Starting phenix.real_space_refine on Sat Mar 16 07:07:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ff4_4255/03_2024/6ff4_4255_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ff4_4255/03_2024/6ff4_4255.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ff4_4255/03_2024/6ff4_4255.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ff4_4255/03_2024/6ff4_4255.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ff4_4255/03_2024/6ff4_4255_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ff4_4255/03_2024/6ff4_4255_updated.pdb" } resolution = 3.4 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 10 6.06 5 P 282 5.49 5 Mg 4 5.21 5 S 339 5.16 5 C 44960 2.51 5 N 12625 2.21 5 O 14172 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 ARG 69": "NH1" <-> "NH2" Residue "1 ARG 108": "NH1" <-> "NH2" Residue "3 ARG 533": "NH1" <-> "NH2" Residue "3 ARG 563": "NH1" <-> "NH2" Residue "3 ARG 565": "NH1" <-> "NH2" Residue "3 ARG 600": "NH1" <-> "NH2" Residue "7 ARG 6": "NH1" <-> "NH2" Residue "8 ARG 515": "NH1" <-> "NH2" Residue "8 PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 554": "NH1" <-> "NH2" Residue "8 TYR 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 49": "NH1" <-> "NH2" Residue "A ARG 79": "NH1" <-> "NH2" Residue "A ARG 114": "NH1" <-> "NH2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A ARG 159": "NH1" <-> "NH2" Residue "A TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 305": "NH1" <-> "NH2" Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 462": "NH1" <-> "NH2" Residue "A ARG 470": "NH1" <-> "NH2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A ARG 510": "NH1" <-> "NH2" Residue "A TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 593": "NH1" <-> "NH2" Residue "A ARG 603": "NH1" <-> "NH2" Residue "A ARG 707": "NH1" <-> "NH2" Residue "A ARG 855": "NH1" <-> "NH2" Residue "A ARG 861": "NH1" <-> "NH2" Residue "A ARG 889": "NH1" <-> "NH2" Residue "A PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 998": "NH1" <-> "NH2" Residue "A PHE 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1094": "NH1" <-> "NH2" Residue "A PHE 1099": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1151": "NH1" <-> "NH2" Residue "A ARG 1163": "NH1" <-> "NH2" Residue "A PHE 1207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1401": "NH1" <-> "NH2" Residue "A ARG 1402": "NH1" <-> "NH2" Residue "A ARG 1427": "NH1" <-> "NH2" Residue "A ARG 1459": "NH1" <-> "NH2" Residue "A ARG 1523": "NH1" <-> "NH2" Residue "A TYR 1620": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1748": "NH1" <-> "NH2" Residue "A ARG 1865": "NH1" <-> "NH2" Residue "A ARG 1949": "NH1" <-> "NH2" Residue "A TYR 2129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 160": "NH1" <-> "NH2" Residue "B PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 342": "NH1" <-> "NH2" Residue "B ARG 354": "NH1" <-> "NH2" Residue "B ARG 367": "NH1" <-> "NH2" Residue "B ARG 417": "NH1" <-> "NH2" Residue "B ARG 543": "NH1" <-> "NH2" Residue "B ARG 578": "NH1" <-> "NH2" Residue "B ARG 711": "NH1" <-> "NH2" Residue "B ARG 803": "NH1" <-> "NH2" Residue "B TYR 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 854": "NH1" <-> "NH2" Residue "B TYR 869": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 931": "NH1" <-> "NH2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C ARG 166": "NH1" <-> "NH2" Residue "C PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 310": "NH1" <-> "NH2" Residue "C ARG 325": "NH1" <-> "NH2" Residue "D ARG 226": "NH1" <-> "NH2" Residue "D TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 337": "NH1" <-> "NH2" Residue "D ARG 383": "NH1" <-> "NH2" Residue "D ARG 476": "NH1" <-> "NH2" Residue "E TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 91": "NH1" <-> "NH2" Residue "O ARG 228": "NH1" <-> "NH2" Residue "O ARG 267": "NH1" <-> "NH2" Residue "O ARG 274": "NH1" <-> "NH2" Residue "O ARG 296": "NH1" <-> "NH2" Residue "O ARG 355": "NH1" <-> "NH2" Residue "O ARG 361": "NH1" <-> "NH2" Residue "O ARG 368": "NH1" <-> "NH2" Residue "O ARG 384": "NH1" <-> "NH2" Residue "O ARG 396": "NH1" <-> "NH2" Residue "P PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 56": "NH1" <-> "NH2" Residue "P ARG 62": "NH1" <-> "NH2" Residue "P ARG 123": "NH1" <-> "NH2" Residue "P ARG 132": "NH1" <-> "NH2" Residue "P ARG 201": "NH1" <-> "NH2" Residue "Q ARG 8": "NH1" <-> "NH2" Residue "Q ARG 72": "NH1" <-> "NH2" Residue "Q ARG 120": "NH1" <-> "NH2" Residue "R ARG 44": "NH1" <-> "NH2" Residue "R ARG 60": "NH1" <-> "NH2" Residue "S ARG 29": "NH1" <-> "NH2" Residue "S ARG 33": "NH1" <-> "NH2" Residue "V ARG 72": "NH1" <-> "NH2" Residue "s ARG 154": "NH1" <-> "NH2" Residue "s PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 145": "NH1" <-> "NH2" Residue "t ARG 154": "NH1" <-> "NH2" Residue "t ARG 179": "NH1" <-> "NH2" Residue "t ARG 190": "NH1" <-> "NH2" Residue "u ARG 451": "NH1" <-> "NH2" Residue "u ARG 495": "NH1" <-> "NH2" Residue "u ARG 517": "NH1" <-> "NH2" Residue "u ARG 590": "NH1" <-> "NH2" Residue "u ARG 614": "NH1" <-> "NH2" Residue "u ARG 684": "NH1" <-> "NH2" Residue "u ARG 736": "NH1" <-> "NH2" Residue "u ARG 767": "NH1" <-> "NH2" Residue "u ARG 822": "NH1" <-> "NH2" Residue "u PHE 914": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 939": "NH1" <-> "NH2" Residue "u ARG 1019": "NH1" <-> "NH2" Residue "u ARG 1027": "NH1" <-> "NH2" Residue "u ARG 1045": "NH1" <-> "NH2" Residue "u ARG 1106": "NH1" <-> "NH2" Residue "u PHE 1126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 1245": "NH1" <-> "NH2" Residue "u TYR 1302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ARG 151": "NH1" <-> "NH2" Residue "v TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ARG 274": "NH1" <-> "NH2" Residue "v ARG 326": "NH1" <-> "NH2" Residue "v ARG 429": "NH1" <-> "NH2" Residue "v ARG 464": "NH1" <-> "NH2" Residue "v ARG 525": "NH1" <-> "NH2" Residue "v ARG 528": "NH1" <-> "NH2" Residue "v ARG 532": "NH1" <-> "NH2" Residue "v ARG 692": "NH1" <-> "NH2" Residue "v ARG 697": "NH1" <-> "NH2" Residue "v PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ARG 815": "NH1" <-> "NH2" Residue "v ARG 895": "NH1" <-> "NH2" Residue "v ARG 1013": "NH1" <-> "NH2" Residue "v ARG 1079": "NH1" <-> "NH2" Residue "v TYR 1166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 4": "NH1" <-> "NH2" Residue "y ARG 21": "NH1" <-> "NH2" Residue "z ARG 19": "NH1" <-> "NH2" Residue "z ARG 24": "NH1" <-> "NH2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 72392 Number of models: 1 Model: "" Number of chains: 35 Chain: "1" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 981 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "2" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1262 Classifications: {'RNA': 60} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 19, 'rna3p_pyr': 30} Link IDs: {'rna2p': 11, 'rna3p': 48} Chain breaks: 2 Chain: "3" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 981 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "5" Number of atoms: 1470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 1470 Classifications: {'RNA': 70} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 5, 'rna3p_pur': 18, 'rna3p_pyr': 36} Link IDs: {'rna2p': 16, 'rna3p': 53} Chain: "6" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 2035 Classifications: {'RNA': 95} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 47, 'rna3p_pyr': 34} Link IDs: {'rna2p': 14, 'rna3p': 80} Chain: "7" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 733 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "8" Number of atoms: 1211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1211 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 9, 'TRANS': 134} Chain: "A" Number of atoms: 18569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2238, 18569 Classifications: {'peptide': 2238} Link IDs: {'PCIS': 1, 'PTRANS': 125, 'TRANS': 2111} Chain breaks: 2 Chain: "B" Number of atoms: 7137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 902, 7137 Classifications: {'peptide': 902} Link IDs: {'PTRANS': 55, 'TRANS': 846} Chain: "C" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2287 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 19, 'TRANS': 266} Chain breaks: 1 Chain: "D" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2517 Classifications: {'peptide': 320} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 306} Chain: "E" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1054 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 7, 'TRANS': 122} Chain breaks: 1 Chain: "L" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 858 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "O" Number of atoms: 2235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2235 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 3, 'TRANS': 249} Chain: "P" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2305 Classifications: {'peptide': 286} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 267} Chain breaks: 1 Chain: "Q" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1153 Classifications: {'peptide': 138} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 130} Chain: "R" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 869 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 2, 'TRANS': 99} Chain breaks: 1 Chain: "S" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 261 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 3, 'TRANS': 30} Chain: "V" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1236 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 149} Chain: "Y" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 762 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain: "Z" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 1013 Classifications: {'RNA': 48} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 5, 'rna3p_pur': 14, 'rna3p_pyr': 21} Link IDs: {'rna2p': 12, 'rna3p': 35} Chain breaks: 1 Chain: "s" Number of atoms: 1377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1377 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 164} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "t" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1415 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 8, 'TRANS': 163} Chain breaks: 2 Chain: "u" Number of atoms: 7013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 881, 7013 Classifications: {'peptide': 881} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 841} Chain breaks: 1 Chain: "v" Number of atoms: 9315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1189, 9315 Classifications: {'peptide': 1189} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 58, 'TRANS': 1127} Chain breaks: 4 Chain: "x" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 656 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "y" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 766 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "z" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 839 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "6" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "t" 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 43414 SG CYS P 24 50.953 74.167 65.199 1.00 41.59 S ATOM 43436 SG CYS P 27 49.863 77.360 66.381 1.00 41.94 S ATOM 43879 SG CYS P 81 53.773 74.914 67.691 1.00 46.73 S ATOM 43901 SG CYS P 84 50.445 74.668 68.727 1.00 47.23 S ATOM 44547 SG CYS P 165 36.296 90.945 78.391 1.00 58.25 S ATOM 44613 SG CYS P 173 34.621 95.389 77.896 1.00 58.03 S ATOM 44661 SG CYS P 179 36.261 93.192 75.546 1.00 53.98 S ATOM 43585 SG CYS P 45 63.006 79.513 74.280 1.00 45.52 S ATOM 43608 SG CYS P 48 66.538 79.166 74.994 1.00 45.69 S ATOM 43804 SG CYS P 71 65.447 78.780 70.799 1.00 43.75 S ATOM 43826 SG CYS P 74 65.118 76.281 73.385 1.00 43.70 S ATOM 46486 SG CYS Q 101 40.670 109.804 60.592 1.00 39.22 S ATOM 46492 SG CYS Q 102 44.149 112.736 62.950 1.00 36.50 S ATOM 46767 SG CYS Q 137 43.100 109.415 63.230 1.00 32.19 S ATOM 46486 SG CYS Q 101 40.670 109.804 60.592 1.00 39.22 S ATOM 46625 SG CYS Q 119 38.412 106.994 60.263 1.00 37.25 S ATOM 46517 SG CYS Q 105 42.936 107.048 60.714 1.00 28.89 S ATOM 46611 SG CYS Q 117 42.917 103.370 61.047 1.00 32.48 S ATOM 46744 SG CYS Q 134 42.156 105.455 63.861 1.00 33.57 S ATOM 53022 SG CYS t 202 87.501 107.541 114.162 1.00 18.13 S ATOM 53097 SG CYS t 211 90.287 105.137 114.991 1.00 20.91 S ATOM 53136 SG CYS t 217 90.646 109.082 114.676 1.00 17.46 S ATOM 70787 SG CYS y 11 103.838 97.988 173.098 1.00 17.72 S ATOM 71050 SG CYS y 46 101.346 100.583 174.992 1.00 17.87 S ATOM 71073 SG CYS y 49 103.454 101.281 171.835 1.00 21.41 S ATOM 71344 SG CYS y 85 100.267 97.860 172.921 1.00 17.85 S ATOM 70874 SG CYS y 23 97.863 104.289 157.105 1.00 23.88 S ATOM 70898 SG CYS y 26 98.064 100.805 155.928 1.00 23.69 S ATOM 71145 SG CYS y 58 98.400 103.089 160.489 1.00 23.30 S ATOM 71166 SG CYS y 61 101.024 102.504 156.776 1.00 25.80 S ATOM 70925 SG CYS y 30 92.594 91.888 161.724 1.00 17.61 S ATOM 71241 SG CYS y 72 90.204 89.815 159.834 1.00 15.01 S ATOM 71265 SG CYS y 75 92.838 88.736 163.402 1.00 15.43 S Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ASN C 413 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASN C 413 " occ=0.00 residue: pdb=" N GLN C 414 " occ=0.00 ... (7 atoms not shown) pdb=" NE2 GLN C 414 " occ=0.00 residue: pdb=" N SER C 415 " occ=0.00 ... (4 atoms not shown) pdb=" OG SER C 415 " occ=0.00 Time building chain proxies: 28.16, per 1000 atoms: 0.39 Number of scatterers: 72392 At special positions: 0 Unit cell: (193.72, 207.64, 251.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 10 29.99 S 339 16.00 P 282 15.00 Mg 4 11.99 O 14172 8.00 N 12625 7.00 C 44960 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS 7 56 " - pdb=" SG CYS 7 59 " distance=2.03 Simple disulfide: pdb=" SG CYS s 44 " - pdb=" SG CYS s 164 " distance=2.03 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 22.15 Conformation dependent library (CDL) restraints added in 8.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN P 501 " pdb="ZN ZN P 501 " - pdb=" SG CYS P 27 " pdb="ZN ZN P 501 " - pdb=" SG CYS P 81 " pdb="ZN ZN P 501 " - pdb=" SG CYS P 84 " pdb="ZN ZN P 501 " - pdb=" SG CYS P 24 " pdb=" ZN P 502 " pdb="ZN ZN P 502 " - pdb=" SG CYS P 173 " pdb="ZN ZN P 502 " - pdb=" SG CYS P 179 " pdb="ZN ZN P 502 " - pdb=" SG CYS P 165 " pdb=" ZN P 503 " pdb="ZN ZN P 503 " - pdb=" SG CYS P 71 " pdb="ZN ZN P 503 " - pdb=" SG CYS P 48 " pdb="ZN ZN P 503 " - pdb=" SG CYS P 45 " pdb="ZN ZN P 503 " - pdb=" SG CYS P 74 " pdb=" ZN Q 201 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 137 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 101 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 102 " pdb=" ZN Q 202 " pdb="ZN ZN Q 202 " - pdb=" SG CYS Q 119 " pdb="ZN ZN Q 202 " - pdb=" SG CYS Q 101 " pdb=" ZN Q 203 " pdb="ZN ZN Q 203 " - pdb=" SG CYS Q 105 " pdb="ZN ZN Q 203 " - pdb=" SG CYS Q 134 " pdb="ZN ZN Q 203 " - pdb=" SG CYS Q 117 " pdb=" ZN t 401 " pdb="ZN ZN t 401 " - pdb=" SG CYS t 202 " pdb="ZN ZN t 401 " - pdb=" SG CYS t 211 " pdb="ZN ZN t 401 " - pdb=" SG CYS t 217 " pdb=" ZN y 201 " pdb="ZN ZN y 201 " - pdb=" SG CYS y 46 " pdb="ZN ZN y 201 " - pdb=" SG CYS y 49 " pdb="ZN ZN y 201 " - pdb=" SG CYS y 85 " pdb="ZN ZN y 201 " - pdb=" SG CYS y 11 " pdb=" ZN y 202 " pdb="ZN ZN y 202 " - pdb=" SG CYS y 23 " pdb="ZN ZN y 202 " - pdb=" SG CYS y 26 " pdb="ZN ZN y 202 " - pdb=" SG CYS y 61 " pdb="ZN ZN y 202 " - pdb=" SG CYS y 58 " pdb=" ZN y 203 " pdb="ZN ZN y 203 " - pdb=" SG CYS y 75 " pdb="ZN ZN y 203 " - pdb=" SG CYS y 30 " pdb="ZN ZN y 203 " - pdb=" SG CYS y 72 " Number of angles added : 24 16292 Ramachandran restraints generated. 8146 Oldfield, 0 Emsley, 8146 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15506 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 264 helices and 65 sheets defined 32.4% alpha, 10.3% beta 64 base pairs and 131 stacking pairs defined. Time for finding SS restraints: 25.11 Creating SS restraints... Processing helix chain '1' and resid 5 through 20 removed outlier: 3.556A pdb=" N ASN 1 14 " --> pdb=" O ILE 1 10 " (cutoff:3.500A) Processing helix chain '1' and resid 49 through 59 removed outlier: 4.665A pdb=" N GLN 1 58 " --> pdb=" O CYS 1 54 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N TYR 1 59 " --> pdb=" O VAL 1 55 " (cutoff:3.500A) Processing helix chain '1' and resid 87 through 96 Processing helix chain '3' and resid 502 through 518 Processing helix chain '3' and resid 531 through 537 removed outlier: 4.537A pdb=" N ARG 3 536 " --> pdb=" O ASP 3 532 " (cutoff:3.500A) Processing helix chain '3' and resid 546 through 549 No H-bonds generated for 'chain '3' and resid 546 through 549' Processing helix chain '3' and resid 594 through 615 removed outlier: 3.767A pdb=" N GLU 3 609 " --> pdb=" O LYS 3 605 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS 3 613 " --> pdb=" O GLU 3 609 " (cutoff:3.500A) Processing helix chain '7' and resid 19 through 41 Processing helix chain '7' and resid 66 through 69 No H-bonds generated for 'chain '7' and resid 66 through 69' Processing helix chain '7' and resid 81 through 89 removed outlier: 3.569A