.8751 (tp30) cc_final: 0.8281 (tp30) REVERT: J 140 GLN cc_start: 0.8406 (tp40) cc_final: 0.8003 (tp-100) REVERT: J 154 GLN cc_start: 0.8527 (tt0) cc_final: 0.8239 (tt0) REVERT: L 39 ASN cc_start: 0.8160 (t0) cc_final: 0.7801 (p0) REVERT: L 48 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7992 (tppt) REVERT: L 130 GLU cc_start: 0.8539 (tt0) cc_final: 0.8273 (tt0) REVERT: N 27 LYS cc_start: 0.8710 (pttt) cc_final: 0.8276 (mmtt) REVERT: N 49 GLN cc_start: 0.8972 (mm-40) cc_final: 0.8515 (mt0) REVERT: N 86 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7895 (tt0) REVERT: O 86 LYS cc_start: 0.9300 (tppp) cc_final: 0.9069 (mmmt) REVERT: O 87 GLU cc_start: 0.8355 (tp30) cc_final: 0.7932 (mt-10) REVERT: O 143 LYS cc_start: 0.8552 (tmmt) cc_final: 0.8186 (tppt) REVERT: O 147 ARG cc_start: 0.8911 (tpt90) cc_final: 0.8152 (mtm110) REVERT: O 150 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7812 (mtt180) REVERT: V 4 ASP cc_start: 0.8486 (t70) cc_final: 0.8142 (p0) REVERT: V 32 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8207 (pt) REVERT: V 64 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8230 (mt-10) REVERT: W 31 SER cc_start: 0.9072 (t) cc_final: 0.8757 (p) REVERT: W 76 SER cc_start: 0.9416 (t) cc_final: 0.9066 (p) REVERT: W 84 LYS cc_start: 0.8798 (mttt) cc_final: 0.8330 (pttm) REVERT: W 104 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8554 (pp) REVERT: W 117 ARG cc_start: 0.8409 (tpp80) cc_final: 0.8132 (mtp85) REVERT: X 7 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8686 (tt) REVERT: X 50 ILE cc_start: 0.9096 (mt) cc_final: 0.8760 (pt) REVERT: X 61 GLN cc_start: 0.8530 (tp40) cc_final: 0.8172 (tp40) REVERT: X 69 CYS cc_start: 0.8671 (m) cc_final: 0.8223 (m) REVERT: X 127 ASN cc_start: 0.8966 (m-40) cc_final: 0.8705 (t0) REVERT: Y 18 LEU cc_start: 0.9009 (mt) cc_final: 0.8781 (mp) REVERT: Y 19 GLN cc_start: 0.9194 (mp10) cc_final: 0.8832 (mp10) REVERT: Y 42 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8729 (mt-10) REVERT: Y 53 ASP cc_start: 0.9180 (m-30) cc_final: 0.8903 (p0) REVERT: Y 61 ARG cc_start: 0.9028 (tpt170) cc_final: 0.8632 (mmm-85) REVERT: Y 68 LYS cc_start: 0.8894 (mttt) cc_final: 0.8668 (mppt) REVERT: Y 70 THR cc_start: 0.9016 (m) cc_final: 0.8768 (p) REVERT: Y 85 ASN cc_start: 0.8832 (m-40) cc_final: 0.8611 (m-40) REVERT: Y 109 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8081 (mt-10) REVERT: b 34 ASP cc_start: 0.8097 (t0) cc_final: 0.7106 (p0) REVERT: b 72 ARG cc_start: 0.8861 (ptt180) cc_final: 0.8412 (ptm-80) REVERT: e 25 LYS cc_start: 0.8392 (pttt) cc_final: 0.7992 (mmtm) REVERT: e 37 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8579 (mt0) REVERT: e 40 ARG cc_start: 0.8749 (ttt180) cc_final: 0.8522 (mtm180) REVERT: x 80 VAL cc_start: 0.9575 (OUTLIER) cc_final: 0.9346 (m) REVERT: x 88 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8807 (tt) REVERT: x 91 ASN cc_start: 0.8581 (m-40) cc_final: 0.8373 (m-40) REVERT: x 145 GLN cc_start: 0.8677 (tt0) cc_final: 0.8388 (mm110) REVERT: x 147 GLU cc_start: 0.8736 (mp0) cc_final: 0.8488 (mt-10) REVERT: x 172 LYS cc_start: 0.9040 (mptt) cc_final: 0.8739 (mtpp) REVERT: x 240 ASN cc_start: 0.8950 (m-40) cc_final: 0.8655 (m-40) REVERT: y 64 ARG cc_start: 0.8577 (mtt180) cc_final: 0.8036 (mtm-85) REVERT: y 75 ASP cc_start: 0.8373 (m-30) cc_final: 0.8002 (m-30) REVERT: y 85 GLN cc_start: 0.8406 (mm110) cc_final: 0.7927 (mt0) REVERT: y 109 LYS cc_start: 0.8157 (mmmm) cc_final: 0.7700 (ttpp) REVERT: y 251 HIS cc_start: 0.8267 (OUTLIER) cc_final: 0.7383 (m-70) REVERT: y 278 SER cc_start: 0.9221 (m) cc_final: 0.8709 (p) REVERT: y 342 GLU cc_start: 0.8846 (pm20) cc_final: 0.8354 (tp30) REVERT: u 219 LYS cc_start: 0.8780 (pttt) cc_final: 0.8340 (tttp) REVERT: u 225 THR cc_start: 0.7736 (OUTLIER) cc_final: 0.7507 (p) REVERT: u 228 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8199 (mt-10) REVERT: u 401 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8530 (tt0) REVERT: u 481 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8592 (tp30) REVERT: u 482 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7947 (tp30) REVERT: u 738 ARG cc_start: 0.8272 (mmt180) cc_final: 0.7957 (ttm110) REVERT: u 766 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8344 (pp) REVERT: w 194 LYS cc_start: 0.8654 (mttt) cc_final: 0.8088 (tmtt) REVERT: w 267 ARG cc_start: 0.8165 (ptt90) cc_final: 0.7143 (ttt180) REVERT: w 389 TYR cc_start: 0.6648 (m-80) cc_final: 0.4484 (m-80) REVERT: w 407 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7976 (mt) REVERT: v 30 HIS cc_start: 0.5822 (t70) cc_final: 0.5510 (t70) REVERT: v 123 LYS cc_start: 0.6516 (mtpp) cc_final: 0.6264 (mtpp) REVERT: v 183 ARG cc_start: 0.7564 (mtm-85) cc_final: 0.7176 (ttm-80) REVERT: v 213 MET cc_start: 0.8033 (mmm) cc_final: 0.7705 (mmm) REVERT: v 274 MET cc_start: 0.8311 (ptm) cc_final: 0.8002 (mtt) REVERT: v 507 ARG cc_start: 0.7703 (mtt180) cc_final: 0.7465 (mtp85) REVERT: v 523 LYS cc_start: 0.6112 (mttt) cc_final: 0.5245 (tptt) REVERT: t 250 MET cc_start: 0.4508 (OUTLIER) cc_final: 0.3991 (pmm) REVERT: t 259 HIS cc_start: 0.6659 (p-80) cc_final: 0.5288 (t-90) REVERT: t 304 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7415 (tt0) REVERT: t 313 ASN cc_start: 0.7320 (t0) cc_final: 0.6935 (t0) REVERT: t 440 GLU cc_start: 0.8408 (mt-10) cc_final: 0.7956 (tm-30) REVERT: t 456 LYS cc_start: 0.8475 (tttp) cc_final: 0.8224 (ttpt) REVERT: t 462 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7662 (tm-30) outliers start: 312 outliers final: 191 residues processed: 1255 average time/residue: 0.8021 time to fit residues: 1709.7718 Evaluate side-chains 1224 residues out of total 5267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 997 time to evaluate : 5.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 79 HIS Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain P residue 30 TYR Chi-restraints excluded: chain P residue 50 ARG Chi-restraints excluded: chain P residue 82 ASP Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 25 CYS Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 43 GLU Chi-restraints excluded: chain Q residue 72 VAL Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 11 LYS Chi-restraints excluded: chain R residue 24 LEU Chi-restraints excluded: chain R residue 70 SER Chi-restraints excluded: chain R residue 77 GLU Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain R residue 110 ASP Chi-restraints excluded: chain R residue 116 ASN Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 99 LEU Chi-restraints excluded: chain S residue 106 LYS Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 49 ASP Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain c residue 9 ILE Chi-restraints excluded: chain c residue 26 GLN Chi-restraints excluded: chain c residue 57 THR Chi-restraints excluded: chain c residue 59 LEU Chi-restraints excluded: chain c residue 61 SER Chi-restraints excluded: chain f residue 102 VAL Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 114 ILE Chi-restraints excluded: chain f residue 147 THR Chi-restraints excluded: chain g residue 46 THR Chi-restraints excluded: chain g residue 64 HIS Chi-restraints excluded: chain g residue 87 LEU Chi-restraints excluded: chain g residue 93 THR Chi-restraints excluded: chain g residue 118 ARG Chi-restraints excluded: chain g residue 157 SER Chi-restraints excluded: chain g residue 240 CYS Chi-restraints excluded: chain g residue 249 CYS Chi-restraints excluded: chain g residue 297 THR Chi-restraints excluded: chain g residue 303 THR Chi-restraints excluded: chain A residue 11 LYS Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 172 ASN Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 159 ASP Chi-restraints excluded: chain H residue 165 ASN Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 138 ASN Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 73 GLU Chi-restraints excluded: chain J residue 146 SER Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 48 LYS Chi-restraints excluded: chain L residue 60 CYS Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 80 MET Chi-restraints excluded: chain L residue 116 CYS Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain N residue 9 LYS Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 77 SER Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain N residue 143 SER Chi-restraints excluded: chain O residue 40 THR Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain O residue 150 ARG Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 70 LEU Chi-restraints excluded: chain W residue 42 MET Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 121 THR Chi-restraints excluded: chain X residue 7 LEU Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 45 SER Chi-restraints excluded: chain X residue 110 HIS Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Y residue 109 GLU Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain b residue 37 CYS Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 36 MET Chi-restraints excluded: chain e residue 37 GLN Chi-restraints excluded: chain x residue 78 ILE Chi-restraints excluded: chain x residue 80 VAL Chi-restraints excluded: chain x residue 88 LEU Chi-restraints excluded: chain x residue 102 HIS Chi-restraints excluded: chain x residue 118 ILE Chi-restraints excluded: chain x residue 130 LEU Chi-restraints excluded: chain x residue 152 LEU Chi-restraints excluded: chain x residue 160 LEU Chi-restraints excluded: chain x residue 162 SER Chi-restraints excluded: chain y residue 15 LEU Chi-restraints excluded: chain y residue 34 VAL Chi-restraints excluded: chain y residue 69 PHE Chi-restraints excluded: chain y residue 116 ILE Chi-restraints excluded: chain y residue 235 LEU Chi-restraints excluded: chain y residue 251 HIS Chi-restraints excluded: chain y residue 253 LEU Chi-restraints excluded: chain y residue 281 SER Chi-restraints excluded: chain y residue 303 ASP Chi-restraints excluded: chain y residue 351 LEU Chi-restraints excluded: chain y residue 359 THR Chi-restraints excluded: chain y residue 371 SER Chi-restraints excluded: chain y residue 389 ASP Chi-restraints excluded: chain y residue 404 SER Chi-restraints excluded: chain u residue 88 VAL Chi-restraints excluded: chain u residue 103 LEU Chi-restraints excluded: chain u residue 136 THR Chi-restraints excluded: chain u residue 207 LEU Chi-restraints excluded: chain u residue 217 HIS Chi-restraints excluded: chain u residue 222 LEU Chi-restraints excluded: chain u residue 225 THR Chi-restraints excluded: chain u residue 235 GLN Chi-restraints excluded: chain u residue 297 PHE Chi-restraints excluded: chain u residue 348 ASP Chi-restraints excluded: chain u residue 401 GLN Chi-restraints excluded: chain u residue 488 VAL Chi-restraints excluded: chain u residue 644 LEU Chi-restraints excluded: chain u residue 658 ILE Chi-restraints excluded: chain u residue 687 VAL Chi-restraints excluded: chain u residue 761 SER Chi-restraints excluded: chain u residue 766 LEU Chi-restraints excluded: chain u residue 778 THR Chi-restraints excluded: chain u residue 783 VAL Chi-restraints excluded: chain w residue 184 VAL Chi-restraints excluded: chain w residue 226 THR Chi-restraints excluded: chain w residue 306 ILE Chi-restraints excluded: chain w residue 317 ILE Chi-restraints excluded: chain w residue 407 LEU Chi-restraints excluded: chain w residue 414 SER Chi-restraints excluded: chain v residue 27 MET Chi-restraints excluded: chain v residue 101 MET Chi-restraints excluded: chain v residue 260 TRP Chi-restraints excluded: chain v residue 278 SER Chi-restraints excluded: chain t residue 250 MET Chi-restraints excluded: chain t residue 261 GLU Chi-restraints excluded: chain t residue 297 VAL Chi-restraints excluded: chain t residue 310 VAL Chi-restraints excluded: chain t residue 454 LEU Chi-restraints excluded: chain t residue 469 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 757 random chunks: chunk 609 optimal weight: 9.9990 chunk 415 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 544 optimal weight: 0.9990 chunk 301 optimal weight: 5.9990 chunk 624 optimal weight: 0.4980 chunk 505 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 373 optimal weight: 3.9990 chunk 656 optimal weight: 0.0970 chunk 184 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 GLN Z 106 GLN g 51 ASN ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 ASN E 201 HIS G 65 GLN G 110 ASN ** G 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 GLN ** O 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 GLN ** Y 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 29 ASN ** b 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 22 GLN e 37 GLN ** u 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 617 HIS ** w 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 201 HIS v 513 GLN t 469 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 88868 Z= 0.184 Angle : 0.573 14.109 127913 Z= 0.290 Chirality : 0.037 0.321 15645 Planarity : 0.004 0.054 10091 Dihedral : 23.117 179.873 32629 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.90 % Favored : 95.98 % Rotamer: Outliers : 5.66 % Allowed : 21.54 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.11), residues: 5968 helix: 1.36 (0.12), residues: 2076 sheet: -0.68 (0.15), residues: 1013 loop : -1.18 (0.11), residues: 2879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP w 213 HIS 0.008 0.001 HIS y 307 PHE 0.030 0.001 PHE w 249 TYR 0.020 0.001 TYR I 113 ARG 0.010 0.000 ARG P 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11936 Ramachandran restraints generated. 5968 Oldfield, 0 Emsley, 5968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11936 Ramachandran restraints generated. 5968 Oldfield, 0 Emsley, 5968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1338 residues out of total 5267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 1042 time to evaluate : 5.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 77 MET cc_start: 0.9065 (ptt) cc_final: 0.8855 (ptt) REVERT: F 79 HIS cc_start: 0.6485 (OUTLIER) cc_final: 0.6123 (t70) REVERT: F 81 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8155 (ptt90) REVERT: F 98 GLU cc_start: 0.8379 (tp30) cc_final: 0.7929 (tp30) REVERT: F 106 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8365 (tt0) REVERT: F 124 ASP cc_start: 0.8644 (t0) cc_final: 0.8403 (t0) REVERT: M 63 LYS cc_start: 0.7693 (mtmm) cc_final: 0.7204 (pttp) REVERT: M 91 LEU cc_start: 0.4623 (OUTLIER) cc_final: 0.3698 (mt) REVERT: P 30 TYR cc_start: 0.7870 (OUTLIER) cc_final: 0.6840 (t80) REVERT: P 31 GLU cc_start: 0.8725 (tt0) cc_final: 0.8485 (mp0) REVERT: P 32 GLN cc_start: 0.8978 (tt0) cc_final: 0.8582 (mp10) REVERT: P 41 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8660 (mm-40) REVERT: P 50 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7957 (mmt180) REVERT: P 51 ARG cc_start: 0.8877 (ttt90) cc_final: 0.8448 (ttm110) REVERT: P 104 GLN cc_start: 0.9123 (mm-40) cc_final: 0.8868 (mm-40) REVERT: P 112 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.7989 (mt) REVERT: P 130 ARG cc_start: 0.5950 (OUTLIER) cc_final: 0.5164 (mmt-90) REVERT: Q 27 ARG cc_start: 0.7938 (ptt90) cc_final: 0.7643 (ttp80) REVERT: Q 29 ASN cc_start: 0.7998 (m-40) cc_final: 0.7548 (t0) REVERT: Q 66 VAL cc_start: 0.7161 (OUTLIER) cc_final: 0.6815 (p) REVERT: Q 107 GLU cc_start: 0.8277 (tp30) cc_final: 0.7990 (pt0) REVERT: Q 129 SER cc_start: 0.7146 (t) cc_final: 0.6767 (m) REVERT: R 7 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.8049 (tppt) REVERT: R 11 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7880 (mtpt) REVERT: R 77 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7438 (mp0) REVERT: R 84 TYR cc_start: 0.8506 (t80) cc_final: 0.8221 (t80) REVERT: R 87 GLU cc_start: 0.8500 (pm20) cc_final: 0.8178 (tp30) REVERT: R 92 ASP cc_start: 0.8634 (t70) cc_final: 0.8274 (t70) REVERT: R 97 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7586 (mp0) REVERT: R 107 LYS cc_start: 0.9183 (tttt) cc_final: 0.8855 (mtpp) REVERT: S 77 TYR cc_start: 0.9076 (m-80) cc_final: 0.8766 (m-80) REVERT: S 107 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8397 (tt) REVERT: S 109 GLU cc_start: 0.9211 (tt0) cc_final: 0.8786 (mm-30) REVERT: S 112 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8084 (tt0) REVERT: T 24 LYS cc_start: 0.8836 (mmtt) cc_final: 0.8484 (ptmm) REVERT: T 122 LYS cc_start: 0.8097 (pttt) cc_final: 0.7832 (pptt) REVERT: T 126 GLN cc_start: 0.8566 (tt0) cc_final: 0.8141 (tm-30) REVERT: T 129 ARG cc_start: 0.8083 (mtt90) cc_final: 0.7694 (mtp-110) REVERT: Z 101 SER cc_start: 0.8080 (t) cc_final: 0.7430 (p) REVERT: Z 106 GLN cc_start: 0.8989 (tp-100) cc_final: 0.8754 (mm-40) REVERT: f 114 ILE cc_start: 0.3129 (OUTLIER) cc_final: 0.2785 (tp) REVERT: f 118 ARG cc_start: 0.5323 (ttm-80) cc_final: 0.5085 (ttt90) REVERT: f 146 LEU cc_start: 0.7778 (tt) cc_final: 0.7551 (tt) REVERT: g 21 ILE cc_start: 0.8616 (mt) cc_final: 0.8181 (mm) REVERT: g 101 PHE cc_start: 0.7952 (m-80) cc_final: 0.7692 (m-80) REVERT: g 118 