pdb=" N LYS 7 88 " --> pdb=" O ARG 7 85 " (cutoff:3.500A) Processing helix chain '8' and resid 462 through 468 Processing helix chain '8' and resid 472 through 474 No H-bonds generated for 'chain '8' and resid 472 through 474' Processing helix chain '8' and resid 479 through 481 No H-bonds generated for 'chain '8' and resid 479 through 481' Processing helix chain '8' and resid 485 through 491 Processing helix chain '8' and resid 502 through 504 No H-bonds generated for 'chain '8' and resid 502 through 504' Processing helix chain '8' and resid 526 through 531 removed outlier: 4.238A pdb=" N THR 8 531 " --> pdb=" O PHE 8 527 " (cutoff:3.500A) Processing helix chain '8' and resid 533 through 546 removed outlier: 3.928A pdb=" N GLN 8 546 " --> pdb=" O GLU 8 542 " (cutoff:3.500A) Processing helix chain '8' and resid 549 through 554 Processing helix chain '8' and resid 569 through 575 Processing helix chain 'A' and resid 29 through 44 removed outlier: 4.791A pdb=" N ALA A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ALA A 42 " --> pdb=" O GLN A 38 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS A 43 " --> pdb=" O GLN A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 73 Processing helix chain 'A' and resid 79 through 92 removed outlier: 3.617A pdb=" N ARG A 82 " --> pdb=" O ARG A 79 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N HIS A 83 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS A 85 " --> pdb=" O ARG A 82 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ARG A 86 " --> pdb=" O HIS A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 105 removed outlier: 3.522A pdb=" N LYS A 101 " --> pdb=" O HIS A 97 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASN A 105 " --> pdb=" O LYS A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 156 Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 232 through 241 removed outlier: 3.805A pdb=" N LEU A 238 " --> pdb=" O MET A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 268 Processing helix chain 'A' and resid 291 through 297 Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 399 through 405 Processing helix chain 'A' and resid 441 through 459 removed outlier: 4.002A pdb=" N TYR A 453 " --> pdb=" O LYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 477 No H-bonds generated for 'chain 'A' and resid 474 through 477' Processing helix chain 'A' and resid 489 through 510 removed outlier: 4.177A pdb=" N LEU A 506 " --> pdb=" O ASN A 502 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 565 removed outlier: 3.963A pdb=" N CYS A 547 " --> pdb=" O ALA A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 583 Processing helix chain 'A' and resid 596 through 616 removed outlier: 3.840A pdb=" N ASP A 607 " --> pdb=" O MET A 604 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS A 609 " --> pdb=" O LYS A 606 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR A 614 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N PHE A 616 " --> pdb=" O TYR A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 661 removed outlier: 4.284A pdb=" N VAL A 636 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET A 641 " --> pdb=" O TRP A 637 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY A 643 " --> pdb=" O PHE A 639 " (cutoff:3.500A) Proline residue: A 646 - end of helix Processing helix chain 'A' and resid 678 through 693 removed outlier: 3.739A pdb=" N ASP A 682 " --> pdb=" O GLU A 678 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU A 683 " --> pdb=" O SER A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 721 Processing helix chain 'A' and resid 733 through 763 removed outlier: 3.644A pdb=" N TYR A 756 " --> pdb=" O ASN A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 795 removed outlier: 3.768A pdb=" N GLY A 777 " --> pdb=" O LYS A 773 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU A 779 " --> pdb=" O ASN A 775 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LEU A 782 " --> pdb=" O ARG A 778 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 795 " --> pdb=" O GLN A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 820 removed outlier: 4.121A pdb=" N VAL A 809 " --> pdb=" O GLU A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 849 removed outlier: 4.054A pdb=" N LEU A 841 " --> pdb=" O LYS A 837 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ALA A 849 " --> pdb=" O ARG A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 872 Processing helix chain 'A' and resid 874 through 886 removed outlier: 3.665A pdb=" N LYS A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 932 removed outlier: 4.148A pdb=" N THR A 918 " --> pdb=" O LEU A 914 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR A 928 " --> pdb=" O GLN A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 951 Processing helix chain 'A' and resid 956 through 960 Processing helix chain 'A' and resid 990 through 996 Processing helix chain 'A' and resid 1003 through 1011 removed outlier: 4.092A pdb=" N TYR A1008 " --> pdb=" O ASN A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1052 removed outlier: 4.383A pdb=" N SER A1038 " --> pdb=" O GLN A1035 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL A1041 " --> pdb=" O SER A1038 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN A1042 " --> pdb=" O PHE A1039 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR A1044 " --> pdb=" O VAL A1041 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A1050 " --> pdb=" O VAL A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1062 Processing helix chain 'A' and resid 1078 through 1081 No H-bonds generated for 'chain 'A' and resid 1078 through 1081' Processing helix chain 'A' and resid 1103 through 1114 Processing helix chain 'A' and resid 1144 through 1158 Processing helix chain 'A' and resid 1199 through 1201 No H-bonds generated for 'chain 'A' and resid 1199 through 1201' Processing helix chain 'A' and resid 1234 through 1252 removed outlier: 4.735A pdb=" N GLY A1252 " --> pdb=" O LEU A1248 " (cutoff:3.500A) Processing helix chain 'A' and resid 1256 through 1271 Processing helix chain 'A' and resid 1276 through 1280 removed outlier: 3.776A pdb=" N ASN A1280 " --> pdb=" O ALA A1277 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1302 removed outlier: 3.509A pdb=" N LEU A1287 " --> pdb=" O GLU A1283 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A1289 " --> pdb=" O LEU A1285 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN A1293 " --> pdb=" O VAL A1289 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY A1302 " --> pdb=" O ARG A1298 " (cutoff:3.500A) Processing helix chain 'A' and resid 1369 through 1371 No H-bonds generated for 'chain 'A' and resid 1369 through 1371' Processing helix chain 'A' and resid 1375 through 1398 removed outlier: 3.576A pdb=" N ARG A1384 " --> pdb=" O ILE A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1419 through 1421 No H-bonds generated for 'chain 'A' and resid 1419 through 1421' Processing helix chain 'A' and resid 1427 through 1430 No H-bonds generated for 'chain 'A' and resid 1427 through 1430' Processing helix chain 'A' and resid 1441 through 1445 Processing helix chain 'A' and resid 1458 through 1461 No H-bonds generated for 'chain 'A' and resid 1458 through 1461' Processing helix chain 'A' and resid 1469 through 1478 Processing helix chain 'A' and resid 1521 through 1524 No H-bonds generated for 'chain 'A' and resid 1521 through 1524' Processing helix chain 'A' and resid 1528 through 1537 removed outlier: 3.669A pdb=" N THR A1535 " --> pdb=" O ASN A1531 " (cutoff:3.500A) Processing helix chain 'A' and resid 1539 through 1542 No H-bonds generated for 'chain 'A' and resid 1539 through 1542' Processing helix chain 'A' and resid 1567 through 1574 Processing helix chain 'A' and resid 1581 through 1598 removed outlier: 4.904A pdb=" N PHE A1597 " --> pdb=" O LEU A1593 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASP A1598 " --> pdb=" O CYS A1594 " (cutoff:3.500A) Processing helix chain 'A' and resid 1676 through 1688 removed outlier: 3.573A pdb=" N ARG A1681 " --> pdb=" O GLU A1677 " (cutoff:3.500A) Processing helix chain 'A' and resid 1723 through 1735 removed outlier: 3.802A pdb=" N GLN A1728 " --> pdb=" O PRO A1724 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE A1733 " --> pdb=" O ALA A1729 " (cutoff:3.500A) Processing helix chain 'A' and resid 1739 through 1749 removed outlier: 4.212A pdb=" N ARG A1744 " --> pdb=" O LEU A1740 " (cutoff:3.500A) Processing helix chain 'A' and resid 1824 through 1826 No H-bonds generated for 'chain 'A' and resid 1824 through 1826' Processing helix chain 'A' and resid 1833 through 1851 removed outlier: 4.311A pdb=" N ALA A1837 " --> pdb=" O LEU A1833 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LYS A1838 " --> pdb=" O GLY A1834 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N TRP A1839 " --> pdb=" O GLN A1835 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA A1842 " --> pdb=" O LYS A1838 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU A1843 " --> pdb=" O TRP A1839 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU A1844 " --> pdb=" O LYS A1840 " (cutoff:3.500A) Processing helix chain 'A' and resid 1869 through 1875 Processing helix chain 'A' and resid 1895 through 1897 No H-bonds generated for 'chain 'A' and resid 1895 through 1897' Processing helix chain 'A' and resid 1900 through 1907 removed outlier: 3.842A pdb=" N LEU A1905 " --> pdb=" O LYS A1901 " (cutoff:3.500A) Processing helix chain 'A' and resid 1929 through 1945 removed outlier: 3.899A pdb=" N LEU A1938 " --> pdb=" O SER A1934 " (cutoff:3.500A) Processing helix chain 'A' and resid 1947 through 1953 Processing helix chain 'A' and resid 1973 through 1994 Processing helix chain 'A' and resid 2004 through 2011 Processing helix chain 'A' and resid 2069 through 2086 removed outlier: 4.033A pdb=" N ARG A2074 " --> pdb=" O LYS A2070 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ILE A2078 " --> pdb=" O ARG A2074 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N SER A2079 " --> pdb=" O VAL A2075 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ALA A2080 " --> pdb=" O ARG A2076 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ALA A2081 " --> pdb=" O ALA A2077 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ASN A2082 " --> pdb=" O ILE A2078 " (cutoff:3.500A) Processing helix chain 'A' and resid 2108 through 2116 Processing helix chain 'A' and resid 2190 through 2202 Processing helix chain 'A' and resid 2232 through 2240 Processing helix chain 'A' and resid 2253 through 2255 No H-bonds generated for 'chain 'A' and resid 2253 through 2255' Processing helix chain 'A' and resid 2285 through 2287 No H-bonds generated for 'chain 'A' and resid 2285 through 2287' Processing helix chain 'B' and resid 70 through 73 No H-bonds generated for 'chain 'B' and resid 70 through 73' Processing helix chain 'B' and resid 116 through 122 removed outlier: 3.935A pdb=" N ALA B 120 " --> pdb=" O MET B 116 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ASP B 121 " --> pdb=" O ASP B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 126 No H-bonds generated for 'chain 'B' and resid 124 through 126' Processing helix chain 'B' and resid 142 through 153 removed outlier: 3.775A pdb=" N ASP B 147 " --> pdb=" O THR B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 209 through 219 removed outlier: 4.567A pdb=" N ASP B 213 " --> pdb=" O ASN B 210 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU B 214 " --> pdb=" O PHE B 211 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL B 215 " --> pdb=" O SER B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 248 Processing helix chain 'B' and resid 260 through 264 Processing helix chain 'B' and resid 271 through 291 removed outlier: 3.984A pdb=" N MET B 291 " --> pdb=" O GLY B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 329 removed outlier: 4.481A pdb=" N LYS B 325 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 342 No H-bonds generated for 'chain 'B' and resid 340 through 342' Processing helix chain 'B' and resid 374 through 385 Processing helix chain 'B' and resid 392 through 399 Processing helix chain 'B' and resid 405 through 408 No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 412 through 424 Processing helix chain 'B' and resid 428 through 436 removed outlier: 3.519A pdb=" N CYS B 434 " --> pdb=" O PHE B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 452 Processing helix chain 'B' and resid 461 through 464 No H-bonds generated for 'chain 'B' and resid 461 through 464' Processing helix chain 'B' and resid 600 through 613 Processing helix chain 'B' and resid 634 through 646 Processing helix chain 'B' and resid 694 through 701 Processing helix chain 'B' and resid 711 through 721 Processing helix chain 'B' and resid 726 through 729 No H-bonds generated for 'chain 'B' and resid 726 through 729' Processing helix chain 'B' and resid 737 through 739 No H-bonds generated for 'chain 'B' and resid 737 through 739' Processing helix chain 'B' and resid 765 through 774 Processing helix chain 'B' and resid 809 through 821 Processing helix chain 'B' and resid 844 through 851 Processing helix chain 'B' and resid 877 through 879 No H-bonds generated for 'chain 'B' and resid 877 through 879' Processing helix chain 'B' and resid 883 through 890 Processing helix chain 'B' and resid 929 through 938 removed outlier: 4.172A pdb=" N THR B 937 " --> pdb=" O PHE B 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 102 No H-bonds generated for 'chain 'C' and resid 99 through 102' Processing helix chain 'C' and resid 111 through 114 Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 129 through 132 No H-bonds generated for 'chain 'C' and resid 129 through 132' Processing helix chain 'C' and resid 137 through 162 Processing helix chain 'C' and resid 241 through 244 No H-bonds generated for 'chain 'C' and resid 241 through 244' Processing helix chain 'C' and resid 282 through 325 removed outlier: 5.468A pdb=" N GLU C 289 " --> pdb=" O LYS C 286 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ILE C 293 " --> pdb=" O ALA C 290 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG C 299 " --> pdb=" O ARG C 296 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N GLU C 300 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LYS C 317 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N GLU C 318 " --> pdb=" O LYS C 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 462 No H-bonds generated for 'chain 'D' and resid 460 through 462' Processing helix chain 'E' and resid 85 through 89 Processing helix chain 'E' and resid 102 through 105 No H-bonds generated for 'chain 'E' and resid 102 through 105' Processing helix chain 'E' and resid 122 through 135 Processing helix chain 'E' and resid 157 through 161 Processing helix chain 'E' and resid 212 through 219 Processing helix chain 'L' and resid 13 through 25 removed outlier: 4.193A pdb=" N ILE L 18 " --> pdb=" O THR L 14 " (cutoff:3.500A) Processing helix chain 'L' and resid 32 through 37 removed outlier: 4.916A pdb=" N LEU L 37 " --> pdb=" O ARG L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 52 Processing helix chain 'L' and resid 66 through 73 removed outlier: 4.050A pdb=" N HIS L 73 " --> pdb=" O GLU L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 89 No H-bonds generated for 'chain 'L' and resid 86 through 89' Processing helix chain 'L' and resid 96 through 107 Processing helix chain 'O' and resid 216 through 237 Processing helix chain 'O' and resid 243 through 255 removed outlier: 3.562A pdb=" N LEU O 255 " --> pdb=" O TRP O 251 " (cutoff:3.500A) Processing helix chain 'O' and resid 261 through 266 Processing helix chain 'O' and resid 276 through 288 Processing helix chain 'O' and resid 292 through 305 removed outlier: 4.525A pdb=" N ARG O 301 " --> pdb=" O ASN O 297 " (cutoff:3.500A) Processing helix chain 'O' and resid 310 through 322 Processing helix chain 'O' and resid 327 through 338 Processing helix chain 'O' and resid 343 through 355 removed outlier: 3.676A pdb=" N SER O 348 " --> pdb=" O GLN O 344 " (cutoff:3.500A) Processing helix chain 'O' and resid 359 through 370 removed outlier: 3.869A pdb=" N TYR O 366 " --> pdb=" O ALA O 362 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU O 367 " --> pdb=" O ARG O 363 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ARG O 368 " --> pdb=" O THR O 364 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N PHE O 369 " --> pdb=" O ILE O 365 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL O 370 " --> pdb=" O TYR O 366 " (cutoff:3.500A) Processing helix chain 'O' and resid 376 through 382 removed outlier: 3.613A pdb=" N LYS O 381 " --> pdb=" O LYS O 377 " (cutoff:3.500A) Processing helix chain 'O' and resid 385 through 388 No H-bonds generated for 'chain 'O' and resid 385 through 388' Processing helix chain 'O' and resid 392 through 404 Processing helix chain 'O' and resid 411 through 413 No H-bonds generated for 'chain 'O' and resid 411 through 413' Processing helix chain 'O' and resid 415 through 425 Processing helix chain 'O' and resid 432 through 436 removed outlier: 