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8013 (mmm160) REVERT: A 32 PHE cc_start: 0.8848 (OUTLIER) cc_final: 0.8637 (t80) REVERT: A 151 ASP cc_start: 0.8909 (p0) cc_final: 0.8565 (p0) REVERT: A 209 GLU cc_start: 0.8444 (tt0) cc_final: 0.7925 (tp30) REVERT: B 73 ASP cc_start: 0.8541 (m-30) cc_final: 0.8095 (t0) REVERT: B 168 MET cc_start: 0.8546 (ttm) cc_final: 0.8324 (ttm) REVERT: B 175 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8537 (mm-30) REVERT: B 203 SER cc_start: 0.9329 (p) cc_final: 0.8959 (t) REVERT: C 61 MET cc_start: 0.8397 (tpp) cc_final: 0.7466 (pmm) REVERT: C 68 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.7981 (mtp180) REVERT: C 77 SER cc_start: 0.9158 (t) cc_final: 0.8955 (p) REVERT: C 123 ARG cc_start: 0.8089 (ptm160) cc_final: 0.7079 (mpt-90) REVERT: C 144 SER cc_start: 0.8452 (p) cc_final: 0.8176 (p) REVERT: C 145 LYS cc_start: 0.8389 (mttt) cc_final: 0.8014 (mttm) REVERT: C 159 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8495 (mttp) REVERT: C 267 GLN cc_start: 0.8777 (tm-30) cc_final: 0.8180 (tm-30) REVERT: E 22 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8457 (ttmm) REVERT: E 158 ASP cc_start: 0.8743 (m-30) cc_final: 0.8346 (m-30) REVERT: E 197 ASN cc_start: 0.8769 (t0) cc_final: 0.8498 (p0) REVERT: E 224 ASN cc_start: 0.8627 (m110) cc_final: 0.8337 (m-40) REVERT: E 237 SER cc_start: 0.9164 (t) cc_final: 0.8765 (m) REVERT: E 242 LYS cc_start: 0.9031 (mmmt) cc_final: 0.8795 (mptt) REVERT: G 1 MET cc_start: 0.8037 (mmm) cc_final: 0.7572 (tpp) REVERT: G 17 GLU cc_start: 0.8913 (tt0) cc_final: 0.8407 (tm-30) REVERT: G 29 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8371 (mm-30) REVERT: G 103 ASP cc_start: 0.8532 (t70) cc_final: 0.8095 (t70) REVERT: G 163 ASN cc_start: 0.7378 (p0) cc_final: 0.6635 (t0) REVERT: G 203 LYS cc_start: 0.8296 (tttt) cc_final: 0.8049 (mmtt) REVERT: G 204 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8019 (mt-10) REVERT: G 219 GLU cc_start: 0.7280 (tm-30) cc_final: 0.7015 (tm-30) REVERT: G 226 GLU cc_start: 0.8009 (tt0) cc_final: 0.7688 (mt-10) REVERT: H 10 LYS cc_start: 0.9115 (mttt) cc_final: 0.8728 (ptmt) REVERT: H 50 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7583 (tm-30) REVERT: H 58 LYS cc_start: 0.8393 (mttt) cc_final: 0.8038 (pttt) REVERT: H 76 GLN cc_start: 0.8310 (tp40) cc_final: 0.7562 (tt0) REVERT: H 99 ARG cc_start: 0.8392 (mmt90) cc_final: 0.8005 (ttp80) REVERT: H 122 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8595 (tp) REVERT: H 159 ASP cc_start: 0.9199 (OUTLIER) cc_final: 0.8894 (m-30) REVERT: I 73 THR cc_start: 0.8497 (m) cc_final: 0.8155 (p) REVERT: I 95 THR cc_start: 0.9502 (m) cc_final: 0.9123 (p) REVERT: I 139 LYS cc_start: 0.7813 (tmtp) cc_final: 0.7147 (ptmm) REVERT: I 159 SER cc_start: 0.7945 (m) cc_final: 0.7631 (t) REVERT: I 163 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7263 (tp30) REVERT: I 167 GLN cc_start: 0.7839 (mm-40) cc_final: 0.7381 (tp40) REVERT: J 107 GLU cc_start: 0.8738 (tp30) cc_final: 0.8254 (tp30) REVERT: J 154 GLN cc_start: 0.8555 (tt0) cc_final: 0.8255 (tt0) REVERT: L 39 ASN cc_start: 0.8143 (t0) cc_final: 0.7809 (p0) REVERT: L 48 LYS cc_start: 0.8160 (tttp) cc_final: 0.7882 (tppt) REVERT: L 130 GLU cc_start: 0.8534 (tt0) cc_final: 0.8161 (tt0) REVERT: N 27 LYS cc_start: 0.8742 (pttt) cc_final: 0.8331 (mmtt) REVERT: N 49 GLN cc_start: 0.8933 (mm-40) cc_final: 0.8515 (mt0) REVERT: N 86 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8024 (tt0) REVERT: O 86 LYS cc_start: 0.9268 (tppp) cc_final: 0.9027 (mmmt) REVERT: O 87 GLU cc_start: 0.8313 (tp30) cc_final: 0.7877 (mt-10) REVERT: O 143 LYS cc_start: 0.8517 (tmmt) cc_final: 0.8117 (tppt) REVERT: O 147 ARG cc_start: 0.8922 (tpt90) cc_final: 0.8157 (mtm110) REVERT: O 150 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7707 (mtt180) REVERT: V 4 ASP cc_start: 0.8504 (t70) cc_final: 0.8180 (p0) REVERT: V 32 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8187 (pt) REVERT: V 64 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8324 (mt-10) REVERT: V 80 SER cc_start: 0.8263 (t) cc_final: 0.8061 (p) REVERT: W 31 SER cc_start: 0.9044 (t) cc_final: 0.8728 (p) REVERT: W 76 SER cc_start: 0.9354 (t) cc_final: 0.9034 (p) REVERT: W 104 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8534 (pp) REVERT: W 117 ARG cc_start: 0.8420 (tpp80) cc_final: 0.8202 (mtp85) REVERT: X 7 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8740 (tt) REVERT: X 50 ILE cc_start: 0.9104 (mt) cc_final: 0.8764 (pt) REVERT: X 61 GLN cc_start: 0.8413 (tp40) cc_final: 0.7881 (mm-40) REVERT: X 69 CYS cc_start: 0.8657 (m) cc_final: 0.8213 (m) REVERT: X 127 ASN cc_start: 0.8982 (m-40) cc_final: 0.8681 (t0) REVERT: Y 19 GLN cc_start: 0.9159 (mp10) cc_final: 0.8793 (mp10) REVERT: Y 42 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8770 (mt-10) REVERT: Y 53 ASP cc_start: 0.9156 (m-30) cc_final: 0.8908 (p0) REVERT: Y 61 ARG cc_start: 0.9014 (tpt170) cc_final: 0.8556 (mmm-85) REVERT: Y 68 LYS cc_start: 0.8855 (mttt) cc_final: 0.8604 (mppt) REVERT: Y 70 THR cc_start: 0.8946 (m) cc_final: 0.8668 (p) REVERT: Y 85 ASN cc_start: 0.8864 (m-40) cc_final: 0.8652 (m-40) REVERT: Y 108 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7600 (mtpp) REVERT: Y 109 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8092 (mt-10) REVERT: b 34 ASP cc_start: 0.8089 (t0) cc_final: 0.7134 (p0) REVERT: b 72 ARG cc_start: 0.8871 (ptt180) cc_final: 0.8421 (ptm-80) REVERT: e 25 LYS cc_start: 0.8364 (pttt) cc_final: 0.8006 (mmtm) REVERT: e 40 ARG cc_start: 0.8827 (ttt180) cc_final: 0.8578 (mtm180) REVERT: x 88 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8740 (tt) REVERT: x 130 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7577 (tp) REVERT: x 145 GLN cc_start: 0.8620 (tt0) cc_final: 0.8366 (mm110) REVERT: x 147 GLU cc_start: 0.8724 (mp0) cc_final: 0.8494 (mt-10) REVERT: x 172 LYS cc_start: 0.9052 (mptt) cc_final: 0.8756 (mtpp) REVERT: x 240 ASN cc_start: 0.8940 (m-40) cc_final: 0.8637 (m-40) REVERT: y 75 ASP cc_start: 0.8382 (m-30) cc_final: 0.7993 (m-30) REVERT: y 85 GLN cc_start: 0.8354 (mm110) cc_final: 0.7887 (mt0) REVERT: y 109 LYS cc_start: 0.8110 (mmmm) cc_final: 0.7662 (ttpp) REVERT: y 251 HIS cc_start: 0.8219 (OUTLIER) cc_final: 0.7385 (m-70) REVERT: y 278 SER cc_start: 0.9245 (m) cc_final: 0.8533 (p) REVERT: y 280 MET cc_start: 0.8274 (mmm) cc_final: 0.8073 (mpp) REVERT: y 342 GLU cc_start: 0.8799 (pm20) cc_final: 0.8297 (tp30) REVERT: u 96 LEU cc_start: 0.8539 (pp) cc_final: 0.8331 (tt) REVERT: u 148 ASP cc_start: 0.8133 (m-30) cc_final: 0.7919 (m-30) REVERT: u 178 PHE cc_start: 0.9284 (m-80) cc_final: 0.8945 (m-10) REVERT: u 219 LYS cc_start: 0.8739 (pttt) cc_final: 0.8329 (tttp) REVERT: u 222 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7775 (mt) REVERT: u 225 THR cc_start: 0.7715 (OUTLIER) cc_final: 0.7330 (p) REVERT: u 228 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8383 (mt-10) REVERT: u 481 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8632 (tp30) REVERT: u 494 VAL cc_start: 0.8249 (OUTLIER) cc_final: 0.7914 (p) REVERT: u 738 ARG cc_start: 0.8260 (mmt180) cc_final: 0.7989 (ttm110) REVERT: u 766 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8363 (pp) REVERT: w 194 LYS cc_start: 0.8682 (mttt) cc_final: 0.8100 (tmtt) REVERT: w 267 ARG cc_start: 0.8218 (ptt90) cc_final: 0.7108 (mmm-85) REVERT: w 294 LEU cc_start: 0.8586 (tt) cc_final: 0.8206 (pp) REVERT: w 302 LEU cc_start: 0.8650 (mt) cc_final: 0.8433 (mp) REVERT: v 183 ARG cc_start: 0.7619 (mtm-85) cc_final: 0.7228 (ttm-80) REVERT: v 213 MET cc_start: 0.7945 (mmm) cc_final: 0.7608 (mmm) REVERT: v 274 MET cc_start: 0.8333 (ptm) cc_final: 0.8068 (mtt) REVERT: v 496 ILE cc_start: 0.7851 (OUTLIER) cc_final: 0.7033 (tp) REVERT: v 503 GLN cc_start: 0.8358 (tt0) cc_final: 0.7776 (tm-30) REVERT: v 519 ARG cc_start: 0.7585 (ttm110) cc_final: 0.6812 (tpm170) REVERT: v 523 LYS cc_start: 0.6106 (mttt) cc_final: 0.5345 (tptt) REVERT: t 250 MET cc_start: 0.4282 (OUTLIER) cc_final: 0.3871 (pmm) REVERT: t 259 HIS cc_start: 0.6722 (p-80) cc_final: 0.5306 (t-90) REVERT: t 313 ASN cc_start: 0.7248 (t0) cc_final: 0.6894 (t0) REVERT: t 440 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7945 (tm-30) REVERT: t 462 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7581 (tm-30) REVERT: t 466 LEU cc_start: 0.8326 (mt) cc_final: 0.8042 (mt) REVERT: t 471 GLU cc_start: 0.8252 (tt0) cc_final: 0.7521 (pm20) outliers start: 296 outliers final: 191 residues processed: 1231 average time/residue: 0.8749 time to fit residues: 1856.4369 Evaluate side-chains 1212 residues out of total 5267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 984 time to evaluate : 5.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 79 HIS Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 72 HIS Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain P residue 30 TYR Chi-restraints excluded: chain P residue 41 GLN Chi-restraints excluded: chain P residue 50 ARG Chi-restraints excluded: chain P residue 82 ASP Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain P residue 130 ARG Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 25 CYS Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 43 GLU Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 72 VAL Chi-restraints excluded: chain R residue 7 LYS Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 11 LYS Chi-restraints excluded: chain R residue 24 LEU Chi-restraints excluded: chain R residue 70 SER Chi-restraints excluded: chain R residue 77 GLU Chi-restraints excluded: chain R residue 81 ARG Chi-restraints excluded: chain R residue 110 ASP Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 116 ASN Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 68 ILE Chi-restraints excluded: chain S residue 85 ASN Chi-restraints excluded: chain S residue 99 LEU Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 49 ASP Chi-restraints excluded: chain Z residue 97 ILE Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain c residue 9 ILE Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 37 ASP Chi-restraints excluded: chain c residue 57 THR Chi-restraints excluded: chain c residue 59 LEU Chi-restraints excluded: chain c residue 61 SER Chi-restraints excluded: chain f residue 102 VAL Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 114 ILE Chi-restraints excluded: chain f residue 147 THR Chi-restraints excluded: chain g residue 46 THR Chi-restraints excluded: chain g residue 64 HIS Chi-restraints excluded: chain g residue 93 THR Chi-restraints excluded: chain g residue 118 ARG Chi-restraints excluded: chain g residue 157 SER Chi-restraints excluded: chain g residue 203 ASP Chi-restraints excluded: chain g residue 240 CYS Chi-restraints excluded: chain g residue 249 CYS Chi-restraints excluded: chain g residue 265 ILE Chi-restraints excluded: chain g residue 287 THR Chi-restraints excluded: chain g residue 297 THR Chi-restraints excluded: chain g residue 303 THR Chi-restraints excluded: chain A residue 11 LYS Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 159 LYS Chi-restraints excluded: chain C residue 172 ASN Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 159 ASP Chi-restraints excluded: chain H residue 165 ASN Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 138 ASN Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 73 GLU Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain J residue 146 SER Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 60 CYS Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 80 MET Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain N residue 9 LYS Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 77 SER Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 150 ARG Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 70 LEU Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 121 THR Chi-restraints excluded: chain X residue 7 LEU Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 110 HIS Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 55 ILE Chi-restraints excluded: chain Y residue 108 LYS Chi-restraints excluded: chain Y residue 109 GLU Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain b residue 33 MET Chi-restraints excluded: chain b residue 37 CYS Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 48 SER Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain x residue 78 ILE Chi-restraints excluded: chain x residue 88 LEU Chi-restraints excluded: chain x residue 102 HIS Chi-restraints excluded: chain x residue 118 ILE Chi-restraints excluded: chain x residue 130 LEU Chi-restraints excluded: chain x residue 152 LEU Chi-restraints excluded: chain x residue 160 LEU Chi-restraints excluded: chain x residue 218 ILE Chi-restraints excluded: chain y residue 34 VAL Chi-restraints excluded: chain y residue 68 GLU Chi-restraints excluded: chain y residue 69 PHE Chi-restraints excluded: chain y residue 116 ILE Chi-restraints excluded: chain y residue 235 LEU Chi-restraints excluded: chain y residue 251 HIS Chi-restraints excluded: chain y residue 253 LEU Chi-restraints excluded: chain y residue 256 ASN Chi-restraints excluded: chain y residue 260 ILE Chi-restraints excluded: chain y residue 281 SER Chi-restraints excluded: chain y residue 303 ASP Chi-restraints excluded: chain y residue 351 LEU Chi-restraints excluded: chain y residue 359 THR Chi-restraints excluded: chain y residue 360 ASN Chi-restraints excluded: chain y residue 371 SER Chi-restraints excluded: chain y residue 379 SER Chi-restraints excluded: chain y residue 389 ASP Chi-restraints excluded: chain y residue 404 SER Chi-restraints excluded: chain u residue 88 VAL Chi-restraints excluded: chain u residue 136 THR Chi-restraints excluded: chain u residue 207 LEU Chi-restraints excluded: chain u residue 217 HIS Chi-restraints excluded: chain u residue 222 LEU Chi-restraints excluded: chain u residue 225 THR Chi-restraints excluded: chain u residue 297 PHE Chi-restraints excluded: chain u residue 348 ASP Chi-restraints excluded: chain u residue 494 VAL Chi-restraints excluded: chain u residue 630 SER Chi-restraints excluded: chain u residue 644 LEU Chi-restraints excluded: chain u residue 658 ILE Chi-restraints excluded: chain u residue 687 VAL Chi-restraints excluded: chain u residue 761 SER Chi-restraints excluded: chain u residue 766 LEU Chi-restraints excluded: chain u residue 778 THR Chi-restraints excluded: chain w residue 226 THR Chi-restraints excluded: chain w residue 306 ILE Chi-restraints excluded: chain w residue 317 ILE Chi-restraints excluded: chain w residue 403 GLU Chi-restraints excluded: chain w residue 414 SER Chi-restraints excluded: chain v residue 27 MET Chi-restraints excluded: chain v residue 101 MET Chi-restraints excluded: chain v residue 236 LEU Chi-restraints excluded: chain v residue 260 TRP Chi-restraints excluded: chain v residue 278 SER Chi-restraints excluded: chain v residue 496 ILE Chi-restraints excluded: chain v residue 522 GLN Chi-restraints excluded: chain t residue 250 MET Chi-restraints excluded: chain t residue 261 GLU Chi-restraints excluded: chain t residue 297 VAL Chi-restraints excluded: chain t residue 310 VAL Chi-restraints excluded: chain t residue 454 LEU Chi-restraints excluded: chain t residue 469 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 757 random chunks: chunk 246 optimal weight: 6.9990 chunk 658 optimal weight: 1.9990 chunk 144 optimal weight: 10.0000 chunk 429 optimal weight: 7.9990 chunk 180 optimal weight: 1.9990 chunk 732 optimal weight: 0.1980 chunk 608 optimal weight: 3.9990 chunk 339 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 242 optimal weight: 5.9990 chunk 384 optimal weight: 2.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 GLN ** Q 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 103 HIS g 51 ASN ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 ASN C 136 HIS G 65 GLN G 110 ASN ** G 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 GLN ** N 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 GLN ** Y 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 22 GLN e 37 GLN x 91 ASN ** u 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 247 GLN ** w 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 513 GLN t 469 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 88868 Z= 0.244 Angle : 0.600 14.068 127913 Z= 0.304 Chirality : 0.038 0.343 15645 Planarity : 0.004 0.074 10091 Dihedral : 23.094 179.680 32618 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.39 % Favored : 95.49 % Rotamer: Outliers : 5.95 % Allowed : 22.17 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.11), residues: 5968 helix: 1.31 (0.11), residues: 2074 sheet: -0.72 (0.16), residues: 1002 loop : -1.15 (0.11), residues: 2892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP w 213 HIS 0.007 0.001 HIS y 307 PHE 0.023 0.002 PHE S 9 TYR 0.019 0.002 TYR t 361 ARG 0.006 0.000 ARG M 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11936 Ramachandran restraints generated. 5968 Oldfield, 0 Emsley, 5968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11936 Ramachandran restraints generated. 