3.684A pdb=" N TYR O 436 " --> pdb=" O VAL O 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 432 through 436' Processing helix chain 'O' and resid 452 through 460 Processing helix chain 'P' and resid 25 through 28 No H-bonds generated for 'chain 'P' and resid 25 through 28' Processing helix chain 'P' and resid 72 through 76 Processing helix chain 'P' and resid 94 through 100 Processing helix chain 'P' and resid 115 through 126 Processing helix chain 'P' and resid 136 through 138 No H-bonds generated for 'chain 'P' and resid 136 through 138' Processing helix chain 'P' and resid 148 through 150 No H-bonds generated for 'chain 'P' and resid 148 through 150' Processing helix chain 'P' and resid 157 through 159 No H-bonds generated for 'chain 'P' and resid 157 through 159' Processing helix chain 'P' and resid 176 through 178 No H-bonds generated for 'chain 'P' and resid 176 through 178' Processing helix chain 'P' and resid 207 through 217 removed outlier: 3.949A pdb=" N ASP P 211 " --> pdb=" O ASP P 207 " (cutoff:3.500A) Processing helix chain 'P' and resid 245 through 253 Processing helix chain 'P' and resid 277 through 286 Processing helix chain 'Q' and resid 16 through 34 Proline residue: Q 20 - end of helix Processing helix chain 'Q' and resid 47 through 64 Processing helix chain 'Q' and resid 72 through 81 Processing helix chain 'Q' and resid 88 through 92 Processing helix chain 'Q' and resid 103 through 105 No H-bonds generated for 'chain 'Q' and resid 103 through 105' Processing helix chain 'Q' and resid 118 through 120 No H-bonds generated for 'chain 'Q' and resid 118 through 120' Processing helix chain 'Q' and resid 123 through 125 No H-bonds generated for 'chain 'Q' and resid 123 through 125' Processing helix chain 'R' and resid 51 through 53 No H-bonds generated for 'chain 'R' and resid 51 through 53' Processing helix chain 'R' and resid 61 through 70 Processing helix chain 'R' and resid 218 through 226 Processing helix chain 'V' and resid 33 through 44 Processing helix chain 'V' and resid 120 through 122 No H-bonds generated for 'chain 'V' and resid 120 through 122' Processing helix chain 'V' and resid 136 through 144 removed outlier: 3.692A pdb=" N MET V 144 " --> pdb=" O ASN V 140 " (cutoff:3.500A) Processing helix chain 'Y' and resid 33 through 35 No H-bonds generated for 'chain 'Y' and resid 33 through 35' Processing helix chain 'Y' and resid 40 through 42 No H-bonds generated for 'chain 'Y' and resid 40 through 42' Processing helix chain 'Y' and resid 49 through 59 Processing helix chain 'Y' and resid 66 through 74 Processing helix chain 'Y' and resid 82 through 92 removed outlier: 4.221A pdb=" N PHE Y 92 " --> pdb=" O ASN Y 88 " (cutoff:3.500A) Processing helix chain 'Y' and resid 97 through 113 Proline residue: Y 107 - end of helix Processing helix chain 'Y' and resid 121 through 124 No H-bonds generated for 'chain 'Y' and resid 121 through 124' Processing helix chain 's' and resid 34 through 45 Processing helix chain 's' and resid 121 through 123 No H-bonds generated for 'chain 's' and resid 121 through 123' Processing helix chain 's' and resid 138 through 142 Processing helix chain 't' and resid 130 through 143 Processing helix chain 't' and resid 157 through 159 No H-bonds generated for 'chain 't' and resid 157 through 159' Processing helix chain 't' and resid 203 through 207 Processing helix chain 't' and resid 229 through 236 Processing helix chain 't' and resid 283 through 292 Processing helix chain 'u' and resid 401 through 407 Processing helix chain 'u' and resid 476 through 478 No H-bonds generated for 'chain 'u' and resid 476 through 478' Processing helix chain 'u' and resid 496 through 506 Processing helix chain 'u' and resid 509 through 521 Processing helix chain 'u' and resid 523 through 526 No H-bonds generated for 'chain 'u' and resid 523 through 526' Processing helix chain 'u' and resid 528 through 539 Proline residue: u 537 - end of helix Processing helix chain 'u' and resid 546 through 558 Processing helix chain 'u' and resid 571 through 581 removed outlier: 4.092A pdb=" N VAL u 577 " --> pdb=" O LYS u 573 " (cutoff:3.500A) Proline residue: u 580 - end of helix Processing helix chain 'u' and resid 587 through 604 Processing helix chain 'u' and resid 607 through 613 Processing helix chain 'u' and resid 622 through 639 Processing helix chain 'u' and resid 641 through 653 Proline residue: u 646 - end of helix removed outlier: 3.657A pdb=" N LYS u 653 " --> pdb=" O LYS u 649 " (cutoff:3.500A) Processing helix chain 'u' and resid 658 through 674 Processing helix chain 'u' and resid 677 through 679 No H-bonds generated for 'chain 'u' and resid 677 through 679' Processing helix chain 'u' and resid 683 through 692 removed outlier: 4.409A pdb=" N ILE u 689 " --> pdb=" O SER u 685 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE u 690 " --> pdb=" O LEU u 686 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N HIS u 692 " --> pdb=" O GLU u 688 " (cutoff:3.500A) Processing helix chain 'u' and resid 699 through 716 Processing helix chain 'u' and resid 721 through 723 No H-bonds generated for 'chain 'u' and resid 721 through 723' Processing helix chain 'u' and resid 728 through 737 Processing helix chain 'u' and resid 741 through 756 Proline residue: u 755 - end of helix Processing helix chain 'u' and resid 759 through 767 Processing helix chain 'u' and resid 770 through 775 Processing helix chain 'u' and resid 782 through 795 removed outlier: 4.080A pdb=" N LYS u 793 " --> pdb=" O LEU u 789 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN u 794 " --> pdb=" O LYS u 790 " (cutoff:3.500A) Processing helix chain 'u' and resid 803 through 809 Processing helix chain 'u' and resid 811 through 817 Processing helix chain 'u' and resid 822 through 825 No H-bonds generated for 'chain 'u' and resid 822 through 825' Processing helix chain 'u' and resid 827 through 843 removed outlier: 3.776A pdb=" N GLN u 832 " --> pdb=" O ARG u 828 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU u 833 " --> pdb=" O ASN u 829 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU u 839 " --> pdb=" O ASP u 835 " (cutoff:3.500A) Processing helix chain 'u' and resid 846 through 856 removed outlier: 3.641A pdb=" N ARG u 852 " --> pdb=" O GLU u 848 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ASP u 855 " --> pdb=" O SER u 851 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ASP u 856 " --> pdb=" O ARG u 852 " (cutoff:3.500A) Processing helix chain 'u' and resid 862 through 878 Processing helix chain 'u' and resid 889 through 901 Processing helix chain 'u' and resid 909 through 921 Processing helix chain 'u' and resid 926 through 939 removed outlier: 3.629A pdb=" N LEU u 929 " --> pdb=" O LYS u 926 " (cutoff:3.500A) Proline residue: u 930 - end of helix removed outlier: 3.579A pdb=" N CYS u 933 " --> pdb=" O PRO u 930 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY u 934 " --> pdb=" O GLN u 931 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TRP u 938 " --> pdb=" O THR u 935 " (cutoff:3.500A) Processing helix chain 'u' and resid 942 through 944 No H-bonds generated for 'chain 'u' and resid 942 through 944' Processing helix chain 'u' and resid 949 through 958 Processing helix chain 'u' and resid 960 through 963 No H-bonds generated for 'chain 'u' and resid 960 through 963' Processing helix chain 'u' and resid 969 through 980 removed outlier: 4.039A pdb=" N VAL u 976 " --> pdb=" O GLY u 972 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL u 977 " --> pdb=" O HIS u 973 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU u 980 " --> pdb=" O VAL u 976 " (cutoff:3.500A) Processing helix chain 'u' and resid 987 through 1003 removed outlier: 3.646A pdb=" N SER u 992 " --> pdb=" O GLU u 988 " (cutoff:3.500A) Processing helix chain 'u' and resid 1013 through 1015 No H-bonds generated for 'chain 'u' and resid 1013 through 1015' Processing helix chain 'u' and resid 1017 through 1025 Proline residue: u1022 - end of helix removed outlier: 4.061A pdb=" N LYS u1025 " --> pdb=" O THR u1021 " (cutoff:3.500A) Processing helix chain 'u' and resid 1029 through 1045 Processing helix chain 'u' and resid 1054 through 1059 Processing helix chain 'u' and resid 1072 through 1088 removed outlier: 3.894A pdb=" N VAL u1078 " --> pdb=" O ARG u1074 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN u1079 " --> pdb=" O ARG u1075 " (cutoff:3.500A) Processing helix chain 'u' and resid 1093 through 1101 removed outlier: 3.757A pdb=" N LEU u1101 " --> pdb=" O LEU u1097 " (cutoff:3.500A) Processing helix chain 'u' and resid 1110 through 1122 removed outlier: 4.000A pdb=" N ALA u1115 " --> pdb=" O CYS u1111 " (cutoff:3.500A) Processing helix chain 'u' and resid 1129 through 1137 removed outlier: 4.092A pdb=" N TYR u1136 " --> pdb=" O LEU u1132 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ARG u1137 " --> pdb=" O MET u1133 " (cutoff:3.500A) Processing helix chain 'u' and resid 1141 through 1163 removed outlier: 7.229A pdb=" N GLU u1160 " --> pdb=" O GLU u1156 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N MET u1161 " --> pdb=" O TYR u1157 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N GLY u1162 " --> pdb=" O ILE u1158 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N LYS u1163 " --> pdb=" O GLY u1159 " (cutoff:3.500A) Processing helix chain 'u' and resid 1166 through 1177 Proline residue: u1171 - end of helix removed outlier: 3.733A pdb=" N ASP u1175 " --> pdb=" O PRO u1171 " (cutoff:3.500A) Processing helix chain 'u' and resid 1182 through 1198 Processing helix chain 'u' and resid 1205 through 1220 removed outlier: 3.519A pdb=" N ASN u1209 " --> pdb=" O GLU u1205 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN u1213 " --> pdb=" O ASN u1209 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR u1214 " --> pdb=" O HIS u1210 " (cutoff:3.500A) Proline residue: u1217 - end of helix removed outlier: 5.377A pdb=" N PHE u1220 " --> pdb=" O TRP u1216 " (cutoff:3.500A) Processing helix chain 'u' and resid 1224 through 1241 removed outlier: 4.774A pdb=" N VAL u1239 " --> pdb=" O GLU u1235 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA u1240 " --> pdb=" O GLY u1236 " (cutoff:3.500A) Processing helix chain 'u' and resid 1243 through 1250 Processing helix chain 'u' and resid 1259 through 1275 removed outlier: 4.116A pdb=" N VAL u1264 " --> pdb=" O LYS u1260 " (cutoff:3.500A) Processing helix chain 'u' and resid 1298 through 1300 No H-bonds generated for 'chain 'u' and resid 1298 through 1300' Processing helix chain 'v' and resid 190 through 194 Processing helix chain 'v' and resid 430 through 432 No H-bonds generated for 'chain 'v' and resid 430 through 432' Processing helix chain 'v' and resid 809 through 825 Processing helix chain 'v' and resid 837 through 844 Processing helix chain 'v' and resid 849 through 852 No H-bonds generated for 'chain 'v' and resid 849 through 852' Processing helix chain 'v' and resid 1135 through 1151 removed outlier: 3.931A pdb=" N SER v1150 " --> pdb=" O MET v1146 " (cutoff:3.500A) Processing helix chain 'v' and resid 1160 through 1164 Processing helix chain 'v' and resid 1176 through 1184 removed outlier: 3.980A pdb=" N GLN v1181 " --> pdb=" O ASP v1177 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE v1182 " --> pdb=" O LEU v1178 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASN v1183 " --> pdb=" O CYS v1179 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N SER v1184 " --> pdb=" O GLU v1180 " (cutoff:3.500A) Processing helix chain 'v' and resid 1187 through 1196 Processing helix chain 'v' and resid 1201 through 1215 removed outlier: 4.244A pdb=" N ILE v1211 " --> pdb=" O LYS v1207 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ARG v1212 " --> pdb=" O LEU v1208 " (cutoff:3.500A) Processing helix chain 'x' and resid 28 through 45 Processing helix chain 'x' and resid 47 through 56 removed outlier: 3.702A pdb=" N ALA x 56 " --> pdb=" O TYR x 52 " (cutoff:3.500A) Processing helix chain 'x' and resid 61 through 70 Processing helix chain 'y' and resid 52 through 54 No H-bonds generated for 'chain 'y' and resid 52 through 54' Processing helix chain 'y' and resid 73 through 76 No H-bonds generated for 'chain 'y' and resid 73 through 76' Processing helix chain 'y' and resid 97 through 100 No H-bonds generated for 'chain 'y' and resid 97 through 100' Processing helix chain 'z' and resid 33 through 40 Processing helix chain 'z' and resid 67 through 76 Processing sheet with id= A, first strand: chain '1' and resid 108 through 111 removed outlier: 3.925A pdb=" N CYS 1 80 " --> pdb=" O LEU 1 40 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '7' and resid 46 through 48 Processing sheet with id= C, first strand: chain 'A' and resid 482 through 487 Processing sheet with id= D, first strand: chain 'A' and resid 227 through 229 Processing sheet with id= E, first strand: chain 'A' and resid 516 through 518 Processing sheet with id= F, first strand: chain 'A' and resid 894 through 900 removed outlier: 3.565A pdb=" N VAL A 906 " --> pdb=" O MET A 899 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1174 through 1178 removed outlier: 6.581A pdb=" N ARG A1100 " --> pdb=" O ILE A1085 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N ILE A1085 " --> pdb=" O ARG A1100 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1184 through 1189 removed outlier: 3.674A pdb=" N MET A1189 " --> pdb=" O PHE A1192 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU A1223 " --> pdb=" O ASN A1218 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU A1216 " --> pdb=" O THR A1225 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1609 through 1611 removed outlier: 6.308A pdb=" N VAL A1701 " --> pdb=" O ASP A1663 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N GLN A1665 " --> pdb=" O VAL A1701 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ILE A1703 " --> pdb=" O GLN A1665 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ARG A1667 " --> pdb=" O ILE A1703 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE A1705 " --> pdb=" O ARG A1667 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU A1702 " --> pdb=" O TYR A1715 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1915 through 1918 removed outlier: 3.767A pdb=" N GLN A1816 " --> pdb=" O ASN A1811 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLN A1860 " --> pdb=" O TRP A1778 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N VAL A1780 " --> pdb=" O GLN A1860 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE A1862 " --> pdb=" O VAL A1780 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N VAL A1883 " --> pdb=" O ILE A1861 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL A1863 " --> pdb=" O VAL A1883 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LYS A1885 " --> pdb=" O VAL A1863 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 2260 through 2262 removed outlier: 4.136A pdb=" N TYR A2104 " --> pdb=" O GLN A2260 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TYR A2129 " --> pdb=" O ARG A2143 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE A2145 " --> pdb=" O TYR A2127 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N TYR A2127 " --> pdb=" O ILE A2145 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 2144 through 2146 removed outlier: 6.875A pdb=" N PHE A2270 " --> pdb=" O ILE A2145 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'A' and resid 2150 through 2152 Processing sheet with id= N, first strand: chain 'A' and resid 2228 through 2230 Processing sheet with id= O, first strand: chain 'B' and resid 132 through 134 Processing sheet with id= P, first strand: chain 'B' and resid 227 through 230 removed outlier: 3.816A pdb=" N ILE B 229 " --> pdb=" O CYS B 256 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 476 through 478 Processing sheet with id= R, first strand: chain 'B' and resid 480 through 483 Processing sheet with id= S, first strand: chain 'B' and resid 505 through 507 removed outlier: 4.184A pdb=" N GLN B 505 " --> pdb=" O VAL B 527 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL B 527 " --> pdb=" O GLN B 505 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 653 through 655 removed outlier: 3.539A pdb=" N HIS B 627 " --> pdb=" O VAL B 592 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 663 through 666 Processing sheet with id= V, first strand: chain 'B' and resid 896 through 901 removed outlier: 6.833A pdb=" N PHE B 874 " --> pdb=" O VAL B 857 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N VAL B 857 " --> pdb=" O PHE B 874 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 686 through 691 removed outlier: 6.452A pdb=" N ILE B 688 " --> pdb=" O ILE B 791 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ILE B 791 " --> pdb=" O ILE B 688 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLU B 690 " --> pdb=" O PHE B 789 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N PHE B 789 " --> pdb=" O GLU B 690 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 176 through 178 Processing sheet with id= Y, first strand: chain 'D' and resid 210 through 212 removed outlier: 3.702A pdb=" N LEU D 240 " --> pdb=" O