5968 Oldfield, 0 Emsley, 5968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1327 residues out of total 5267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 311 poor density : 1016 time to evaluate : 5.453 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: F 81 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8100 (ptt90) REVERT: F 98 GLU cc_start: 0.8413 (tp30) cc_final: 0.7966 (tp30) REVERT: F 106 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8390 (tt0) REVERT: M 63 LYS cc_start: 0.7717 (mtmm) cc_final: 0.7234 (pttp) REVERT: M 74 ILE cc_start: 0.6501 (mm) cc_final: 0.6272 (mp) REVERT: M 91 LEU cc_start: 0.4758 (OUTLIER) cc_final: 0.3770 (mt) REVERT: P 30 TYR cc_start: 0.7918 (OUTLIER) cc_final: 0.6861 (t80) REVERT: P 31 GLU cc_start: 0.8846 (tt0) cc_final: 0.8620 (mp0) REVERT: P 32 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8741 (mp10) REVERT: P 41 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8509 (mm-40) REVERT: P 50 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.8066 (mmt180) REVERT: P 51 ARG cc_start: 0.8889 (ttt90) cc_final: 0.8448 (ttm110) REVERT: P 56 LEU cc_start: 0.8829 (tt) cc_final: 0.8593 (tt) REVERT: P 104 GLN cc_start: 0.9119 (mm-40) cc_final: 0.8843 (mm-40) REVERT: P 130 ARG cc_start: 0.6116 (OUTLIER) cc_final: 0.5276 (mmt-90) REVERT: Q 27 ARG cc_start: 0.7972 (ptt90) cc_final: 0.7684 (ttp80) REVERT: Q 29 ASN cc_start: 0.7994 (m-40) cc_final: 0.7571 (t0) REVERT: Q 66 VAL cc_start: 0.7318 (t) cc_final: 0.6963 (p) REVERT: Q 107 GLU cc_start: 0.8277 (tp30) cc_final: 0.7996 (pt0) REVERT: Q 129 SER cc_start: 0.6974 (t) cc_final: 0.6573 (m) REVERT: R 7 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8018 (tppt) REVERT: R 11 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7831 (mtpt) REVERT: R 63 ARG cc_start: 0.9199 (mmm-85) cc_final: 0.8715 (mmp80) REVERT: R 77 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7468 (mp0) REVERT: R 84 TYR cc_start: 0.8503 (t80) cc_final: 0.8222 (t80) REVERT: R 87 GLU cc_start: 0.8436 (pm20) cc_final: 0.8209 (tp30) REVERT: R 92 ASP cc_start: 0.8739 (t70) cc_final: 0.8419 (t70) REVERT: R 107 LYS cc_start: 0.9193 (tttt) cc_final: 0.8870 (mtpp) REVERT: S 77 TYR cc_start: 0.9102 (m-80) cc_final: 0.8781 (m-80) REVERT: S 107 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8375 (tt) REVERT: S 109 GLU cc_start: 0.9216 (tt0) cc_final: 0.8801 (mm-30) REVERT: S 112 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8133 (tt0) REVERT: T 13 GLU cc_start: 0.7915 (mp0) cc_final: 0.7557 (tp30) REVERT: T 24 LYS cc_start: 0.8820 (mmtt) cc_final: 0.8470 (ptmm) REVERT: T 122 LYS cc_start: 0.8128 (pttt) cc_final: 0.7852 (pptt) REVERT: T 126 GLN cc_start: 0.8656 (tt0) cc_final: 0.8200 (tm-30) REVERT: T 129 ARG cc_start: 0.8100 (mtt90) cc_final: 0.7740 (mtp-110) REVERT: Z 101 SER cc_start: 0.8185 (t) cc_final: 0.7503 (p) REVERT: f 114 ILE cc_start: 0.3162 (OUTLIER) cc_final: 0.2801 (tp) REVERT: g 21 ILE cc_start: 0.8538 (mt) cc_final: 0.8289 (mm) REVERT: g 101 PHE cc_start: 0.7953 (m-80) cc_final: 0.7676 (m-80) REVERT: g 118 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7911 (ttm-80) REVERT: g 228 TYR cc_start: 0.7067 (m-80) cc_final: 0.6845 (t80) REVERT: g 246 TYR cc_start: 0.7732 (t80) cc_final: 0.7513 (t80) REVERT: A 9 GLN cc_start: 0.9032 (mm110) cc_final: 0.8714 (mm-40) REVERT: A 34 MET cc_start: 0.8969 (mmm) cc_final: 0.8755 (mmm) REVERT: A 151 ASP cc_start: 0.8984 (p0) cc_final: 0.8552 (p0) REVERT: B 73 ASP cc_start: 0.8527 (m-30) cc_final: 0.8121 (t0) REVERT: B 175 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8585 (mm-30) REVERT: B 203 SER cc_start: 0.9388 (p) cc_final: 0.9021 (t) REVERT: C 61 MET cc_start: 0.8390 (tpp) cc_final: 0.7518 (pmm) REVERT: C 68 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8009 (mtp180) REVERT: C 77 SER cc_start: 0.9170 (t) cc_final: 0.8945 (p) REVERT: C 123 ARG cc_start: 0.7997 (ptm160) cc_final: 0.7003 (mpt-90) REVERT: C 145 LYS cc_start: 0.8419 (mttt) cc_final: 0.8088 (mttm) REVERT: C 159 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8497 (mttp) REVERT: C 160 LEU cc_start: 0.8720 (mp) cc_final: 0.8500 (mp) REVERT: C 267 GLN cc_start: 0.8762 (tm-30) cc_final: 0.8490 (tm-30) REVERT: E 158 ASP cc_start: 0.8774 (m-30) cc_final: 0.8433 (m-30) REVERT: E 224 ASN cc_start: 0.8720 (m110) cc_final: 0.8422 (m-40) REVERT: E 237 SER cc_start: 0.9120 (t) cc_final: 0.8743 (m) REVERT: G 1 MET cc_start: 0.8078 (mmm) cc_final: 0.7693 (tpp) REVERT: G 17 GLU cc_start: 0.8934 (tt0) cc_final: 0.8434 (tm-30) REVERT: G 41 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8821 (tp) REVERT: G 103 ASP cc_start: 0.8720 (t70) cc_final: 0.8139 (t70) REVERT: G 163 ASN cc_start: 0.7494 (p0) cc_final: 0.6654 (t0) REVERT: G 203 LYS cc_start: 0.8308 (tttt) cc_final: 0.7978 (mmmt) REVERT: G 204 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8125 (mt-10) REVERT: G 219 GLU cc_start: 0.7372 (tm-30) cc_final: 0.7101 (tm-30) REVERT: G 226 GLU cc_start: 0.8037 (tt0) cc_final: 0.7663 (mt-10) REVERT: H 10 LYS cc_start: 0.9130 (mttt) cc_final: 0.8748 (ptmt) REVERT: H 35 ASP cc_start: 0.7152 (p0) cc_final: 0.6848 (p0) REVERT: H 58 LYS cc_start: 0.8360 (mttt) cc_final: 0.7995 (pttt) REVERT: H 76 GLN cc_start: 0.8292 (tp40) cc_final: 0.7547 (tt0) REVERT: H 78 ARG cc_start: 0.8223 (mtp85) cc_final: 0.7975 (mtp180) REVERT: H 99 ARG cc_start: 0.8414 (mmt90) cc_final: 0.7998 (ttp80) REVERT: H 159 ASP cc_start: 0.9190 (OUTLIER) cc_final: 0.8891 (m-30) REVERT: I 73 THR cc_start: 0.8521 (m) cc_final: 0.8169 (p) REVERT: I 95 THR cc_start: 0.9508 (m) cc_final: 0.9070 (p) REVERT: I 139 LYS cc_start: 0.7838 (tmtp) cc_final: 0.7188 (pttp) REVERT: I 159 SER cc_start: 0.8064 (m) cc_final: 0.7761 (t) REVERT: I 163 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7302 (tp30) REVERT: I 167 GLN cc_start: 0.7791 (mm-40) cc_final: 0.7322 (tp40) REVERT: J 34 GLU cc_start: 0.8818 (tp30) cc_final: 0.8591 (tt0) REVERT: J 107 GLU cc_start: 0.8739 (tp30) cc_final: 0.8271 (tp30) REVERT: J 140 GLN cc_start: 0.8389 (tp40) cc_final: 0.8005 (tp-100) REVERT: J 154 GLN cc_start: 0.8568 (tt0) cc_final: 0.8266 (tt0) REVERT: N 27 LYS cc_start: 0.8756 (pttt) cc_final: 0.8432 (mmtt) REVERT: N 49 GLN cc_start: 0.8980 (mm-40) cc_final: 0.8512 (mt0) REVERT: N 86 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8076 (tt0) REVERT: O 86 LYS cc_start: 0.9301 (tppp) cc_final: 0.9040 (mmmt) REVERT: O 87 GLU cc_start: 0.8302 (tp30) cc_final: 0.7858 (mt-10) REVERT: O 143 LYS cc_start: 0.8537 (tmmt) cc_final: 0.8131 (tppt) REVERT: O 147 ARG cc_start: 0.8970 (tpt90) cc_final: 0.8260 (mtm110) REVERT: O 150 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7717 (mtt180) REVERT: V 4 ASP cc_start: 0.8511 (t70) cc_final: 0.8174 (p0) REVERT: V 32 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8227 (pt) REVERT: V 64 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8364 (mt-10) REVERT: W 31 SER cc_start: 0.9044 (t) cc_final: 0.8623 (p) REVERT: W 76 SER cc_start: 0.9350 (t) cc_final: 0.9018 (p) REVERT: W 104 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8541 (pp) REVERT: W 117 ARG cc_start: 0.8461 (tpp80) cc_final: 0.8211 (mtp85) REVERT: X 7 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8846 (tt) REVERT: X 50 ILE cc_start: 0.9067 (mt) cc_final: 0.8701 (pt) REVERT: X 69 CYS cc_start: 0.8606 (m) cc_final: 0.8164 (m) REVERT: X 127 ASN cc_start: 0.8986 (m-40) cc_final: 0.8668 (t0) REVERT: Y 19 GLN cc_start: 0.9319 (mp10) cc_final: 0.8868 (mp10) REVERT: Y 42 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8818 (mt-10) REVERT: Y 53 ASP cc_start: 0.9196 (m-30) cc_final: 0.8942 (p0) REVERT: Y 61 ARG cc_start: 0.9027 (tpt170) cc_final: 0.8593 (mmm-85) REVERT: Y 68 LYS cc_start: 0.8870 (mttt) cc_final: 0.8603 (mppt) REVERT: Y 70 THR cc_start: 0.8962 (m) cc_final: 0.8718 (t) REVERT: Y 85 ASN cc_start: 0.8848 (m-40) cc_final: 0.8587 (m-40) REVERT: Y 104 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7548 (mtp-110) REVERT: Y 108 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7624 (mtpp) REVERT: Y 109 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8105 (mt-10) REVERT: b 34 ASP cc_start: 0.8077 (t0) cc_final: 0.7204 (p0) REVERT: b 72 ARG cc_start: 0.8896 (ptt180) cc_final: 0.8438 (ptm-80) REVERT: e 25 LYS cc_start: 0.8360 (pttt) cc_final: 0.8059 (mmtm) REVERT: e 40 ARG cc_start: 0.8855 (ttt180) cc_final: 0.8630 (mtm180) REVERT: x 88 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8810 (tt) REVERT: x 130 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7534 (tp) REVERT: x 145 GLN cc_start: 0.8551 (tt0) cc_final: 0.8310 (mm110) REVERT: x 147 GLU cc_start: 0.8715 (mp0) cc_final: 0.8511 (mt-10) REVERT: x 172 LYS cc_start: 0.9067 (mptt) cc_final: 0.8759 (mtpp) REVERT: x 240 ASN cc_start: 0.8941 (m-40) cc_final: 0.8647 (m-40) REVERT: y 75 ASP cc_start: 0.8398 (m-30) cc_final: 0.8142 (m-30) REVERT: y 85 GLN cc_start: 0.8414 (mm110) cc_final: 0.7940 (mt0) REVERT: y 109 LYS cc_start: 0.8117 (mmmm) cc_final: 0.7789 (ttpt) REVERT: y 251 HIS cc_start: 0.8213 (OUTLIER) cc_final: 0.7474 (m-70) REVERT: y 280 MET cc_start: 0.8321 (mmm) cc_final: 0.8110 (mpp) REVERT: y 342 GLU cc_start: 0.8867 (pm20) cc_final: 0.8380 (tp30) REVERT: y 345 ARG cc_start: 0.8440 (ttp-110) cc_final: 0.8199 (ttt180) REVERT: u 96 LEU cc_start: 0.8598 (pp) cc_final: 0.8350 (tt) REVERT: u 123 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8540 (tpp) REVERT: u 148 ASP cc_start: 0.8143 (m-30) cc_final: 0.7940 (m-30) REVERT: u 219 LYS cc_start: 0.8777 (pttt) cc_final: 0.8311 (tttp) REVERT: u 222 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7434 (mt) REVERT: u 225 THR cc_start: 0.7721 (OUTLIER) cc_final: 0.7428 (p) REVERT: u 228 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8341 (mt-10) REVERT: u 395 LYS cc_start: 0.7678 (tptm) cc_final: 0.6717 (mmtt) REVERT: u 476 LYS cc_start: 0.8156 (mttt) cc_final: 0.7839 (mmtt) REVERT: u 481 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8608 (tp30) REVERT: u 494 VAL cc_start: 0.8231 (OUTLIER) cc_final: 0.7883 (p) REVERT: u 738 ARG cc_start: 0.8343 (mmt180) cc_final: 0.8033 (ttm110) REVERT: u 766 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8321 (pp) REVERT: w 194 LYS cc_start: 0.8700 (mttt) cc_final: 0.8072 (tmtt) REVERT: w 267 ARG cc_start: 0.8280 (ptt90) cc_final: 0.7200 (mmm-85) REVERT: w 294 LEU cc_start: 0.8613 (tt) cc_final: 0.8183 (pp) REVERT: w 389 TYR cc_start: 0.6491 (m-80) cc_final: 0.6102 (m-80) REVERT: w 407 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.8005 (mt) REVERT: v 123 LYS cc_start: 0.6207 (OUTLIER) cc_final: 0.5974 (mmmt) REVERT: v 183 ARG cc_start: 0.7689 (mtm-85) cc_final: 0.7289 (ttm-80) REVERT: v 213 MET cc_start: 0.7995 (mmm) cc_final: 0.7749 (mmp) REVERT: v 274 MET cc_start: 0.8382 (ptm) cc_final: 0.8072 (mtt) REVERT: v 496 ILE cc_start: 0.7905 (OUTLIER) cc_final: 0.7184 (tp) REVERT: v 503 GLN cc_start: 0.8326 (tt0) cc_final: 0.7943 (tm-30) REVERT: v 523 LYS cc_start: 0.6206 (mttt) cc_final: 0.5435 (tptt) REVERT: t 250 MET cc_start: 0.4334 (OUTLIER) cc_final: 0.3860 (pmm) REVERT: t 259 HIS cc_start: 0.6605 (p-80) cc_final: 0.5417 (t-90) REVERT: t 304 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7449 (tt0) REVERT: t 313 ASN cc_start: 0.7135 (t0) cc_final: 0.6812 (t0) REVERT: t 366 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8539 (pp) REVERT: t 440 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7912 (tm-30) REVERT: t 462 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7583 (tm-30) REVERT: t 467 LYS cc_start: 0.8305 (mttt) cc_final: 0.7700 (mmtm) REVERT: t 471 GLU cc_start: 0.8185 (tt0) cc_final: 0.7398 (pm20) outliers start: 311 outliers final: 213 residues processed: 1220 average time/residue: 0.7934 time to fit residues: 1644.3212 Evaluate side-chains 1229 residues out of total 5267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 978 time to evaluate : 5.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 72 HIS Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain P residue 30 TYR Chi-restraints excluded: chain P residue 32 GLN Chi-restraints excluded: chain P residue 41 GLN Chi-restraints excluded: chain P residue 50 ARG Chi-restraints excluded: chain P residue 82 ASP Chi-restraints excluded: chain P residue 130 ARG Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 25 CYS Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 43 GLU Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 72 VAL Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain R residue 7 LYS Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 11 LYS Chi-restraints excluded: chain R residue 24 LEU Chi-restraints excluded: chain R residue 70 SER Chi-restraints excluded: chain R residue 77 GLU Chi-restraints excluded: chain R residue 81 ARG Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain R residue 110 ASP Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 116 ASN Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain S residue 19 ASN Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 68 ILE Chi-restraints excluded: chain S residue 99 LEU Chi-restraints excluded: chain S residue 106 LYS Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 49 ASP Chi-restraints excluded: chain T residue 76 THR Chi-restraints excluded: chain Z residue 58 LEU Chi-restraints excluded: chain Z residue 97 ILE Chi-restraints excluded: chain Z residue 99 LEU Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain c residue 9 ILE Chi-restraints excluded: chain c residue 57 THR Chi-restraints excluded: chain c residue 59 LEU Chi-restraints excluded: chain c residue 61 SER Chi-restraints excluded: chain f residue 102 VAL Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 114 ILE Chi-restraints excluded: chain f residue 147 THR Chi-restraints excluded: chain g residue 46 THR Chi-restraints excluded: chain g residue 64 HIS Chi-restraints excluded: chain g residue 93 THR Chi-restraints excluded: chain g residue 118 ARG Chi-restraints excluded: chain g residue 203 ASP Chi-restraints excluded: chain g residue 240 CYS Chi-restraints excluded: chain g residue 249 CYS Chi-restraints excluded: chain g residue 287 THR Chi-restraints excluded: chain g residue 297 THR Chi-restraints excluded: chain g residue 303 THR Chi-restraints excluded: chain A residue 11 LYS Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 95 ASP Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 159 LYS Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 159 ASP Chi-restraints excluded: chain H residue 165 ASN Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 138 ASN Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 73 GLU Chi-restraints excluded: chain J residue 146 SER Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 60 CYS Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 80 MET Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain N residue 9 LYS Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 77 SER Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain N residue 143 SER Chi-restraints excluded: chain O residue 37 PHE Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 150 ARG Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 70 LEU Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain W residue 42 MET Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 121 THR Chi-restraints excluded: chain X residue 7 LEU Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 45 SER Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain X residue 119 ARG Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Y residue 78 SER Chi-restraints excluded: chain Y residue 104 ARG Chi-restraints excluded: chain Y residue 108 LYS Chi-restraints excluded: chain Y residue 109 GLU Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain b residue 33 MET Chi-restraints excluded: chain b residue 37 CYS Chi-restraints excluded: chain b residue 48 SER Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain x residue 78 ILE Chi-restraints excluded: chain x residue 88 LEU Chi-restraints excluded: chain x residue 102 HIS Chi-restraints excluded: chain x residue 118 ILE Chi-restraints excluded: chain x residue 130 LEU Chi-restraints excluded: chain x residue 160 LEU Chi-restraints excluded: chain x residue 218 ILE Chi-restraints excluded: chain y residue 15 LEU Chi-restraints excluded: chain y residue 34 VAL Chi-restraints excluded: chain y residue 68 GLU Chi-restraints excluded: chain y residue 69 PHE Chi-restraints excluded: chain y residue 93 LEU Chi-restraints excluded: chain y residue 116 ILE Chi-restraints excluded: chain y residue 235 LEU Chi-restraints excluded: chain y residue 251 HIS Chi-restraints excluded: chain y residue 253 LEU Chi-restraints excluded: chain y residue 256 ASN Chi-restraints excluded: chain y residue 260 ILE Chi-restraints excluded: chain y residue 281 SER Chi-restraints excluded: chain y residue 303 ASP Chi-restraints excluded: chain y residue 316 VAL Chi-restraints excluded: chain y residue 351 LEU Chi-restraints excluded: chain y residue 359 THR Chi-restraints excluded: chain y residue 360 ASN Chi-restraints excluded: chain y residue 371 SER Chi-restraints excluded: chain y residue 379 SER Chi-restraints excluded: chain y residue 389 ASP Chi-restraints excluded: chain u residue 88 VAL Chi-restraints excluded: chain u residue 123 MET Chi-restraints excluded: chain u residue 136 THR Chi-restraints excluded: chain u residue 152 VAL Chi-restraints excluded: chain u residue 217 HIS Chi-restraints excluded: chain u residue 222 LEU Chi-restraints excluded: chain u residue 225 THR Chi-restraints excluded: chain u residue 235 GLN Chi-restraints excluded: chain u residue 297 PHE Chi-restraints excluded: chain u residue 348 ASP Chi-restraints excluded: chain u residue 494 VAL Chi-restraints excluded: chain u residue 644 LEU Chi-restraints excluded: chain u residue 658 ILE Chi-restraints excluded: chain u residue 687 VAL Chi-restraints excluded: chain u residue 761 SER Chi-restraints excluded: chain u residue 766 LEU Chi-restraints excluded: chain u residue 778 THR Chi-restraints excluded: chain u residue 783 VAL Chi-restraints excluded: chain w residue 226 THR Chi-restraints excluded: chain w residue 306 ILE Chi-restraints excluded: chain w residue 317 ILE Chi-restraints excluded: chain w residue 403 GLU Chi-restraints excluded: chain w residue 407 LEU Chi-restraints excluded: chain w residue 414 SER Chi-restraints excluded: chain v residue 27 MET Chi-restraints excluded: chain v residue 101 MET Chi-restraints excluded: chain v residue 123 LYS Chi-restraints excluded: chain v residue 260 TRP Chi-restraints excluded: chain v residue 278 SER Chi-restraints excluded: chain v residue 290 ILE Chi-restraints excluded: chain v residue 496 ILE Chi-restraints excluded: chain v residue 522 GLN Chi-restraints excluded: chain t residue 250 MET Chi-restraints excluded: chain t residue 261 GLU Chi-restraints excluded: chain t residue 297 VAL Chi-restraints excluded: chain t residue 310 VAL Chi-restraints excluded: chain t residue 366 LEU Chi-restraints excluded: chain t residue 454 LEU Chi-restraints excluded: chain t residue 469 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 757 random chunks: chunk 706 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 417 optimal weight: 7.9990 chunk 534 optimal weight: 0.8980 chunk 414 optimal weight: 0.0570 chunk 616 optimal weight: 9.9990 chunk 408 optimal weight: 5.9990 chunk 729 optimal weight: 0.3980 chunk 456 optimal weight: 9.9990 chunk 444 optimal weight: 9.9990 chunk 336 optimal weight: 0.9980 overall best weight: 1.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 GLN P 46 ASN R 31 ASN ** S 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 51 ASN ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 ASN G 65 GLN G 110 ASN ** G 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 GLN V 49 GLN Y 19 GLN ** Y 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 65 GLN e 22 GLN e 37 GLN ** u 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 112 HIS ** u 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 284 ASN ** u 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 184 HIS t 299 ASN t 469 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 88868 Z= 0.196 Angle : 0.576 13.986 127913 Z= 0.292 Chirality : 0.036 0.319 15645 Planarity : 0.004 0.063 10091 Dihedral : 23.076 179.423 32612 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.16 % Favored : 95.73 % Rotamer: Outliers : 5.72 % Allowed : 22.80 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.11), residues: 5968 helix: 1.40 (0.11), residues: 2082 sheet: -0.67 (0.16), residues: 991 loop : -1.08 (0.11), residues: 2895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 82 HIS 0.007 0.001 HIS y 307 PHE 0.021 0.001 PHE x 96 TYR 0.023 0.001 TYR R 20 ARG 0.013 0.000 ARG P 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11936 Ramachandran restraints generated. 5968 Oldfield, 0 Emsley, 5968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11936 Ramachandran restraints generated. 5968 Oldfield, 0 Emsley, 5968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1320 residues out of total 5267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 299 poor density : 1021 time to evaluate : 5.277 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: F 81 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8052 (ptt90) REVERT: F 98 GLU cc_start: 0.8400 (tp30) cc_final: 0.7995 (tp30) REVERT: F 106 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8378 (tt0) REVERT: M 15 ASN cc_start: 0.6265 (m-40) cc_final: 0.5795 (t0) REVERT: M 63 LYS cc_start: 0.7831 (mtmm) cc_final: 0.7365 (pttp) REVERT: M 74 ILE cc_start: 0.6546 (mm) cc_final: 0.6343 (mp) REVERT: M 91 LEU cc_start: 0.4622 (OUTLIER) cc_final: 0.4107 (mt) REVERT: P 30 TYR cc_start: 0.7929 (OUTLIER) cc_final: 0.6858 (t80) REVERT: P 31 GLU cc_start: 0.8760 (tt0) cc_final: 0.8513 (mp0) REVERT: P 32 GLN cc_start: 0.9053 (tt0) cc_final: 0.8828 (mm110) REVERT: P 37 TYR cc_start: 0.8676 (m-10) cc_final: 0.8263 (m-10) REVERT: P 41 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8506 (mm-40) REVERT: P 50 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8048 (mmt180) REVERT: P 51 ARG cc_start: 0.8885 (ttt90) cc_final: 0.8429 (ttm110) REVERT: P 56 LEU cc_start: 0.8767 (tt) cc_final: 0.8552 (tt) REVERT: P 104 GLN cc_start: 0.9121 (mm-40) cc_final: 0.8878 (mm-40) REVERT: P 130 ARG cc_start: 0.6337 (OUTLIER) cc_final: 0.5480 (mmt-90) REVERT: Q 27 ARG cc_start: 0.7952 (ptt90) cc_final: 0.7671 (ttp80) REVERT: Q 29 ASN cc_start: 0.8012 (m-40) cc_final: 0.7553 (t0) REVERT: Q 66 VAL cc_start: 0.7420 (OUTLIER) cc_final: 0.7068 (p) REVERT: Q 107 GLU cc_start: 0.8260 (tp30) cc_final: 0.7978 (pt0) REVERT: Q 129 SER cc_start: 0.6958 (t) cc_final: 0.6569 (m) REVERT: R 7 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.7762 (tppt) REVERT: R 11 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7777 (mtmm) REVERT: R 63 ARG cc_start: 0.9186 (mmm-85) cc_final: 0.8714 (mmp80) REVERT: R 77 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7580 (mp0) REVERT: R 84 TYR cc_start: 0.8483 (t80) cc_final: 0.8207 (t80) REVERT: R 87 GLU cc_start: 0.8392 (pm20) cc_final: 0.8163 (tp30) REVERT: R 92 ASP cc_start: 0.8617 (t70) cc_final: 0.8250 (t70) REVERT: R 105 MET cc_start: 0.8758 (tmm) cc_final: 0.8451 (ttt) REVERT: R 107 LYS cc_start: 0.9163 (tttt) cc_final: 0.8812 (mtpp) REVERT: S 77 TYR cc_start: 0.9102 (m-80) cc_final: 0.8780 (m-80) REVERT: S 107 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8358 (tt) REVERT: S 109 GLU cc_start: 0.9206 (tt0) cc_final: 0.8805 (mm-30) REVERT: S 112 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8155 (tt0) REVERT: T 13 GLU cc_start: 0.7919 (mp0) cc_final: 0.7542 (tp30) REVERT: T 24 LYS cc_start: 0.8798 (mmtt) cc_final: 0.8457 (ptmm) REVERT: T 122 LYS cc_start: 0.8111 (pttt) cc_final: 0.7892 (pptt) REVERT: T 126 GLN cc_start: 0.8652 (tt0) cc_final: 0.8194 (tm-30) REVERT: T 129 ARG cc_start: 0.8057 (mtt90) cc_final: 0.7721 (mtp-110) REVERT: c 60 GLU cc_start: 0.7025 (tt0) cc_final: 0.6671 (tp30) REVERT: f 95 ARG cc_start: 0.3468 (OUTLIER) cc_final: 0.3195 (ttp-110) REVERT: f 114 ILE cc_start: 0.3230 (OUTLIER) cc_final: 0.2838 (tp) REVERT: g 91 ASP cc_start: 0.8217 (t70) cc_final: 0.7853 (t0) REVERT: g 118 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.7870 (ttm-80) REVERT: A 151 ASP cc_start: 0.8924 (p0) cc_final: 0.8491 (p0) REVERT: A 209 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8390 (tm-30) REVERT: B 73 ASP cc_start: 0.8524 (m-30) cc_final: 0.8130 (t0) REVERT: B 78 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7950 (mm-30) REVERT: B 183 GLU cc_start: 0.8579 (tp30) cc_final: 0.8041 (tp30) REVERT: B 203 SER cc_start: 0.9385 (p) cc_final: 0.9016 (t) REVERT: C 61 MET cc_start: 0.8327 (tpp) cc_final: 0.7428 (pmm) REVERT: C 68 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.7966 (mtp180) REVERT: C 77 SER cc_start: 0.9171 (t) cc_final: 0.8956 (p) REVERT: C 123 ARG cc_start: 0.8074 (ptm160) cc_final: 0.7107 (mpt-90) REVERT: C 145 LYS cc_start: 0.8363 (mttt) cc_final: 0.8003 (mttm) REVERT: C 159 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8364 (mtmm) REVERT: C 267 GLN cc_start: 0.8754 (tm-30) cc_final: 0.8150 (tm-30) REVERT: E 158 ASP cc_start: 0.8808 (m-30) cc_final: 0.8441 (m-30) REVERT: E 224 ASN cc_start: 0.8750 (m110) cc_final: 0.8437 (m-40) REVERT: E 237 SER cc_start: 0.9105 (t) cc_final: 0.8751 (m) REVERT: G 1 MET cc_start: 0.8061 (mmm) cc_final: 0.7689 (tpp) REVERT: G 17 GLU cc_start: 0.8927 (tt0) cc_final: 0.8436 (tm-30) REVERT: G 103 ASP cc_start: 0.8773 (t70) cc_final: 0.8209 (t70) REVERT: G 163 ASN cc_start: 0.7578 (p0) cc_final: 0.6740 (t0) REVERT: G 203 LYS cc_start: 0.8277 (tttt) cc_final: 0.7960 (mmmt) REVERT: G 204 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8144 (mt-10) REVERT: G 219 GLU cc_start: 0.7461 (tm-30) cc_final: 0.7192 (tm-30) REVERT: G 226 GLU cc_start: 0.8037 (tt0) cc_final: 0.7633 (mt-10) REVERT: H 10 LYS cc_start: 0.9115 (mttt) cc_final: 0.8730 (ptmt) REVERT: H 58 LYS cc_start: 0.8335 (mttt) cc_final: 0.8033 (pttt) REVERT: H 99 ARG cc_start: 0.8452 (mmt90) cc_final: 0.8098 (ttp80) REVERT: H 159 ASP cc_start: 0.9180 (OUTLIER) cc_final: 0.8889 (m-30) REVERT: I 73 THR cc_start: 0.8466 (m) cc_final: 0.8113 (p) REVERT: I 95 THR cc_start: 0.9488 (m) cc_final: 0.9080 (p) REVERT: I 139 LYS cc_start: 0.7781 (tmtp) cc_final: 0.7013 (ptmm) REVERT: I 159 SER cc_start: 0.8122 (m) cc_final: 0.7817 (t) REVERT: I 163 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7243 (tp30) REVERT: I 167 GLN cc_start: 0.7775 (mm-40) cc_final: 0.7292 (tp40) REVERT: J 107 GLU cc_start: 0.8774 (tp30) cc_final: 0.8318 (tp30) REVERT: J 154 GLN cc_start: 0.8579 (tt0) cc_final: 0.8263 (tt0) REVERT: N 27 LYS cc_start: 0.8748 (pttt) cc_final: 0.8436 (mmtt) REVERT: N 49 GLN cc_start: 0.8991 (mm-40) cc_final: 0.8539 (mt0) REVERT: O 84 ARG cc_start: 0.8055 (tpt-90) cc_final: 0.7616 (mtp85) REVERT: O 86 LYS cc_start: 0.9283 (tppp) cc_final: 0.9039 (mmmt) REVERT: O 87 GLU cc_start: 0.8332 (tp30) cc_final: 0.7943 (mt-10) REVERT: O 143 LYS cc_start: 0.8516 (tmmt) cc_final: 0.8120 (tppt) REVERT: O 147 ARG cc_start: 0.8938 (tpt90) cc_final: 0.8235 (mtm110) REVERT: O 150 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7692 (mtt180) REVERT: V 4 ASP cc_start: 0.8510 (t70) cc_final: 0.8206 (p0) REVERT: V 13 VAL cc_start: 0.9438 (t) cc_final: 0.9199 (m) REVERT: V 32 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8279 (pt) REVERT: V 64 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8367 (mt-10) REVERT: W 31 SER cc_start: 0.8802 (t) cc_final: 0.8435 (p) REVERT: W 46 TYR cc_start: 0.9091 (m-80) cc_final: 0.8652 (m-80) REVERT: W 76 SER cc_start: 0.9364 (t) cc_final: 0.9010 (p) REVERT: W 104 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8552 (pp) REVERT: W 117 ARG cc_start: 0.8500 (tpp80) cc_final: 0.8277 (mtp85) REVERT: X 50 ILE cc_start: 0.9071 (mt) cc_final: 0.8738 (pt) REVERT: X 58 GLU cc_start: 0.8660 (tt0) cc_final: 0.8426 (tt0) REVERT: X 69 CYS cc_start: 0.8642 (m) cc_final: 0.8189 (m) REVERT: X 127 ASN cc_start: 0.8958 (m-40) cc_final: 0.8646 (t0) REVERT: Y 42 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8805 (mt-10) REVERT: Y 53 ASP cc_start: 0.9200 (m-30) cc_final: 0.8936 (p0) REVERT: Y 61 ARG cc_start: 0.8996 (tpt170) cc_final: 0.8510 (mmm-85) REVERT: Y 68 LYS cc_start: 0.8853 (mttt) cc_final: 0.8618 (mppt) REVERT: Y 86 GLU cc_start: 0.9087 (tp30) cc_final: 0.8814 (tp30) REVERT: Y 104 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7535 (mtp-110) REVERT: Y 108 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7621 (mtpp) REVERT: Y 109 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8124 (mt-10) REVERT: b 34 ASP cc_start: 0.8052 (t0) cc_final: 0.7245 (p0) REVERT: b 72 ARG cc_start: 0.8892 (ptt180) cc_final: 0.8444 (ptm-80) REVERT: e 25 LYS cc_start: 0.8334 (pttt) cc_final: 0.8057 (mmtm) REVERT: e 40 ARG cc_start: 0.8827 (ttt180) cc_final: 0.8593 (mtm180) REVERT: x 130 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7460 (tp) REVERT: x 145 GLN cc_start: 0.8534 (tt0) cc_final: 0.8306 (mm110) REVERT: x 172 LYS cc_start: 0.9073 (mptt) cc_final: 0.8764 (mtpp) REVERT: x 240 ASN cc_start: 0.8926 (m-40) cc_final: 0.8608 (m-40) REVERT: y 75 ASP cc_start: 0.8392 (m-30) cc_final: 0.8158 (m-30) REVERT: y 85 GLN cc_start: 0.8381 (mm110) cc_final: 0.7926 (mt0) REVERT: y 109 LYS cc_start: 0.8155 (mmmm) cc_final: 0.7716 (ttpp) REVERT: y 251 HIS cc_start: 0.8139 (OUTLIER) cc_final: 0.7490 (m-70) REVERT: y 280 MET cc_start: 0.8297 (mmm) cc_final: 0.8083 (mpp) REVERT: y 342 GLU cc_start: 0.8853 (pm20) cc_final: 0.8381 (tp30) REVERT: y 345 ARG cc_start: 0.8375 (ttp-110) cc_final: 0.8085 (ttt180) REVERT: u 96 LEU cc_start: 0.8586 (pp) cc_final: 0.8342 (tt) REVERT: u 144 HIS cc_start: 0.8260 (t-90) cc_final: 0.8031 (m-70) REVERT: u 148 ASP cc_start: 0.8160 (m-30) cc_final: 0.7830 (m-30) REVERT: u 219 LYS cc_start: 0.8764 (pttt) cc_final: 0.8312 (tttp) REVERT: u 222 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7379 (mt) REVERT: u 225 THR cc_start: 0.7696 (OUTLIER) cc_final: 0.7401 (p) REVERT: u 228 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8328 (mt-10) REVERT: u 395 LYS cc_start: 0.7685 (tptm) cc_final: 0.6730 (mmtt) REVERT: u 401 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.8772 (tt0) REVERT: u 476 LYS cc_start: 0.8150 (mttt) cc_final: 0.7848 (mmtt) REVERT: u 481 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8599 (tp30) REVERT: u 738 ARG cc_start: 0.8341 (mmt180) cc_final: 0.8028 (ttm110) REVERT: u 766 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8334 (pp) REVERT: w 194 LYS cc_start: 0.8732 (mttt) cc_final: 0.8107 (tmtt) REVERT: w 213 TRP cc_start: 0.8440 (p-90) cc_final: 0.8207 (p-90) REVERT: w 267 ARG cc_start: 0.8277 (ptt90) cc_final: 0.7411 (ptm160) REVERT: w 328 LYS cc_start: 0.8510 (mmtt) cc_final: 0.8304 (mmtt) REVERT: v 183 ARG cc_start: 0.7698 (mtm-85) cc_final: 0.7292 (ttm-80) REVERT: v 274 MET cc_start: 0.8278 (ptm) cc_final: 0.8039 (mtt) REVERT: v 503 GLN cc_start: 0.8335 (tt0) cc_final: 0.7941 (tm-30) REVERT: v 519 ARG cc_start: 0.7504 (ttm110) cc_final: 0.7131 (tpp-160) REVERT: v 523 LYS cc_start: 0.6177 (mttt) cc_final: 0.5452 (tptt) REVERT: t 250 MET cc_start: 0.4075 (OUTLIER) cc_final: 0.3807 (pmm) REVERT: t 259 HIS cc_start: 0.6659 (p-80) cc_final: 0.5472 (t-90) REVERT: t 304 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7531 (tt0) REVERT: t 305 LYS cc_start: 0.7436 (ttpt) cc_final: 0.7216 (ttmt) REVERT: t 313 ASN cc_start: 0.7036 (t0) cc_final: 0.6764 (t0) REVERT: t 366 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8548 (pp) REVERT: t 440 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7899 (tm-30) REVERT: t 462 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7607 (tm-30) REVERT: t 467 LYS cc_start: 0.8183 (mttt) cc_final: 0.7656 (mmtm) outliers start: 299 outliers final: 221 residues processed: 1213 average time/residue: 0.7954 time to fit residues: 1631.5147 Evaluate side-chains 1233 residues out of total 5267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 981 time to evaluate : 5.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 72 HIS Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain P residue 30 TYR Chi-restraints excluded: chain P residue 41 GLN Chi-restraints excluded: chain P residue 50 ARG Chi-restraints excluded: chain P residue 82 ASP Chi-restraints excluded: chain P residue 130 ARG Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 25 CYS Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 43 GLU Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain R residue 7 LYS Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 11 LYS Chi-restraints excluded: chain R residue 24 LEU Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 70 SER Chi-restraints excluded: chain R residue 77 GLU Chi-restraints excluded: chain R residue 81 ARG Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain R residue 110 ASP Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 116 ASN Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain S residue 19 ASN Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 99 LEU Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 76 THR Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain Z residue 97 ILE Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain c residue 9 ILE Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 37 ASP Chi-restraints excluded: chain c residue 57 THR Chi-restraints excluded: chain c residue 59 LEU Chi-restraints excluded: chain c residue 61 SER Chi-restraints excluded: chain f residue 95 ARG Chi-restraints excluded: chain f residue 102 VAL Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 114 ILE Chi-restraints excluded: chain f residue 147 THR Chi-restraints excluded: chain g residue 46 THR Chi-restraints excluded: chain g residue 64 HIS Chi-restraints excluded: chain g residue 93 THR Chi-restraints excluded: chain g residue 118 ARG Chi-restraints excluded: chain g residue 203 ASP Chi-restraints excluded: chain g residue 240 CYS Chi-restraints excluded: chain g residue 249 CYS Chi-restraints excluded: chain g residue 265 ILE Chi-restraints excluded: chain g residue 287 THR Chi-restraints excluded: chain g residue 297 THR Chi-restraints excluded: chain g residue 303 THR Chi-restraints excluded: chain A residue 11 LYS Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 95 ASP Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 159 LYS Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 159 ASP Chi-restraints excluded: chain H residue 165 ASN Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 138 ASN Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 73 GLU Chi-restraints excluded: chain J residue 146 SER Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 60 CYS Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 80 MET Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain N residue 9 LYS Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 77 SER Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 143 SER Chi-restraints excluded: chain O residue 37 PHE Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 150 ARG Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 42 VAL Chi-restraints excluded: chain V residue 50 PHE Chi-restraints excluded: chain V residue 70 LEU Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain W residue 42 MET Chi-restraints excluded: chain W residue 64 ASN Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 121 THR Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 28 LYS Chi-restraints excluded: chain X residue 110 HIS Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain X residue 119 ARG Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Y residue 55 ILE Chi-restraints excluded: chain Y residue 78 SER Chi-restraints excluded: chain Y residue 104 ARG Chi-restraints excluded: chain Y residue 108 LYS Chi-restraints excluded: chain Y residue 109 GLU Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain b residue 33 MET Chi-restraints excluded: chain b residue 37 CYS Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 48 SER Chi-restraints excluded: chain b residue 60 SER Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 36 MET Chi-restraints excluded: chain e residue 37 GLN Chi-restraints excluded: chain x residue 77 LYS Chi-restraints excluded: chain x residue 78 ILE Chi-restraints excluded: chain x residue 102 HIS Chi-restraints excluded: chain x residue 118 ILE Chi-restraints excluded: chain x residue 130 LEU Chi-restraints excluded: chain x residue 152 LEU Chi-restraints excluded: chain x residue 160 LEU Chi-restraints excluded: chain x residue 218 ILE Chi-restraints excluded: chain y residue 34 VAL Chi-restraints excluded: chain y residue 68 GLU Chi-restraints excluded: chain y residue 69 PHE Chi-restraints excluded: chain y residue 116 ILE Chi-restraints excluded: chain y residue 235 LEU Chi-restraints excluded: chain y residue 251 HIS Chi-restraints excluded: chain y residue 253 LEU Chi-restraints excluded: chain y residue 256 ASN Chi-restraints excluded: chain y residue 260 ILE Chi-restraints excluded: chain y residue 281 SER Chi-restraints excluded: chain y residue 303 ASP Chi-restraints excluded: chain y residue 316 VAL Chi-restraints excluded: chain y residue 351 LEU Chi-restraints excluded: chain y residue 359 THR Chi-restraints excluded: chain y residue 360 ASN Chi-restraints excluded: chain y residue 371 SER Chi-restraints excluded: chain y residue 389 ASP Chi-restraints excluded: chain y residue 404 SER Chi-restraints excluded: chain u residue 88 VAL Chi-restraints excluded: chain u residue 136 THR Chi-restraints excluded: chain u residue 152 VAL Chi-restraints excluded: chain u residue 212 GLU Chi-restraints excluded: chain u residue 217 HIS Chi-restraints excluded: chain u residue 222 LEU Chi-restraints excluded: chain u residue 225 THR Chi-restraints excluded: chain u residue 235 GLN Chi-restraints excluded: chain u residue 297 PHE Chi-restraints excluded: chain u residue 348 ASP Chi-restraints excluded: chain u residue 401 GLN Chi-restraints excluded: chain u residue 644 LEU Chi-restraints excluded: chain u residue 658 ILE Chi-restraints excluded: chain u residue 687 VAL Chi-restraints excluded: chain u residue 761 SER Chi-restraints excluded: chain u residue 766 LEU Chi-restraints excluded: chain u residue 778 THR Chi-restraints excluded: chain w residue 226 THR Chi-restraints excluded: chain w residue 302 LEU Chi-restraints excluded: chain w residue 306 ILE Chi-restraints excluded: chain w residue 377 LEU Chi-restraints excluded: chain w residue 403 GLU Chi-restraints excluded: chain w residue 414 SER Chi-restraints excluded: chain v residue 101 MET Chi-restraints excluded: chain v residue 278 SER Chi-restraints excluded: chain v residue 290 ILE Chi-restraints excluded: chain v residue 295 THR Chi-restraints excluded: chain t residue 250 MET Chi-restraints excluded: chain t residue 261 GLU Chi-restraints excluded: chain t residue 297 VAL Chi-restraints excluded: chain t residue 310 VAL Chi-restraints excluded: chain t residue 366 LEU Chi-restraints excluded: chain t residue 454 LEU Chi-restraints excluded: chain t residue 469 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 757 random chunks: chunk 451 optimal weight: 0.3980 chunk 291 optimal weight: 6.9990 chunk 435 optimal weight: 4.9990 chunk 219 optimal weight: 10.0000 chunk 143 optimal weight: 8.9990 chunk 141 optimal weight: 5.9990 chunk 463 optimal weight: 0.8980 chunk 497 optimal weight: 5.9990 chunk 360 optimal weight: 0.9990 chunk 67 optimal weight: 8.9990 chunk 573 optimal weight: 7.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 GLN R 74 GLN S 72 GLN ** S 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 106 GLN g 51 ASN ** g 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 9 GLN ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN G 110 ASN ** G 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN I 165 GLN V 49 GLN X 110 HIS ** Y 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 65 GLN e 22 GLN x 145 GLN y 102 HIS ** y 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 299 ASN t 469 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 88868 Z= 0.276 Angle : 0.620 13.984 127913 Z= 0.313 Chirality : 0.038 0.344 15645 Planarity : 0.004 0.058 10091 Dihedral : 23.068 179.317 32606 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.71 % Favored : 95.21 % Rotamer: Outliers : 5.85 % Allowed : 23.28 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.11), residues: 5968 helix: 1.28 (0.11), residues: 2084 sheet: -0.72 (0.16), residues: 1013 loop : -1.09 (0.11), residues: 2871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 82 HIS 0.007 0.001 HIS y 102 PHE 0.020 0.002 PHE x 96 TYR 0.019 0.002 TYR R 21 ARG 0.008 0.000 ARG M 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11936 Ramachandran restraints generated. 5968 Oldfield, 0 Emsley, 5968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11936 Ramachandran restraints generated. 5968 Oldfield, 0 Emsley, 5968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1314 residues out of total 5267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 306 poor density : 1008 time to evaluate : 5.223 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: F 81 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.7997 (ptt90) REVERT: F 98 GLU cc_start: 0.8454 (tp30) cc_final: 0.8035 (tp30) REVERT: F 106 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8421 (tt0) REVERT: M 91 LEU cc_start: 0.4654 (OUTLIER) cc_final: 0.4245 (mt) REVERT: M 96 ARG cc_start: 0.6106 (mmm160) cc_final: 0.5079 (mmp80) REVERT: P 30 TYR cc_start: 0.7792 (OUTLIER) cc_final: 0.6620 (t80) REVERT: P 31 GLU cc_start: 0.8847 (tt0) cc_final: 0.8604 (mp0) REVERT: P 32 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8854 (mm110) REVERT: P 37 TYR cc_start: 0.8757 (m-10) cc_final: 0.8320 (m-10) REVERT: P 41 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8529 (mm-40) REVERT: P 50 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8293 (mmt180) REVERT: P 51 ARG cc_start: 0.8910 (ttt90) cc_final: 0.8535 (ttm110) REVERT: P 56 LEU cc_start: 0.8823 (tt) cc_final: 0.8614 (tt) REVERT: P 130 ARG cc_start: 0.6347 (OUTLIER) cc_final: 0.5503 (mmt-90) REVERT: Q 27 ARG cc_start: 0.7927 (ptt90) cc_final: 0.7641 (ttp80) REVERT: Q 29 ASN cc_start: 0.7956 (m-40) cc_final: 0.7473 (t0) REVERT: Q 66 VAL cc_start: 0.7519 (OUTLIER) cc_final: 0.7171 (p) REVERT: Q 107 GLU cc_start: 0.8280 (tp30) cc_final: 0.7956 (pt0) REVERT: Q 129 SER cc_start: 0.6806 (t) cc_final: 0.6385 (m) REVERT: R 7 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.7755 (tppt) REVERT: R 11 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7811 (mtmm) REVERT: R 74 GLN cc_start: 0.7236 (OUTLIER) cc_final: 0.7032 (tt0) REVERT: R 77 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7596 (mp0) REVERT: R 84 TYR cc_start: 0.8439 (t80) cc_final: 0.8171 (t80) REVERT: R 87 GLU cc_start: 0.8439 (pm20) cc_final: 0.8162 (tp30) REVERT: R 92 ASP cc_start: 0.8737 (t70) cc_final: 0.8373 (t0) REVERT: R 107 LYS cc_start: 0.9148 (tttt) cc_final: 0.8794 (mtpp) REVERT: S 107 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8322 (tt) REVERT: S 109 GLU cc_start: 0.9219 (tt0) cc_final: 0.8813 (mm-30) REVERT: S 112 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8194 (tt0) REVERT: T 13 GLU cc_start: 0.7925 (mp0) cc_final: 0.7635 (tp30) REVERT: T 24 LYS cc_start: 0.8853 (mmtt) cc_final: 0.8472 (ptmm) REVERT: T 122 LYS cc_start: 0.8141 (pttt) cc_final: 0.7910 (pptt) REVERT: T 126 GLN cc_start: 0.8824 (tt0) cc_final: 0.8308 (tm-30) REVERT: T 129 ARG cc_start: 0.8069 (mtt90) cc_final: 0.7744 (mtp-110) REVERT: c 60 GLU cc_start: 0.7076 (tt0) cc_final: 0.6804 (tp30) REVERT: f 95 ARG cc_start: 0.3422 (OUTLIER) cc_final: 0.3138 (ttp-110) REVERT: f 114 ILE cc_start: 0.2828 (OUTLIER) cc_final: 0.2541 (tp) REVERT: g 36 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8642 (mtt90) REVERT: g 91 ASP cc_start: 0.8173 (t70) cc_final: 0.7818 (t0) REVERT: g 118 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7780 (ttm-80) REVERT: A 136 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.7395 (mp0) REVERT: A 151 ASP cc_start: 0.8987 (p0) cc_final: 0.8630 (p0) REVERT: A 166 LYS cc_start: 0.8952 (mttm) cc_final: 0.8717 (mtmt) REVERT: B 73 ASP cc_start: 0.8557 (m-30) cc_final: 0.8158 (t0) REVERT: B 78 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7940 (mm-30) REVERT: B 183 GLU cc_start: 0.8619 (tp30) cc_final: 0.8092 (tp30) REVERT: B 203 SER cc_start: 0.9397 (p) cc_final: 0.9002 (t) REVERT: B 211 PHE cc_start: 0.9107 (m-80) cc_final: 0.8820 (m-80) REVERT: C 61 MET cc_start: 0.8438 (tpp) cc_final: 0.7503 (pmm) REVERT: C 68 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8008 (mtp180) REVERT: C 77 SER cc_start: 0.9173 (t) cc_final: 0.8945 (p) REVERT: C 123 ARG cc_start: 0.8006 (ptm160) cc_final: 0.7007 (mpt-90) REVERT: C 145 LYS cc_start: 0.8394 (mttt) cc_final: 0.8040 (mttm) REVERT: C 159 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8449 (mttp) REVERT: C 160 LEU cc_start: 0.8727 (mp) cc_final: 0.8501 (mp) REVERT: C 267 GLN cc_start: 0.8773 (tm-30) cc_final: 0.8497 (tm-30) REVERT: E 104 ASP cc_start: 0.8663 (t0) cc_final: 0.7871 (p0) REVERT: E 158 ASP cc_start: 0.8783 (m-30) cc_final: 0.8439 (m-30) REVERT: E 197 ASN cc_start: 0.9130 (OUTLIER) cc_final: 0.8925 (p0) REVERT: E 199 GLU cc_start: 0.8722 (pm20) cc_final: 0.8402 (mp0) REVERT: E 224 ASN cc_start: 0.8735 (m110) cc_final: 0.8471 (m-40) REVERT: E 237 SER cc_start: 0.9050 (t) cc_final: 0.8697 (m) REVERT: G 1 MET cc_start: 0.8057 (mmm) cc_final: 0.7706 (tpp) REVERT: G 17 GLU cc_start: 0.8963 (tt0) cc_final: 0.8492 (tm-30) REVERT: G 41 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8800 (tp) REVERT: G 103 ASP cc_start: 0.8808 (t70) cc_final: 0.8500 (t70) REVERT: G 155 GLN cc_start: 0.8082 (mm110) cc_final: 0.7818 (mm-40) REVERT: G 163 ASN cc_start: 0.7657 (p0) cc_final: 0.6870 (t0) REVERT: G 203 LYS cc_start: 0.8267 (tttt) cc_final: 0.7950 (mmmt) REVERT: G 204 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8108 (mt-10) REVERT: G 219 GLU cc_start: 0.7422 (tm-30) cc_final: 0.7137 (tm-30) REVERT: G 226 GLU cc_start: 0.7914 (tt0) cc_final: 0.7498 (mt-10) REVERT: H 10 LYS cc_start: 0.9089 (mttt) cc_final: 0.8713 (ptmt) REVERT: H 58 LYS cc_start: 0.8346 (mttt) cc_final: 0.8042 (pttt) REVERT: H 78 ARG cc_start: 0.8285 (mtp85) cc_final: 0.8066 (mtp180) REVERT: H 99 ARG cc_start: 0.8480 (mmt90) cc_final: 0.8097 (ttp80) REVERT: H 159 ASP cc_start: 0.9173 (OUTLIER) cc_final: 0.8872 (m-30) REVERT: I 73 THR cc_start: 0.8516 (m) cc_final: 0.8154 (p) REVERT: I 119 LEU cc_start: 0.8220 (mp) cc_final: 0.7964 (mp) REVERT: I 139 LYS cc_start: 0.7804 (tmtp) cc_final: 0.7165 (pttp) REVERT: I 141 ARG cc_start: 0.8145 (mtt180) cc_final: 0.7632 (mtp180) REVERT: I 159 SER cc_start: 0.8077 (m) cc_final: 0.7763 (t) REVERT: I 163 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7211 (tp30) REVERT: I 167 GLN cc_start: 0.7753 (mm-40) cc_final: 0.7268 (tp40) REVERT: J 107 GLU cc_start: 0.8827 (tp30) cc_final: 0.8366 (tp30) REVERT: J 140 GLN cc_start: 0.8386 (tp40) cc_final: 0.8074 (tp-100) REVERT: N 27 LYS cc_start: 0.8815 (pttt) cc_final: 0.8506 (mmtt) REVERT: N 49 GLN cc_start: 0.9025 (mm-40) cc_final: 0.8543 (mt0) REVERT: O 86 LYS cc_start: 0.9304 (tppp) cc_final: 0.9087 (mmmt) REVERT: O 87 GLU cc_start: 0.8330 (tp30) cc_final: 0.7924 (mt-10) REVERT: O 138 ASP cc_start: 0.8409 (m-30) cc_final: 0.8184 (m-30) REVERT: O 143 LYS cc_start: 0.8575 (tmmt) cc_final: 0.8171 (tppt) REVERT: O 147 ARG cc_start: 0.8972 (tpt90) cc_final: 0.8280 (mtm110) REVERT: O 150 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7704 (mtt180) REVERT: V 4 ASP cc_start: 0.8513 (t70) cc_final: 0.8176 (p0) REVERT: V 13 VAL cc_start: 0.9448 (t) cc_final: 0.9206 (m) REVERT: V 32 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8248 (pt) REVERT: V 64 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8405 (mt-10) REVERT: W 31 SER cc_start: 0.8893 (t) cc_final: 0.8401 (m) REVERT: W 76 SER cc_start: 0.9339 (t) cc_final: 0.9003 (p) REVERT: W 104 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8587 (pp) REVERT: W 117 ARG cc_start: 0.8537 (tpp80) cc_final: 0.8283 (mtp85) REVERT: X 50 ILE cc_start: 0.9062 (mt) cc_final: 0.8708 (pt) REVERT: X 58 GLU cc_start: 0.8601 (tt0) cc_final: 0.8382 (tt0) REVERT: X 69 CYS cc_start: 0.8602 (m) cc_final: 0.8152 (m) REVERT: X 127 ASN cc_start: 0.8967 (m-40) cc_final: 0.8617 (t0) REVERT: Y 53 ASP cc_start: 0.9218 (m-30) cc_final: 0.8922 (p0) REVERT: Y 61 ARG cc_start: 0.8988 (tpt170) cc_final: 0.8529 (mmm-85) REVERT: Y 68 LYS cc_start: 0.8915 (mttt) cc_final: 0.8662 (mppt) REVERT: Y 86 GLU cc_start: 0.9080 (tp30) cc_final: 0.8727 (tp30) REVERT: Y 104 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7538 (mtp-110) REVERT: Y 108 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7717 (mtpp) REVERT: Y 109 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8105 (mt-10) REVERT: b 34 ASP cc_start: 0.8064 (t0) cc_final: 0.7216 (p0) REVERT: b 72 ARG cc_start: 0.8894 (ptt180) cc_final: 0.8460 (ptm-80) REVERT: e 25 LYS cc_start: 0.8275 (pttt) cc_final: 0.8038 (mmtm) REVERT: e 40 ARG cc_start: 0.8879 (ttt180) cc_final: 0.8522 (ttp80) REVERT: x 172 LYS cc_start: 0.9062 (mptt) cc_final: 0.8756 (mtpp) REVERT: x 240 ASN cc_start: 0.8934 (m-40) cc_final: 0.8633 (m-40) REVERT: y 75 ASP cc_start: 0.8360 (m-30) cc_final: 0.8060 (m-30) REVERT: y 85 GLN cc_start: 0.8413 (mm110) cc_final: 0.7936 (mt0) REVERT: y 109 LYS cc_start: 0.8109 (mmmm) cc_final: 0.7693 (ttpp) REVERT: y 120 GLU cc_start: 0.9146 (mp0) cc_final: 0.8293 (mp0) REVERT: y 280 MET cc_start: 0.8350 (mmm) cc_final: 0.8115 (mpp) REVERT: y 342 GLU cc_start: 0.8876 (pm20) cc_final: 0.8429 (tp30) REVERT: y 345 ARG cc_start: 0.8424 (ttp-110) cc_final: 0.8139 (ttt180) REVERT: y 367 ILE cc_start: 0.8532 (pt) cc_final: 0.8255 (mm) REVERT: u 96 LEU cc_start: 0.8596 (pp) cc_final: 0.8233 (tt) REVERT: u 100 MET cc_start: 0.7993 (mmm) cc_final: 0.7708 (mmm) REVERT: u 101 GLN cc_start: 0.8596 (mm110) cc_final: 0.8373 (mm110) REVERT: u 148 ASP cc_start: 0.8073 (m-30) cc_final: 0.7791 (m-30) REVERT: u 219 LYS cc_start: 0.8795 (pttt) cc_final: 0.8338 (tttp) REVERT: u 225 THR cc_start: 0.7771 (OUTLIER) cc_final: 0.7480 (p) REVERT: u 228 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8360 (mt-10) REVERT: u 395 LYS cc_start: 0.7705 (tptm) cc_final: 0.6702 (mmtt) REVERT: u 401 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.8811 (tt0) REVERT: u 476 LYS cc_start: 0.8141 (mttt) cc_final: 0.7832 (mmtt) REVERT: u 481 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8620 (tp30) REVERT: u 738 ARG cc_start: 0.8390 (mmt180) cc_final: 0.8079 (ttm110) REVERT: u 766 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8327 (pp) REVERT: w 194 LYS cc_start: 0.8688 (mttt) cc_final: 0.8140 (tmtt) REVERT: w 213 TRP cc_start: 0.8339 (p-90) cc_final: 0.7901 (p-90) REVERT: w 267 ARG cc_start: 0.8359 (ptt90) cc_final: 0.7524 (ptm160) REVERT: w 294 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8259 (pp) REVERT: w 389 TYR cc_start: 0.6456 (m-80) cc_final: 0.5210 (m-80) REVERT: w 407 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8064 (mt) REVERT: v 177 LYS cc_start: 0.8270 (tttt) cc_final: 0.7908 (mttm) REVERT: v 274 MET cc_start: 0.8287 (ptm) cc_final: 0.8068 (mtt) REVERT: v 503 GLN cc_start: 0.8364 (tt0) cc_final: 0.7986 (tm-30) REVERT: v 519 ARG cc_start: 0.7501 (ttm110) cc_final: 0.7107 (tpp-160) REVERT: v 523 LYS cc_start: 0.6322 (mttt) cc_final: 0.5632 (tptt) REVERT: t 249 VAL cc_start: 0.6522 (t) cc_final: 0.6256 (t) REVERT: t 250 MET cc_start: 0.4218 (OUTLIER) cc_final: 0.3875 (pmm) REVERT: t 259 HIS cc_start: 0.6679 (p-80) cc_final: 0.5541 (t-90) REVERT: t 304 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7601 (tt0) REVERT: t 313 ASN cc_start: 0.7040 (t0) cc_final: 0.6817 (t0) REVERT: t 366 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8580 (pp) REVERT: t 440 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7873 (tm-30) REVERT: t 462 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7610 (tm-30) REVERT: t 467 LYS cc_start: 0.8233 (mttt) cc_final: 0.7709 (mmtm) outliers start: 306 outliers final: 227 residues processed: 1207 average time/residue: 0.8021 time to fit residues: 1643.2727 Evaluate side-chains 1240 residues out of total 5267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 977 time to evaluate : 5.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 72 HIS Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain P residue 30 TYR Chi-restraints excluded: chain P residue 32 GLN Chi-restraints excluded: chain P residue 41 GLN Chi-restraints excluded: chain P residue 50 ARG Chi-restraints excluded: chain P residue 82 ASP Chi-restraints excluded: chain P residue 130 ARG Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 25 CYS Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 43 GLU Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 72 VAL Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain Q residue 97 GLN Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 7 LYS Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 11 LYS Chi-restraints excluded: chain R residue 24 LEU Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 70 SER Chi-restraints excluded: chain R residue 74 GLN Chi-restraints excluded: chain R residue 77 GLU Chi-restraints excluded: chain R residue 81 ARG Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain R residue 110 ASP Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 116 ASN Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain S residue 19 ASN Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 99 LEU Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 76 THR Chi-restraints excluded: chain Z residue 58 LEU Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain Z residue 97 ILE Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain c residue 9 ILE Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 37 ASP Chi-restraints excluded: chain c residue 57 THR Chi-restraints excluded: chain c residue 59 LEU Chi-restraints excluded: chain c residue 61 SER Chi-restraints excluded: chain f residue 95 ARG Chi-restraints excluded: chain f residue 102 VAL Chi-restraints excluded: chain f residue 114 ILE Chi-restraints excluded: chain f residue 147 THR Chi-restraints excluded: chain g residue 36 ARG Chi-restraints excluded: chain g residue 46 THR Chi-restraints excluded: chain g residue 93 THR Chi-restraints excluded: chain g residue 118 ARG Chi-restraints excluded: chain g residue 203 ASP Chi-restraints excluded: chain g residue 228 TYR Chi-restraints excluded: chain g residue 240 CYS Chi-restraints excluded: chain g residue 249 CYS Chi-restraints excluded: chain g residue 287 THR Chi-restraints excluded: chain g residue 297 THR Chi-restraints excluded: chain g residue 303 THR Chi-restraints excluded: chain A residue 11 LYS Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 95 ASP Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 159 LYS Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 159 ASP Chi-restraints excluded: chain H residue 165 ASN Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 138 ASN Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 21 GLU Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 73 GLU Chi-restraints excluded: chain J residue 146 SER Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 60 CYS Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain N residue 9 LYS Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 77 SER Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 143 SER Chi-restraints excluded: chain O residue 37 PHE Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 135 ILE Chi-restraints excluded: chain O residue 150 ARG Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 42 VAL Chi-restraints excluded: chain V residue 50 PHE Chi-restraints excluded: chain V residue 70 LEU Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain W residue 42 MET Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 121 THR Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 28 LYS Chi-restraints excluded: chain X residue 45 SER Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Y residue 78 SER Chi-restraints excluded: chain Y residue 104 ARG Chi-restraints excluded: chain Y residue 108 LYS Chi-restraints excluded: chain Y residue 109 GLU Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain b residue 33 MET Chi-restraints excluded: chain b residue 37 CYS Chi-restraints excluded: chain b residue 48 SER Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 60 SER Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 36 MET Chi-restraints excluded: chain x residue 77 LYS Chi-restraints excluded: chain x residue 78 ILE Chi-restraints excluded: chain x residue 102 HIS Chi-restraints excluded: chain x residue 118 ILE Chi-restraints excluded: chain x residue 152 LEU Chi-restraints excluded: chain x residue 160 LEU Chi-restraints excluded: chain x residue 218 ILE Chi-restraints excluded: chain y residue 15 LEU Chi-restraints excluded: chain y residue 34 VAL Chi-restraints excluded: chain y residue 69 PHE Chi-restraints excluded: chain y residue 93 LEU Chi-restraints excluded: chain y residue 116 ILE Chi-restraints excluded: chain y residue 230 VAL Chi-restraints excluded: chain y residue 235 LEU Chi-restraints excluded: chain y residue 251 HIS Chi-restraints excluded: chain y residue 256 ASN Chi-restraints excluded: chain y residue 260 ILE Chi-restraints excluded: chain y residue 281 SER Chi-restraints excluded: chain y residue 303 ASP Chi-restraints excluded: chain y residue 351 LEU Chi-restraints excluded: chain y residue 359 THR Chi-restraints excluded: chain y residue 360 ASN Chi-restraints excluded: chain y residue 371 SER Chi-restraints excluded: chain y residue 389 ASP Chi-restraints excluded: chain u residue 88 VAL Chi-restraints excluded: chain u residue 136 THR Chi-restraints excluded: chain u residue 212 GLU Chi-restraints excluded: chain u residue 217 HIS Chi-restraints excluded: chain u residue 225 THR Chi-restraints excluded: chain u residue 235 GLN Chi-restraints excluded: chain u residue 297 PHE Chi-restraints excluded: chain u residue 348 ASP Chi-restraints excluded: chain u residue 397 THR Chi-restraints excluded: chain u residue 401 GLN Chi-restraints excluded: chain u residue 644 LEU Chi-restraints excluded: chain u residue 658 ILE Chi-restraints excluded: chain u residue 687 VAL Chi-restraints excluded: chain u residue 761 SER Chi-restraints excluded: chain u residue 766 LEU Chi-restraints excluded: chain u residue 778 THR Chi-restraints excluded: chain w residue 226 THR Chi-restraints excluded: chain w residue 294 LEU Chi-restraints excluded: chain w residue 302 LEU Chi-restraints excluded: chain w residue 306 ILE Chi-restraints excluded: chain w residue 377 LEU Chi-restraints excluded: chain w residue 403 GLU Chi-restraints excluded: chain w residue 407 LEU Chi-restraints excluded: chain w residue 413 LEU Chi-restraints excluded: chain w residue 414 SER Chi-restraints excluded: chain v residue 59 HIS Chi-restraints excluded: chain v residue 101 MET Chi-restraints excluded: chain v residue 260 TRP Chi-restraints excluded: chain v residue 278 SER Chi-restraints excluded: chain v residue 290 ILE Chi-restraints excluded: chain v residue 295 THR Chi-restraints excluded: chain v residue 517 VAL Chi-restraints excluded: chain v residue 522 GLN Chi-restraints excluded: chain t residue 250 MET Chi-restraints excluded: chain t residue 260 ASP Chi-restraints excluded: chain t residue 261 GLU Chi-restraints excluded: chain t residue 297 VAL Chi-restraints excluded: chain t residue 310 VAL Chi-restraints excluded: chain t residue 366 LEU Chi-restraints excluded: chain t residue 454 LEU Chi-restraints excluded: chain t residue 469 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 757 random chunks: chunk 663 optimal weight: 0.4980 chunk 698 optimal weight: 2.9990 chunk 637 optimal weight: 1.9990 chunk 679 optimal weight: 4.9990 chunk 409 optimal weight: 3.9990 chunk 296 optimal weight: 7.9990 chunk 533 optimal weight: 4.9990 chunk 208 optimal weight: 5.9990 chunk 614 optimal weight: 7.9990 chunk 643 optimal weight: 6.9990 chunk 677 optimal weight: 0.6980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 GLN R 74 GLN ** S 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 106 GLN g 51 ASN ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 ASN G 65 GLN G 110 ASN ** G 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 GLN V 49 GLN ** Y 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 65 GLN e 22 GLN e 37 GLN x 145 GLN y 102 HIS ** y 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 182 ASN t 299 ASN t 469 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 88868 Z= 0.225 Angle : 0.597 13.925 127913 Z= 0.302 Chirality : 0.037 0.322 15645 Planarity : 0.004 0.054 10091 Dihedral : 23.066 179.506 32603 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.41 % Favored : 95.51 % Rotamer: Outliers : 5.45 % Allowed : 23.74 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.11), residues: 5968 helix: 1.31 (0.11), residues: 2085 sheet: -0.67 (0.16), residues: 999 loop : -1.06 (0.11), residues: 2884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 82 HIS 0.007 0.001 HIS y 307 PHE 0.021 0.002 PHE x 96 TYR 0.019 0.001 TYR G 28 ARG 0.016 0.000 ARG P 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11936 Ramachandran restraints generated. 5968 Oldfield, 0 Emsley, 5968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11936 Ramachandran restraints generated. 5968 Oldfield, 0 Emsley, 5968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1288 residues out of total 5267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 1003 time to evaluate : 5.333 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: F 81 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.7998 (ptt90) REVERT: F 98 GLU cc_start: 0.8424 (tp30) cc_final: 0.7996 (tp30) REVERT: F 106 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8461 (tt0) REVERT: M 96 ARG cc_start: 0.6153 (mmm160) cc_final: 0.5473 (mmp80) REVERT: P 30 TYR cc_start: 0.7737 (OUTLIER) cc_final: 0.6583 (t80) REVERT: P 31 GLU cc_start: 0.8890 (tt0) cc_final: 0.8636 (mp0) REVERT: P 32 GLN cc_start: 0.9256 (OUTLIER) cc_final: 0.8939 (mm110) REVERT: P 37 TYR cc_start: 0.8730 (m-10) cc_final: 0.8309 (m-10) REVERT: P 41 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8524 (mm-40) REVERT: P 50 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8084 (mmt180) REVERT: P 51 ARG cc_start: 0.8905 (ttt90) cc_final: 0.8452 (ttm110) REVERT: P 56 LEU cc_start: 0.8778 (tt) cc_final: 0.8550 (tt) REVERT: P 104 GLN cc_start: 0.9119 (mm-40) cc_final: 0.8831 (mm-40) REVERT: P 130 ARG cc_start: 0.6245 (OUTLIER) cc_final: 0.5415 (mmt-90) REVERT: Q 27 ARG cc_start: 0.7910 (ptt90) cc_final: 0.7632 (ttp80) REVERT: Q 29 ASN cc_start: 0.7960 (m-40) cc_final: 0.7466 (t0) REVERT: Q 49 TYR cc_start: 0.8486 (m-80) cc_final: 0.8230 (m-10) REVERT: Q 66 VAL cc_start: 0.7604 (OUTLIER) cc_final: 0.7264 (p) REVERT: Q 107 GLU cc_start: 0.8287 (tp30) cc_final: 0.7978 (pt0) REVERT: Q 129 SER cc_start: 0.6730 (t) cc_final: 0.6341 (m) REVERT: R 7 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7683 (tppt) REVERT: R 11 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.7906 (mtmm) REVERT: R 27 ASP cc_start: 0.8798 (t0) cc_final: 0.8577 (t0) REVERT: R 77 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7502 (mp0) REVERT: R 84 TYR cc_start: 0.8384 (t80) cc_final: 0.8113 (t80) REVERT: R 87 GLU cc_start: 0.8374 (pm20) cc_final: 0.8097 (tp30) REVERT: R 92 ASP cc_start: 0.8642 (t70) cc_final: 0.8296 (t0) REVERT: R 107 LYS cc_start: 0.9150 (tttt) cc_final: 0.8787 (mtpp) REVERT: S 107 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8335 (tt) REVERT: S 109 GLU cc_start: 0.9191 (tt0) cc_final: 0.8800 (mm-30) REVERT: S 112 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8235 (tt0) REVERT: T 13 GLU cc_start: 0.7896 (mp0) cc_final: 0.7609 (tp30) REVERT: T 24 LYS cc_start: 0.8844 (mmtt) cc_final: 0.8404 (ptmm) REVERT: T 122 LYS cc_start: 0.8108 (pttt) cc_final: 0.7881 (pptt) REVERT: T 126 GLN cc_start: 0.8815 (tt0) cc_final: 0.8303 (tm-30) REVERT: T 129 ARG cc_start: 0.8070 (mtt90) cc_final: 0.7758 (mtp-110) REVERT: Z 106 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8618 (mm110) REVERT: c 60 GLU cc_start: 0.7102 (tt0) cc_final: 0.6832 (tp30) REVERT: f 95 ARG cc_start: 0.3471 (OUTLIER) cc_final: 0.3209 (ttp-110) REVERT: g 36 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8657 (mtt90) REVERT: g 91 ASP cc_start: 0.8197 (t70) cc_final: 0.7843 (t0) REVERT: g 118 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7663 (ttm-80) REVERT: g 246 TYR cc_start: 0.7595 (t80) cc_final: 0.7278 (t80) REVERT: A 136 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.7623 (mp0) REVERT: A 151 ASP cc_start: 0.9010 (p0) cc_final: 0.8607 (p0) REVERT: B 73 ASP cc_start: 0.8553 (m-30) cc_final: 0.8152 (t0) REVERT: B 78 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7899 (mm-30) REVERT: B 183 GLU cc_start: 0.8628 (tp30) cc_final: 0.8093 (tp30) REVERT: B 203 SER cc_start: 0.9398 (p) cc_final: 0.9012 (t) REVERT: B 211 PHE cc_start: 0.9094 (m-80) cc_final: 0.8783 (m-80) REVERT: C 61 MET cc_start: 0.8401 (tpp) cc_final: 0.7453 (pmm) REVERT: C 68 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.7978 (mtp180) REVERT: C 77 SER cc_start: 0.9184 (t) cc_final: 0.8959 (p) REVERT: C 123 ARG cc_start: 0.8032 (ptm160) cc_final: 0.7046 (mpt-90) REVERT: C 145 LYS cc_start: 0.8363 (mttt) cc_final: 0.8004 (mttm) REVERT: C 159 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8468 (mttp) REVERT: C 267 GLN cc_start: 0.8769 (tm-30) cc_final: 0.8488 (tm-30) REVERT: E 104 ASP cc_start: 0.8684 (t0) cc_final: 0.7901 (p0) REVERT: E 158 ASP cc_start: 0.8774 (m-30) cc_final: 0.8463 (m-30) REVERT: E 197 ASN cc_start: 0.9093 (OUTLIER) cc_final: 0.8859 (p0) REVERT: E 199 GLU cc_start: 0.8750 (pm20) cc_final: 0.8474 (mp0) REVERT: E 224 ASN cc_start: 0.8747 (m110) cc_final: 0.8461 (m-40) REVERT: E 237 SER cc_start: 0.9031 (t) cc_final: 0.8688 (m) REVERT: G 1 MET cc_start: 0.8056 (mmm) cc_final: 0.7702 (tpp) REVERT: G 17 GLU cc_start: 0.8965 (tt0) cc_final: 0.8493 (tm-30) REVERT: G 103 ASP cc_start: 0.8820 (t70) cc_final: 0.8504 (t70) REVERT: G 163 ASN cc_start: 0.7724 (p0) cc_final: 0.6832 (t0) REVERT: G 203 LYS cc_start: 0.8292 (tttt) cc_final: 0.7944 (mmmt) REVERT: G 204 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8131 (mt-10) REVERT: G 219 GLU cc_start: 0.7421 (tm-30) cc_final: 0.7136 (tm-30) REVERT: G 226 GLU cc_start: 0.7919 (tt0) cc_final: 0.7489 (mt-10) REVERT: H 10 LYS cc_start: 0.9068 (mttt) cc_final: 0.8694 (ptmt) REVERT: H 58 LYS cc_start: 0.8300 (mttt) cc_final: 0.8014 (pttt) REVERT: H 78 ARG cc_start: 0.8248 (mtp85) cc_final: 0.7973 (mtp180) REVERT: H 99 ARG cc_start: 0.8481 (mmt90) cc_final: 0.8106 (ttp80) REVERT: H 159 ASP cc_start: 0.9164 (OUTLIER) cc_final: 0.8871 (m-30) REVERT: I 73 THR cc_start: 0.8444 (m) cc_final: 0.8085 (p) REVERT: I 119 LEU cc_start: 0.8079 (mp) cc_final: 0.7801 (mp) REVERT: I 139 LYS cc_start: 0.7839 (tmtp) cc_final: 0.7188 (pttp) REVERT: I 141 ARG cc_start: 0.8120 (mtt180) cc_final: 0.7480 (mtp180) REVERT: I 159 SER cc_start: 0.8042 (m) cc_final: 0.7717 (t) REVERT: I 163 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7155 (tp30) REVERT: I 167 GLN cc_start: 0.7747 (mm-40) cc_final: 0.7185 (tp40) REVERT: J 107 GLU cc_start: 0.8829 (tp30) cc_final: 0.8361 (tp30) REVERT: J 140 GLN cc_start: 0.8410 (tp40) cc_final: 0.8074 (tp-100) REVERT: J 154 GLN cc_start: 0.8777 (tt0) cc_final: 0.8451 (tt0) REVERT: N 27 LYS cc_start: 0.8833 (pttt) cc_final: 0.8524 (mmtt) REVERT: N 49 GLN cc_start: 0.9016 (mm-40) cc_final: 0.8542 (mt0) REVERT: O 86 LYS cc_start: 0.9302 (tppp) cc_final: 0.9085 (mmmt) REVERT: O 87 GLU cc_start: 0.8312 (tp30) cc_final: 0.7933 (mt-10) REVERT: O 143 LYS cc_start: 0.8552 (tmmt) cc_final: 0.8144 (tppt) REVERT: O 147 ARG cc_start: 0.8966 (tpt90) cc_final: 0.8151 (ttp-110) REVERT: O 150 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7690 (mtt180) REVERT: V 4 ASP cc_start: 0.8474 (t70) cc_final: 0.8152 (p0) REVERT: V 13 VAL cc_start: 0.9435 (t) cc_final: 0.9196 (m) REVERT: V 32 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8271 (pt) REVERT: V 64 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8389 (mt-10) REVERT: W 31 SER cc_start: 0.8850 (t) cc_final: 0.8287 (m) REVERT: W 76 SER cc_start: 0.9350 (t) cc_final: 0.9001 (p) REVERT: W 104 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8567 (pp) REVERT: W 117 ARG cc_start: 0.8564 (tpp80) cc_final: 0.8344 (mtp85) REVERT: X 50 ILE cc_start: 0.9056 (mt) cc_final: 0.8722 (pt) REVERT: X 69 CYS cc_start: 0.8577 (m) cc_final: 0.8139 (m) REVERT: X 127 ASN cc_start: 0.8923 (m-40) cc_final: 0.8567 (t0) REVERT: Y 53 ASP cc_start: 0.9193 (m-30) cc_final: 0.8958 (p0) REVERT: Y 61 ARG cc_start: 0.8972 (tpt170) cc_final: 0.8552 (mmm-85) REVERT: Y 68 LYS cc_start: 0.8908 (mttt) cc_final: 0.8658 (mppt) REVERT: Y 72 PHE cc_start: 0.8621 (OUTLIER) cc_final: 0.8350 (m-80) REVERT: Y 86 GLU cc_start: 0.9051 (tp30) cc_final: 0.8716 (tp30) REVERT: Y 104 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7523 (mtp-110) REVERT: Y 108 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7742 (mtpp) REVERT: Y 109 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8069 (mt-10) REVERT: b 34 ASP cc_start: 0.8066 (t0) cc_final: 0.7218 (p0) REVERT: b 72 ARG cc_start: 0.8867 (ptt180) cc_final: 0.8448 (ptm-80) REVERT: x 172 LYS cc_start: 0.9060 (mptt) cc_final: 0.8758 (mtpp) REVERT: x 240 ASN cc_start: 0.8929 (m-40) cc_final: 0.8617 (m-40) REVERT: y 75 ASP cc_start: 0.8370 (m-30) cc_final: 0.8060 (m-30) REVERT: y 85 GLN cc_start: 0.8393 (mm110) cc_final: 0.7920 (mt0) REVERT: y 109 LYS cc_start: 0.8123 (mmmm) cc_final: 0.7702 (ttpp) REVERT: y 120 GLU cc_start: 0.9139 (mp0) cc_final: 0.8270 (mp0) REVERT: y 251 HIS cc_start: 0.8275 (OUTLIER) cc_final: 0.7570 (m-70) REVERT: y 342 GLU cc_start: 0.8871 (pm20) cc_final: 0.8413 (tp30) REVERT: y 345 ARG cc_start: 0.8363 (ttp-110) cc_final: 0.8079 (ttt180) REVERT: y 367 ILE cc_start: 0.8560 (pt) cc_final: 0.8291 (mm) REVERT: u 96 LEU cc_start: 0.8588 (pp) cc_final: 0.8300 (tt) REVERT: u 101 GLN cc_start: 0.8618 (mm110) cc_final: 0.8321 (mm-40) REVERT: u 219 LYS cc_start: 0.8782 (pttt) cc_final: 0.8335 (tttp) REVERT: u 225 THR cc_start: 0.7738 (OUTLIER) cc_final: 0.7313 (p) REVERT: u 228 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8394 (mt-10) REVERT: u 395 LYS cc_start: 0.7528 (tptm) cc_final: 0.6439 (mmtt) REVERT: u 401 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8749 (tt0) REVERT: u 476 LYS cc_start: 0.8098 (mttt) cc_final: 0.7790 (mmtt) REVERT: u 481 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8620 (tp30) REVERT: u 738 ARG cc_start: 0.8388 (mmt180) cc_final: 0.8073 (ttm110) REVERT: u 766 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8331 (pp) REVERT: w 194 LYS cc_start: 0.8662 (mttt) cc_final: 0.8153 (tmtt) REVERT: w 213 TRP cc_start: 0.8195 (p-90) cc_final: 0.7566 (p-90) REVERT: w 267 ARG cc_start: 0.8261 (ptt90) cc_final: 0.7442 (ptm160) REVERT: w 328 LYS cc_start: 0.8415 (mmtt) cc_final: 0.8165 (mmtt) REVERT: w 407 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.8047 (mt) REVERT: v 213 MET cc_start: 0.8097 (mmp) cc_final: 0.7299 (mmm) REVERT: v 274 MET cc_start: 0.8264 (ptm) cc_final: 0.8062 (mtt) REVERT: v 519 ARG cc_start: 0.7618 (ttm110) cc_final: 0.7251 (tpp-160) REVERT: v 523 LYS cc_start: 0.6297 (mttt) cc_final: 0.5608 (tptt) REVERT: t 259 HIS cc_start: 0.6716 (p-80) cc_final: 0.5539 (t-90) REVERT: t 304 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7569 (tt0) REVERT: t 366 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8593 (pp) REVERT: t 440 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7878 (tm-30) REVERT: t 462 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7621 (tm-30) REVERT: t 467 LYS cc_start: 0.8151 (mttt) cc_final: 0.7686 (mmtm) outliers start: 285 outliers final: 229 residues processed: 1190 average time/residue: 0.8045 time to fit residues: 1621.5036 Evaluate side-chains 1226 residues out of total 5267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 964 time to evaluate : 5.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 72 HIS Chi-restraints excluded: chain P residue 30 TYR Chi-restraints excluded: chain P residue 32 GLN Chi-restraints excluded: chain P residue 41 GLN Chi-restraints excluded: chain P residue 50 ARG Chi-restraints excluded: chain P residue 82 ASP Chi-restraints excluded: chain P residue 130 ARG Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 25 CYS Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 43 GLU Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain Q residue 97 GLN Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 7 LYS Chi-restraints excluded: chain R residue 11 LYS Chi-restraints excluded: chain R residue 24 LEU Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 70 SER Chi-restraints excluded: chain R residue 77 GLU Chi-restraints excluded: chain R residue 81 ARG Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain R residue 110 ASP Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 116 ASN Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain S residue 19 ASN Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 99 LEU Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 39 LEU Chi-restraints excluded: chain Z residue 58 LEU Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain Z residue 97 ILE Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 106 GLN Chi-restraints excluded: chain c residue 9 ILE Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 37 ASP Chi-restraints excluded: chain c residue 57 THR Chi-restraints excluded: chain c residue 59 LEU Chi-restraints excluded: chain f residue 95 ARG Chi-restraints excluded: chain f residue 102 VAL Chi-restraints excluded: chain f residue 147 THR Chi-restraints excluded: chain g residue 36 ARG Chi-restraints excluded: chain g residue 46 THR Chi-restraints excluded: chain g residue 64 HIS Chi-restraints excluded: chain g residue 93 THR Chi-restraints excluded: chain g residue 118 ARG Chi-restraints excluded: chain g residue 203 ASP Chi-restraints excluded: chain g residue 228 TYR Chi-restraints excluded: chain g residue 240 CYS Chi-restraints excluded: chain g residue 249 CYS Chi-restraints excluded: chain g residue 265 ILE Chi-restraints excluded: chain g residue 287 THR Chi-restraints excluded: chain g residue 297 THR Chi-restraints excluded: chain g residue 303 THR Chi-restraints excluded: chain A residue 11 LYS Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 95 ASP Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 159 LYS Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 159 ASP Chi-restraints excluded: chain H residue 165 ASN Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 138 ASN Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 21 GLU Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 73 GLU Chi-restraints excluded: chain J residue 146 SER Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 60 CYS Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain N residue 9 LYS Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 77 SER Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 143 SER Chi-restraints excluded: chain O residue 37 PHE Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 135 ILE Chi-restraints excluded: chain O residue 150 ARG Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 42 VAL Chi-restraints excluded: chain V residue 50 PHE Chi-restraints excluded: chain V residue 70 LEU Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain W residue 42 MET Chi-restraints excluded: chain W residue 64 ASN Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 121 THR Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 28 LYS Chi-restraints excluded: chain X residue 45 SER Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain X residue 119 ARG Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Y residue 55 ILE Chi-restraints excluded: chain Y residue 72 PHE Chi-restraints excluded: chain Y residue 104 ARG Chi-restraints excluded: chain Y residue 108 LYS Chi-restraints excluded: chain Y residue 109 GLU Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain b residue 33 MET Chi-restraints excluded: chain b residue 37 CYS Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain b residue 48 SER Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 60 SER Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain x residue 77 LYS Chi-restraints excluded: chain x residue 78 ILE Chi-restraints excluded: chain x residue 102 HIS Chi-restraints excluded: chain x residue 152 LEU Chi-restraints excluded: chain x residue 160 LEU Chi-restraints excluded: chain x residue 218 ILE Chi-restraints excluded: chain y residue 15 LEU Chi-restraints excluded: chain y residue 34 VAL Chi-restraints excluded: chain y residue 68 GLU Chi-restraints excluded: chain y residue 69 PHE Chi-restraints excluded: chain y residue 93 LEU Chi-restraints excluded: chain y residue 116 ILE Chi-restraints excluded: chain y residue 230 VAL Chi-restraints excluded: chain y residue 235 LEU Chi-restraints excluded: chain y residue 251 HIS Chi-restraints excluded: chain y residue 253 LEU Chi-restraints excluded: chain y residue 256 ASN Chi-restraints excluded: chain y residue 260 ILE Chi-restraints excluded: chain y residue 281 SER Chi-restraints excluded: chain y residue 303 ASP Chi-restraints excluded: chain y residue 351 LEU Chi-restraints excluded: chain y residue 359 THR Chi-restraints excluded: chain y residue 360 ASN Chi-restraints excluded: chain y residue 371 SER Chi-restraints excluded: chain y residue 379 SER Chi-restraints excluded: chain y residue 389 ASP Chi-restraints excluded: chain u residue 88 VAL Chi-restraints excluded: chain u residue 212 GLU Chi-restraints excluded: chain u residue 217 HIS Chi-restraints excluded: chain u residue 225 THR Chi-restraints excluded: chain u residue 235 GLN Chi-restraints excluded: chain u residue 297 PHE Chi-restraints excluded: chain u residue 348 ASP Chi-restraints excluded: chain u residue 397 THR Chi-restraints excluded: chain u residue 401 GLN Chi-restraints excluded: chain u residue 644 LEU Chi-restraints excluded: chain u residue 658 ILE Chi-restraints excluded: chain u residue 687 VAL Chi-restraints excluded: chain u residue 761 SER Chi-restraints excluded: chain u residue 766 LEU Chi-restraints excluded: chain u residue 778 THR Chi-restraints excluded: chain w residue 226 THR Chi-restraints excluded: chain w residue 302 LEU Chi-restraints excluded: chain w residue 306 ILE Chi-restraints excluded: chain w residue 377 LEU Chi-restraints excluded: chain w residue 403 GLU Chi-restraints excluded: chain w residue 407 LEU Chi-restraints excluded: chain w residue 413 LEU Chi-restraints excluded: chain w residue 414 SER Chi-restraints excluded: chain v residue 59 HIS Chi-restraints excluded: chain v residue 101 MET Chi-restraints excluded: chain v residue 260 TRP Chi-restraints excluded: chain v residue 278 SER Chi-restraints excluded: chain v residue 290 ILE Chi-restraints excluded: chain v residue 295 THR Chi-restraints excluded: chain v residue 517 VAL Chi-restraints excluded: chain v residue 522 GLN Chi-restraints excluded: chain t residue 250 MET Chi-restraints excluded: chain t residue 261 GLU Chi-restraints excluded: chain t residue 297 VAL Chi-restraints excluded: chain t residue 310 VAL Chi-restraints excluded: chain t residue 366 LEU Chi-restraints excluded: chain t residue 454 LEU Chi-restraints excluded: chain t residue 469 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 757 random chunks: chunk 446 optimal weight: 3.9990 chunk 718 optimal weight: 20.0000 chunk 438 optimal weight: 0.6980 chunk 341 optimal weight: 3.9990 chunk 499 optimal weight: 0.0060 chunk 754 optimal weight: 2.9990 chunk 694 optimal weight: 7.9990 chunk 600 optimal weight: 0.7980 chunk 62 optimal weight: 20.0000 chunk 463 optimal weight: 2.9990 chunk 368 optimal weight: 0.8980 overall best weight: 1.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 ASN G 65 GLN G 110 ASN ** G 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 GLN V 49 GLN ** Y 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 65 GLN e 22 GLN e 37 GLN e 39 ASN x 145 GLN ** y 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 247 GLN ** w 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 299 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.255 88868 Z= 0.247 Angle : 0.673 59.200 127913 Z= 0.358 Chirality : 0.037 0.423 15645 Planarity : 0.004 0.153 10091 Dihedral : 23.066 179.428 32600 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.44 % Favored : 95.48 % Rotamer: Outliers : 5.38 % Allowed : 23.91 % Favored : 70.71 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.11), residues: 5968 helix: 1.32 (0.11), residues: 2085 sheet: -0.67 (0.16), residues: 999 loop : -1.05 (0.11), residues: 2884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP w 213 HIS 0.032 0.001 HIS u 144 PHE 0.021 0.001 PHE x 96 TYR 0.083 0.002 TYR g 228 ARG 0.008 0.000 ARG Z 76 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11936 Ramachandran restraints generated. 5968 Oldfield, 0 Emsley, 5968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11936 Ramachandran restraints generated. 5968 Oldfield, 0 Emsley, 5968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1247 residues out of total 5267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 966 time to evaluate : 5.344 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: F 81 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.7991 (ptt90) REVERT: F 98 GLU cc_start: 0.8419 (tp30) cc_final: 0.7992 (tp30) REVERT: F 106 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8457 (tt0) REVERT: M 96 ARG cc_start: 0.6151 (mmm160) cc_final: 0.5471 (mmp80) REVERT: P 30 TYR cc_start: 0.7737 (OUTLIER) cc_final: 0.6565 (t80) REVERT: P 31 GLU cc_start: 0.8875 (tt0) cc_final: 0.8632 (mp0) REVERT: P 32 GLN cc_start: 0.9230 (OUTLIER) cc_final: 0.8905 (mm110) REVERT: P 37 TYR cc_start: 0.8730 (m-10) cc_final: 0.8305 (m-10) REVERT: P 41 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8517 (mm-40) REVERT: P 50 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.8082 (mmt180) REVERT: P 51 ARG cc_start: 0.8908 (ttt90) cc_final: 0.8497 (ttm110) REVERT: P 56 LEU cc_start: 0.8760 (tt) cc_final: 0.8542 (tt) REVERT: P 104 GLN cc_start: 0.9119 (mm-40) cc_final: 0.8827 (mm-40) REVERT: P 130 ARG cc_start: 0.6243 (OUTLIER) cc_final: 0.5411 (mmt-90) REVERT: Q 27 ARG cc_start: 0.7913 (ptt90) cc_final: 0.7627 (ttp80) REVERT: Q 29 ASN cc_start: 0.7950 (m-40) cc_final: 0.7464 (t0) REVERT: Q 49 TYR cc_start: 0.8484 (m-80) cc_final: 0.8229 (m-10) REVERT: Q 66 VAL cc_start: 0.7603 (OUTLIER) cc_final: 0.7266 (p) REVERT: Q 107 GLU cc_start: 0.8277 (tp30) cc_final: 0.7977 (pt0) REVERT: Q 129 SER cc_start: 0.6729 (t) cc_final: 0.6341 (m) REVERT: R 7 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7682 (tppt) REVERT: R 11 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.7916 (mtmm) REVERT: R 27 ASP cc_start: 0.8798 (t0) cc_final: 0.8575 (t0) REVERT: R 77 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7509 (mp0) REVERT: R 84 TYR cc_start: 0.8381 (t80) cc_final: 0.8111 (t80) REVERT: R 87 GLU cc_start: 0.8372 (pm20) cc_final: 0.8095 (tp30) REVERT: R 92 ASP cc_start: 0.8641 (t70) cc_final: 0.8290 (t0) REVERT: R 107 LYS cc_start: 0.9150 (tttt) cc_final: 0.8787 (mtpp) REVERT: S 23 ARG cc_start: 0.8357 (ptt-90) cc_final: 0.7966 (ptm-80) REVERT: S 107 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8335 (tt) REVERT: S 109 GLU cc_start: 0.9191 (tt0) cc_final: 0.8799 (mm-30) REVERT: S 112 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8234 (tt0) REVERT: T 13 GLU cc_start: 0.7893 (mp0) cc_final: 0.7604 (tp30) REVERT: T 24 LYS cc_start: 0.8845 (mmtt) cc_final: 0.8403 (ptmm) REVERT: T 83 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7760 (tt0) REVERT: T 122 LYS cc_start: 0.8108 (pttt) cc_final: 0.7881 (pptt) REVERT: T 126 GLN cc_start: 0.8815 (tt0) cc_final: 0.8303 (tm-30) REVERT: T 129 ARG cc_start: 0.8068 (mtt90) cc_final: 0.7756 (mtp-110) REVERT: c 60 GLU cc_start: 0.7114 (tt0) cc_final: 0.6829 (tp30) REVERT: f 95 ARG cc_start: 0.3471 (OUTLIER) cc_final: 0.3205 (ttp-110) REVERT: g 36 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8656 (mtt90) REVERT: g 91 ASP cc_start: 0.8194 (t70) cc_final: 0.7836 (t0) REVERT: g 118 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7663 (ttm-80) REVERT: g 246 TYR cc_start: 0.7592 (t80) cc_final: 0.7274 (t80) REVERT: A 136 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.7613 (mp0) REVERT: A 151 ASP cc_start: 0.9008 (p0) cc_final: 0.8601 (p0) REVERT: B 73 ASP cc_start: 0.8552 (m-30) cc_final: 0.8150 (t0) REVERT: B 78 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7900 (mm-30) REVERT: B 183 GLU cc_start: 0.8626 (tp30) cc_final: 0.8090 (tp30) REVERT: B 203 SER cc_start: 0.9396 (p) cc_final: 0.9008 (t) REVERT: B 211 PHE cc_start: 0.9093 (m-80) cc_final: 0.8775 (m-80) REVERT: C 61 MET cc_start: 0.8400 (tpp) cc_final: 0.7453 (pmm) REVERT: C 68 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.7974 (mtp180) REVERT: C 77 SER cc_start: 0.9184 (t) cc_final: 0.8956 (p) REVERT: C 123 ARG cc_start: 0.8031 (ptm160) cc_final: 0.7042 (mpt-90) REVERT: C 145 LYS cc_start: 0.8361 (mttt) cc_final: 0.7997 (mttm) REVERT: C 159 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8462 (mttp) REVERT: C 267 GLN cc_start: 0.8764 (tm-30) cc_final: 0.8486 (tm-30) REVERT: E 104 ASP cc_start: 0.8682 (t0) cc_final: 0.7899 (p0) REVERT: E 158 ASP cc_start: 0.8775 (m-30) cc_final: 0.8462 (m-30) REVERT: E 199 GLU cc_start: 0.8724 (pm20) cc_final: 0.8488 (mp0) REVERT: E 224 ASN cc_start: 0.8743 (m110) cc_final: 0.8457 (m-40) REVERT: E 237 SER cc_start: 0.9029 (t) cc_final: 0.8686 (m) REVERT: G 1 MET cc_start: 0.8053 (mmm) cc_final: 0.7700 (tpp) REVERT: G 17 GLU cc_start: 0.8965 (tt0) cc_final: 0.8493 (tm-30) REVERT: G 103 ASP cc_start: 0.8824 (t70) cc_final: 0.8500 (t70) REVERT: G 163 ASN cc_start: 0.7722 (p0) cc_final: 0.6830 (t0) REVERT: G 203 LYS cc_start: 0.8291 (tttt) cc_final: 0.7942 (mmmt) REVERT: G 204 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8137 (mt-10) REVERT: G 219 GLU cc_start: 0.7421 (tm-30) cc_final: 0.7136 (tm-30) REVERT: G 226 GLU cc_start: 0.7920 (tt0) cc_final: 0.7488 (mt-10) REVERT: H 10 LYS cc_start: 0.9066 (mttt) cc_final: 0.8692 (ptmt) REVERT: H 58 LYS cc_start: 0.8285 (mttt) cc_final: 0.7947 (pttm) REVERT: H 78 ARG cc_start: 0.8249 (mtp85) cc_final: 0.7974 (mtp180) REVERT: H 99 ARG cc_start: 0.8479 (mmt90) cc_final: 0.8100 (ttp80) REVERT: H 159 ASP cc_start: 0.9164 (OUTLIER) cc_final: 0.8869 (m-30) REVERT: I 73 THR cc_start: 0.8441 (m) cc_final: 0.8083 (p) REVERT: I 139 LYS cc_start: 0.7844 (tmtp) cc_final: 0.7187 (pttp) REVERT: I 141 ARG cc_start: 0.8120 (mtt180) cc_final: 0.7474 (mtp180) REVERT: I 159 SER cc_start: 0.8039 (m) cc_final: 0.7715 (t) REVERT: I 163 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7152 (tp30) REVERT: I 167 GLN cc_start: 0.7742 (mm-40) cc_final: 0.7181 (tp40) REVERT: J 107 GLU cc_start: 0.8827 (tp30) cc_final: 0.8357 (tp30) REVERT: J 140 GLN cc_start: 0.8404 (tp40) cc_final: 0.8063 (tp-100) REVERT: J 154 GLN cc_start: 0.8771 (tt0) cc_final: 0.8445 (tt0) REVERT: N 27 LYS cc_start: 0.8832 (pttt) cc_final: 0.8524 (mmtt) REVERT: N 49 GLN cc_start: 0.9014 (mm-40) cc_final: 0.8540 (mt0) REVERT: O 86 LYS cc_start: 0.9309 (tppp) cc_final: 0.9082 (mmmt) REVERT: O 87 GLU cc_start: 0.8307 (tp30) cc_final: 0.7935 (mt-10) REVERT: O 143 LYS cc_start: 0.8547 (tmmt) cc_final: 0.8139 (tppt) REVERT: O 147 ARG cc_start: 0.8965 (tpt90) cc_final: 0.8150 (ttp-110) REVERT: O 150 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7687 (mtt180) REVERT: V 4 ASP cc_start: 0.8473 (t70) cc_final: 0.8150 (p0) REVERT: V 13 VAL cc_start: 0.9434 (t) cc_final: 0.9198 (m) REVERT: V 32 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8268 (pt) REVERT: V 64 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8386 (mt-10) REVERT: W 31 SER cc_start: 0.8846 (t) cc_final: 0.8284 (m) REVERT: W 76 SER cc_start: 0.9349 (t) cc_final: 0.8997 (p) REVERT: W 104 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8562 (pp) REVERT: W 117 ARG cc_start: 0.8560 (tpp80) cc_final: 0.8341 (mtp85) REVERT: X 50 ILE cc_start: 0.9053 (mt) cc_final: 0.8717 (pt) REVERT: X 69 CYS cc_start: 0.8562 (m) cc_final: 0.8117 (m) REVERT: X 127 ASN cc_start: 0.8920 (m-40) cc_final: 0.8566 (t0) REVERT: Y 53 ASP cc_start: 0.9194 (m-30) cc_final: 0.8957 (p0) REVERT: Y 61 ARG cc_start: 0.8971 (tpt170) cc_final: 0.8550 (mmm-85) REVERT: Y 68 LYS cc_start: 0.8904 (mttt) cc_final: 0.8656 (mppt) REVERT: Y 72 PHE cc_start: 0.8614 (OUTLIER) cc_final: 0.8339 (m-80) REVERT: Y 86 GLU cc_start: 0.9063 (tp30) cc_final: 0.8715 (tp30) REVERT: Y 104 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7517 (mtp-110) REVERT: Y 108 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7738 (mtpp) REVERT: Y 109 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8067 (mt-10) REVERT: b 34 ASP cc_start: 0.8061 (t0) cc_final: 0.7215 (p0) REVERT: b 72 ARG cc_start: 0.8866 (ptt180) cc_final: 0.8446 (ptm-80) REVERT: x 172 LYS cc_start: 0.9057 (mptt) cc_final: 0.8756 (mtpp) REVERT: x 240 ASN cc_start: 0.8929 (m-40) cc_final: 0.8616 (m-40) REVERT: y 85 GLN cc_start: 0.8382 (mm110) cc_final: 0.7917 (mt0) REVERT: y 109 LYS cc_start: 0.8123 (mmmm) cc_final: 0.7698 (ttpp) REVERT: y 120 GLU cc_start: 0.9135 (mp0) cc_final: 0.8265 (mp0) REVERT: y 251 HIS cc_start: 0.8276 (OUTLIER) cc_final: 0.7571 (m-70) REVERT: y 342 GLU cc_start: 0.8870 (pm20) cc_final: 0.8413 (tp30) REVERT: y 345 ARG cc_start: 0.8357 (ttp-110) cc_final: 0.8075 (ttt180) REVERT: y 367 ILE cc_start: 0.8559 (pt) cc_final: 0.8289 (mm) REVERT: u 96 LEU cc_start: 0.8589 (pp) cc_final: 0.8297 (tt) REVERT: u 101 GLN cc_start: 0.8617 (mm110) cc_final: 0.8317 (mm-40) REVERT: u 219 LYS cc_start: 0.8777 (pttt) cc_final: 0.8334 (tttp) REVERT: u 225 THR cc_start: 0.7736 (OUTLIER) cc_final: 0.7312 (p) REVERT: u 228 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8391 (mt-10) REVERT: u 395 LYS cc_start: 0.7525 (tptm) cc_final: 0.6434 (mmtt) REVERT: u 401 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8748 (tt0) REVERT: u 476 LYS cc_start: 0.8094 (mttt) cc_final: 0.7788 (mmtt) REVERT: u 481 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8617 (tp30) REVERT: u 738 ARG cc_start: 0.8385 (mmt180) cc_final: 0.8070 (ttm110) REVERT: u 766 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8323 (pp) REVERT: w 194 LYS cc_start: 0.8660 (mttt) cc_final: 0.8152 (tmtt) REVERT: w 213 TRP cc_start: 0.8151 (p-90) cc_final: 0.7569 (p-90) REVERT: w 267 ARG cc_start: 0.8259 (ptt90) cc_final: 0.7440 (ptm160) REVERT: w 407 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8047 (mt) REVERT: v 274 MET cc_start: 0.8268 (ptm) cc_final: 0.8063 (mtt) REVERT: v 519 ARG cc_start: 0.7616 (ttm110) cc_final: 0.7249 (tpp-160) REVERT: v 523 LYS cc_start: 0.6296 (mttt) cc_final: 0.5607 (tptt) REVERT: t 259 HIS cc_start: 0.6715 (p-80) cc_final: 0.5538 (t-90) REVERT: t 304 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7570 (tt0) REVERT: t 366 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8592 (pp) REVERT: t 440 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7876 (tm-30) REVERT: t 462 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7616 (tm-30) REVERT: t 467 LYS cc_start: 0.8155 (mttt) cc_final: 0.7683 (mmtm) outliers start: 281 outliers final: 240 residues processed: 1150 average time/residue: 0.7973 time to fit residues: 1559.2737 Evaluate side-chains 1235 residues out of total 5267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 963 time to evaluate : 5.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 202 SER Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 72 HIS Chi-restraints excluded: chain P residue 30 TYR Chi-restraints excluded: chain P residue 32 GLN Chi-restraints excluded: chain P residue 41 GLN Chi-restraints excluded: chain P residue 50 ARG Chi-restraints excluded: chain P residue 82 ASP Chi-restraints excluded: chain P residue 130 ARG Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 25 CYS Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 43 GLU Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 72 VAL Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 93 VAL Chi-restraints excluded: chain Q residue 97 GLN Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 7 LYS Chi-restraints excluded: chain R residue 11 LYS Chi-restraints excluded: chain R residue 24 LEU Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 70 SER Chi-restraints excluded: chain R residue 77 GLU Chi-restraints excluded: chain R residue 81 ARG Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain R residue 110 ASP Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 116 ASN Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain S residue 19 ASN Chi-restraints excluded: chain S residue 43 VAL Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 99 LEU Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 39 LEU Chi-restraints excluded: chain T residue 76 THR Chi-restraints excluded: chain T residue 83 GLN Chi-restraints excluded: chain Z residue 58 LEU Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain Z residue 97 ILE Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain c residue 9 ILE Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 37 ASP Chi-restraints excluded: chain c residue 57 THR Chi-restraints excluded: chain c residue 59 LEU Chi-restraints excluded: chain f residue 95 ARG Chi-restraints excluded: chain f residue 102 VAL Chi-restraints excluded: chain f residue 147 THR Chi-restraints excluded: chain g residue 36 ARG Chi-restraints excluded: chain g residue 46 THR Chi-restraints excluded: chain g residue 64 HIS Chi-restraints excluded: chain g residue 93 THR Chi-restraints excluded: chain g residue 118 ARG Chi-restraints excluded: chain g residue 191 HIS Chi-restraints excluded: chain g residue 203 ASP Chi-restraints excluded: chain g residue 228 TYR Chi-restraints excluded: chain g residue 240 CYS Chi-restraints excluded: chain g residue 249 CYS Chi-restraints excluded: chain g residue 265 ILE Chi-restraints excluded: chain g residue 287 THR Chi-restraints excluded: chain g residue 297 THR Chi-restraints excluded: chain g residue 303 THR Chi-restraints excluded: chain A residue 11 LYS Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 95 ASP Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 159 LYS Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 159 ASP Chi-restraints excluded: chain H residue 165 ASN Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 138 ASN Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 21 GLU Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 73 GLU Chi-restraints excluded: chain J residue 146 SER Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 60 CYS Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 80 MET Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain N residue 9 LYS Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 77 SER Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 143 SER Chi-restraints excluded: chain O residue 37 PHE Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 103 ASN Chi-restraints excluded: chain O residue 135 ILE Chi-restraints excluded: chain O residue 150 ARG Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 42 VAL Chi-restraints excluded: chain V residue 50 PHE Chi-restraints excluded: chain V residue 70 LEU Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain W residue 42 MET Chi-restraints excluded: chain W residue 64 ASN Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 121 THR Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 28 LYS Chi-restraints excluded: chain X residue 36 LEU Chi-restraints excluded: chain X residue 45 SER Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 115 ILE Chi-restraints excluded: chain X residue 119 ARG Chi-restraints excluded: chain Y residue 6 THR Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Y residue 55 ILE Chi-restraints excluded: chain Y residue 72 PHE Chi-restraints excluded: chain Y residue 104 ARG Chi-restraints excluded: chain Y residue 108 LYS Chi-restraints excluded: chain Y residue 109 GLU Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain b residue 33 MET Chi-restraints excluded: chain b residue 37 CYS Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain b residue 48 SER Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 60 SER Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 37 GLN Chi-restraints excluded: chain x residue 77 LYS Chi-restraints excluded: chain x residue 78 ILE Chi-restraints excluded: chain x residue 102 HIS Chi-restraints excluded: chain x residue 152 LEU Chi-restraints excluded: chain x residue 160 LEU Chi-restraints excluded: chain x residue 218 ILE Chi-restraints excluded: chain y residue 15 LEU Chi-restraints excluded: chain y residue 34 VAL Chi-restraints excluded: chain y residue 68 GLU Chi-restraints excluded: chain y residue 69 PHE Chi-restraints excluded: chain y residue 93 LEU Chi-restraints excluded: chain y residue 116 ILE Chi-restraints excluded: chain y residue 230 VAL Chi-restraints excluded: chain y residue 235 LEU Chi-restraints excluded: chain y residue 251 HIS Chi-restraints excluded: chain y residue 253 LEU Chi-restraints excluded: chain y residue 256 ASN Chi-restraints excluded: chain y residue 260 ILE Chi-restraints excluded: chain y residue 281 SER Chi-restraints excluded: chain y residue 303 ASP Chi-restraints excluded: chain y residue 351 LEU Chi-restraints excluded: chain y residue 359 THR Chi-restraints excluded: chain y residue 360 ASN Chi-restraints excluded: chain y residue 371 SER Chi-restraints excluded: chain y residue 379 SER Chi-restraints excluded: chain y residue 389 ASP Chi-restraints excluded: chain u residue 88 VAL Chi-restraints excluded: chain u residue 212 GLU Chi-restraints excluded: chain u residue 217 HIS Chi-restraints excluded: chain u residue 225 THR Chi-restraints excluded: chain u residue 235 GLN Chi-restraints excluded: chain u residue 297 PHE Chi-restraints excluded: chain u residue 348 ASP Chi-restraints excluded: chain u residue 397 THR Chi-restraints excluded: chain u residue 401 GLN Chi-restraints excluded: chain u residue 644 LEU Chi-restraints excluded: chain u residue 658 ILE Chi-restraints excluded: chain u residue 687 VAL Chi-restraints excluded: chain u residue 761 SER Chi-restraints excluded: chain u residue 766 LEU Chi-restraints excluded: chain u residue 778 THR Chi-restraints excluded: chain w residue 216 ILE Chi-restraints excluded: chain w residue 226 THR Chi-restraints excluded: chain w residue 302 LEU Chi-restraints excluded: chain w residue 306 ILE Chi-restraints excluded: chain w residue 377 LEU Chi-restraints excluded: chain w residue 403 GLU Chi-restraints excluded: chain w residue 407 LEU Chi-restraints excluded: chain w residue 413 LEU Chi-restraints excluded: chain w residue 414 SER Chi-restraints excluded: chain v residue 59 HIS Chi-restraints excluded: chain v residue 101 MET Chi-restraints excluded: chain v residue 260 TRP Chi-restraints excluded: chain v residue 278 SER Chi-restraints excluded: chain v residue 290 ILE Chi-restraints excluded: chain v residue 295 THR Chi-restraints excluded: chain v residue 517 VAL Chi-restraints excluded: chain v residue 522 GLN Chi-restraints excluded: chain t residue 250 MET Chi-restraints excluded: chain t residue 261 GLU Chi-restraints excluded: chain t residue 297 VAL Chi-restraints excluded: chain t residue 310 VAL Chi-restraints excluded: chain t residue 366 LEU Chi-restraints excluded: chain t residue 454 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 757 random chunks: chunk 477 optimal weight: 10.0000 chunk 639 optimal weight: 5.9990 chunk 183 optimal weight: 30.0000 chunk 553 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 601 optimal weight: 4.9990 chunk 251 optimal weight: 8.9990 chunk 617 optimal weight: 3.9990 chunk 76 optimal weight: 8.9990 chunk 110 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 114 HIS Q 86 GLN ** R 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 145 HIS ** g 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 117 ASN g 188 HIS A 36 GLN ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 GLN ** E 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 165 ASN I 22 HIS I 165 GLN J 140 GLN ** L 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 ASN V 49 GLN ** Y 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 65 GLN e 22 GLN x 145 GLN y 124 HIS ** y 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 53 GLN ** u 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 284 ASN ** u 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.113545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.087006 restraints weight = 159106.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.087362 restraints weight = 110886.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.088950 restraints weight = 93458.704| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.123 88868 Z= 0.623 Angle : 0.889 15.260 127913 Z= 0.443 Chirality : 0.049 0.404 15645 Planarity : 0.007 0.088 10091 Dihedral : 23.197 179.817 32600 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.32 % Favored : 93.55 % Rotamer: Outliers : 5.41 % Allowed : 23.95 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.10), residues: 5968 helix: 0.53 (0.11), residues: 2082 sheet: -1.02 (0.15), residues: 987 loop : -1.33 (0.11), residues: 2899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 175 HIS 0.014 0.002 HIS F 79 PHE 0.032 0.003 PHE u 704 TYR 0.046 0.003 TYR e 38 ARG 0.016 0.001 ARG P 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24231.29 seconds wall clock time: 426 minutes 15.57 seconds (25575.57 seconds total)