ILE D 230 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ASP D 232 " --> pdb=" O LEU D 238 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU D 238 " --> pdb=" O ASP D 232 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 270 through 274 Processing sheet with id= AA, first strand: chain 'D' and resid 291 through 296 removed outlier: 6.515A pdb=" N CYS D 306 " --> pdb=" O TYR D 292 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU D 294 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL D 304 " --> pdb=" O LEU D 294 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N LEU D 296 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N VAL D 302 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA D 312 " --> pdb=" O LEU D 326 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS D 324 " --> pdb=" O ILE D 314 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ASP D 316 " --> pdb=" O SER D 322 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N SER D 322 " --> pdb=" O ASP D 316 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 333 through 338 removed outlier: 7.118A pdb=" N GLY D 348 " --> pdb=" O ALA D 334 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL D 336 " --> pdb=" O ILE D 346 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE D 346 " --> pdb=" O VAL D 336 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE D 345 " --> pdb=" O TRP D 357 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N THR D 353 " --> pdb=" O SER D 349 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'D' and resid 436 through 438 Processing sheet with id= AD, first strand: chain 'D' and resid 195 through 200 removed outlier: 7.136A pdb=" N VAL D 488 " --> pdb=" O TYR D 197 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL D 199 " --> pdb=" O ILE D 486 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE D 486 " --> pdb=" O VAL D 199 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR D 485 " --> pdb=" O GLU D 481 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 375 through 379 removed outlier: 6.551A pdb=" N GLY D 390 " --> pdb=" O ARG D 376 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL D 378 " --> pdb=" O ALA D 388 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ALA D 388 " --> pdb=" O VAL D 378 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'E' and resid 137 through 139 removed outlier: 3.613A pdb=" N ALA E 138 " --> pdb=" O ILE E 153 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'P' and resid 36 through 38 Processing sheet with id= AH, first strand: chain 'P' and resid 235 through 237 Processing sheet with id= AI, first strand: chain 'P' and resid 262 through 264 Processing sheet with id= AJ, first strand: chain 'V' and resid 13 through 17 removed outlier: 3.547A pdb=" N VAL V 24 " --> pdb=" O GLN V 134 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN V 134 " --> pdb=" O VAL V 24 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLU V 26 " --> pdb=" O VAL V 132 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N VAL V 132 " --> pdb=" O GLU V 26 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU V 98 " --> pdb=" O PHE V 129 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE V 97 " --> pdb=" O THR V 115 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET V 61 " --> pdb=" O ILE V 57 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 's' and resid 131 through 133 Processing sheet with id= AL, first strand: chain 's' and resid 56 through 58 removed outlier: 3.995A pdb=" N ARG s 56 " --> pdb=" O GLN s 64 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'v' and resid 1173 through 1175 removed outlier: 6.923A pdb=" N LEU v 3 " --> pdb=" O ILE v1174 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE v1126 " --> pdb=" O LEU v 8 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR v1107 " --> pdb=" O SER v1116 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER v1103 " --> pdb=" O THR v1120 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'v' and resid 16 through 20 removed outlier: 3.687A pdb=" N PHE v 16 " --> pdb=" O SER v 33 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU v 54 " --> pdb=" O LEU v 40 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ARG v 42 " --> pdb=" O THR v 52 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N THR v 52 " --> pdb=" O ARG v 42 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'v' and resid 62 through 69 removed outlier: 6.931A pdb=" N GLY v 81 " --> pdb=" O ARG v 63 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LEU v 65 " --> pdb=" O VAL v 79 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL v 79 " --> pdb=" O LEU v 65 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ALA v 67 " --> pdb=" O TYR v 77 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TYR v 77 " --> pdb=" O ALA v 67 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ASP v 76 " --> pdb=" O TYR v 92 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N TYR v 92 " --> pdb=" O ASP v 76 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER v 82 " --> pdb=" O ARG v 86 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ARG v 86 " --> pdb=" O SER v 82 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLU v 91 " --> pdb=" O LYS v 101 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N LYS v 101 " --> pdb=" O GLU v 91 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLN v 93 " --> pdb=" O PHE v 99 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N PHE v 99 " --> pdb=" O GLN v 93 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'v' and resid 120 through 123 Processing sheet with id= AQ, first strand: chain 'v' and resid 144 through 147 Processing sheet with id= AR, first strand: chain 'v' and resid 165 through 167 removed outlier: 3.535A pdb=" N TYR v 224 " --> pdb=" O PHE v 210 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLU v 212 " --> pdb=" O ARG v 222 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ARG v 222 " --> pdb=" O GLU v 212 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ASP v 214 " --> pdb=" O VAL v 220 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL v 220 " --> pdb=" O ASP v 214 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'v' and resid 170 through 173 removed outlier: 4.254A pdb=" N MET v 181 " --> pdb=" O VAL v 173 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'v' and resid 267 through 270 removed outlier: 3.898A pdb=" N GLY v 247 " --> pdb=" O VAL v 238 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE v 234 " --> pdb=" O CYS v 251 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'v' and resid 292 through 294 removed outlier: 6.563A pdb=" N PHE v 299 " --> pdb=" O LEU v 315 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LEU v 315 " --> pdb=" O PHE v 299 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU v 316 " --> pdb=" O GLU v 324 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU v 324 " --> pdb=" O GLU v 316 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'v' and resid 336 through 342 removed outlier: 7.105A pdb=" N ALA v 350 " --> pdb=" O ALA v 337 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N MET v 339 " --> pdb=" O PHE v 348 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N PHE v 348 " --> pdb=" O MET v 339 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL v 341 " --> pdb=" O PHE v 346 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N PHE v 346 " --> pdb=" O VAL v 341 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N GLN v 360 " --> pdb=" O LEU v 397 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LEU v 397 " --> pdb=" O GLN v 360 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'v' and resid 410 through 413 removed outlier: 3.650A pdb=" N ARG v 439 " --> pdb=" O ASN v 775 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'v' and resid 458 through 462 removed outlier: 3.812A pdb=" N VAL v 462 " --> pdb=" O TYR v 473 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR v 473 " --> pdb=" O VAL v 462 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'v' and resid 507 through 510 Processing sheet with id= AZ, first strand: chain 'v' and resid 589 through 594 removed outlier: 4.293A pdb=" N ALA v 593 " --> pdb=" O PHE v 604 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE v 604 " --> pdb=" O ALA v 593 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE v 616 " --> pdb=" O SER v 629 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER v 629 " --> pdb=" O ILE v 616 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N SER v 618 " --> pdb=" O PRO v 627 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'v' and resid 672 through 675 Processing sheet with id= BB, first strand: chain 'v' and resid 700 through 706 removed outlier: 3.681A pdb=" N VAL v 712 " --> pdb=" O SER v 722 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'v' and resid 743 through 746 Processing sheet with id= BD, first strand: chain 'v' and resid 785 through 791 removed outlier: 7.239A pdb=" N ILE v 800 " --> pdb=" O ARG v 786 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N PHE v 788 " --> pdb=" O ILE v 798 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE v 798 " --> pdb=" O PHE v 788 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ILE v 790 " --> pdb=" O ASN v 796 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ASN v 796 " --> pdb=" O ILE v 790 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ASN v 870 " --> pdb=" O THR v 876 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR v 876 " --> pdb=" O ASN v 870 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'v' and resid 887 through 895 removed outlier: 6.574A pdb=" N GLY v 908 " --> pdb=" O PHE v 889 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL v 891 " --> pdb=" O LEU v 906 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU v 906 " --> pdb=" O VAL v 891 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL v 893 " --> pdb=" O TYR v 904 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TYR v 904 " --> pdb=" O VAL v 893 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'v' and resid 951 through 955 removed outlier: 3.839A pdb=" N ALA v 951 " --> pdb=" O GLY v 962 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL v 959 " --> pdb=" O TYR v 970 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'v' and resid 990 through 995 removed outlier: 6.492A pdb=" N SER v1003 " --> pdb=" O SER v 991 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE v 993 " --> pdb=" O ILE v1001 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE v1001 " --> pdb=" O ILE v 993 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N THR v 995 " --> pdb=" O ARG v 999 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ARG v 999 " --> pdb=" O THR v 995 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N PHE v1009 " --> pdb=" O ASP v1027 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP v1027 " --> pdb=" O PHE v1009 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA v1025 " --> pdb=" O TRP v1011 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ARG v1013 " --> pdb=" O ILE v1023 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ILE v1023 " --> pdb=" O ARG v1013 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLN v1087 " --> pdb=" O ASP v1026 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'v' and resid 1033 through 1038 removed outlier: 7.024A pdb=" N ALA v1047 " --> pdb=" O THR v1034 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ALA v1036 " --> pdb=" O ALA v1045 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA v1045 " --> pdb=" O ALA v1036 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP v1048 " --> pdb=" O ASN v1052 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ASN v1052 " --> pdb=" O ASP v1048 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET v1093 " --> pdb=" O VAL v1055 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ARG v1057 " --> pdb=" O VAL v1091 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N VAL v1091 " --> pdb=" O ARG v1057 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'v' and resid 309 through 311 Processing sheet with id= BJ, first strand: chain 'v' and resid 444 through 450 removed outlier: 6.826A pdb=" N ILE v 764 " --> pdb=" O MET v 447 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL v 449 " --> pdb=" O LEU v 762 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU v 762 " --> pdb=" O VAL v 449 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'y' and resid 21 through 23 Processing sheet with id= BL, first strand: chain 'y' and resid 39 through 42 removed outlier: 6.491A pdb=" N TYR y 71 " --> pdb=" O CYS y 40 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'z' and resid 88 through 90 1949 hydrogen bonds defined for protein. 5382 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 155 hydrogen bonds 276 hydrogen bond angles 0 basepair planarities 64 basepair parallelities 131 stacking parallelities Total time for adding SS restraints: 35.31 Time building geometry restraints manager: 24.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 15652 1.33 - 1.45: 18441 1.45 - 1.57: 39415 1.57 - 1.69: 549 1.69 - 1.82: 535 Bond restraints: 74592 Sorted by residual: bond pdb=" C PRO z 14 " pdb=" N PRO z 15 " ideal model delta sigma weight residual 1.334 1.460 -0.126 2.34e-02 1.83e+03 2.90e+01 bond pdb=" C THR A 733 " pdb=" N PRO A 734 " ideal model delta sigma weight residual 1.336 1.391 -0.055 1.20e-02 6.94e+03 2.08e+01 bond pdb=" C ARG v1057 " pdb=" N LEU v1058 " ideal model delta sigma weight residual 1.330 1.271 0.059 1.47e-02 4.63e+03 1.63e+01 bond pdb=" CB THR u1113 " pdb=" CG2 THR u1113 " ideal model delta sigma weight residual 1.521 1.401 0.120 3.30e-02 9.18e+02 1.32e+01 bond pdb=" O12 IHP A3001 " pdb=" P2 IHP A3001 " ideal model delta sigma weight residual 1.675 1.603 0.072 2.00e-02 2.50e+03 1.28e+01 ... (remaining 74587 not shown) Histogram of bond angle deviations from ideal: 94.64 - 103.96: 2118 103.96 - 113.29: 41066 113.29 - 122.61: 49188 122.61 - 131.93: 9615 131.93 - 141.25: 254 Bond angle restraints: 102241 Sorted by residual: angle pdb=" C VAL R 201 " pdb=" N ASP R 202 " pdb=" CA ASP R 202 " ideal model delta sigma weight residual 126.45 138.70 -12.25 1.77e+00 3.19e-01 4.79e+01 angle pdb=" N GLY A1483 " pdb=" CA GLY A1483 " pdb=" C GLY A1483 " ideal model delta sigma weight residual 115.61 103.68 11.93 1.74e+00 3.30e-01 4.70e+01 angle pdb=" C VAL D 317 " pdb=" N ARG D 318 " pdb=" CA ARG D 318 " ideal model delta sigma weight residual 121.54 133.93 -12.39 1.91e+00 2.74e-01 4.21e+01 angle pdb=" N VAL 3 587 " pdb=" CA VAL 3 587 " pdb=" C VAL 3 587 " ideal model delta sigma weight residual 106.21 113.10 -6.89 1.07e+00 8.73e-01 4.15e+01 angle pdb=" C HIS E 146 " pdb=" N GLN E 147 " pdb=" CA GLN E 147 " ideal model delta sigma weight residual 121.54 133.72 -12.18 1.91e+00 2.74e-01 4.06e+01 ... (remaining 102236 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.04: 44172 35.04 - 70.08: 1116 70.08 - 105.12: 141 105.12 - 140.17: 12 140.17 - 175.21: 7 Dihedral angle restraints: 45448 sinusoidal: 21434 harmonic: 24014 Sorted by residual: dihedral pdb=" CA LYS B 352 " pdb=" C LYS B 352 " pdb=" N THR B 353 " pdb=" CA THR B 353 " ideal model delta harmonic sigma weight residual -180.00 -121.20 -58.80 0 5.00e+00 4.00e-02 1.38e+02 dihedral pdb=" CA SER v 584 " pdb=" C SER v 584 " pdb=" N ALA v 585 " pdb=" CA ALA v 585 " ideal model delta harmonic sigma weight residual -180.00 -123.61 -56.39 0 5.00e+00 4.00e-02 1.27e+02 dihedral pdb=" CA CYS z 83 " pdb=" C CYS z 83 " pdb=" N ASN z 84 " pdb=" CA ASN z 84 " ideal model delta harmonic sigma weight residual -180.00 -126.54 -53.46 0 5.00e+00 4.00e-02 1.14e+02 ... (remaining 45445 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.965: 11352 0.965 - 1.931: 0 1.931 - 2.896: 0 2.896 - 3.861: 0 3.861 - 4.827: 4 Chirality restraints: 11356 Sorted by residual: chirality pdb=" C3 IHP A3001 " pdb=" C2 IHP A3001 " pdb=" C4 IHP A3001 " pdb=" O13 IHP A3001 " both_signs ideal model delta sigma weight residual False -2.34 2.49 -4.83 2.00e-01 2.50e+01 5.82e+02 chirality pdb=" C2 IHP A3001 " pdb=" C1 IHP A3001 " pdb=" C3 IHP A3001 " pdb=" O12 IHP A3001 " both_signs ideal model delta sigma weight residual False -2.52 2.23 -4.75 2.00e-01 2.50e+01 5.65e+02 chirality pdb=" C1 IHP A3001 " pdb=" C2 IHP A3001 " pdb=" C6 IHP A3001 " pdb=" O11 IHP A3001 " both_signs ideal model delta sigma weight residual False 2.32 -2.43 4.75 2.00e-01 2.50e+01 5.64e+02 ... (remaining 11353 not shown) Planarity restraints: 12180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU u 464 " -0.103 5.00e-02 4.00e+02 1.57e-01 3.96e+01 pdb=" N PRO u 465 " 0.272 5.00e-02 4.00e+02 pdb=" CA PRO u 465 " -0.089 5.00e-02 4.00e+02 pdb=" CD PRO u 465 " -0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 383 " 0.024 2.00e-02 2.50e+03 4.76e-02 2.27e+01 pdb=" C ARG D 383 " -0.082 2.00e-02 2.50e+03 pdb=" O ARG D 383 " 0.030 2.00e-02 2.50e+03 pdb=" N HIS D 384 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 384 " -0.024 2.00e-02 2.50e+03 4.73e-02 2.23e+01 pdb=" C HIS D 384 " 0.082 2.00e-02 2.50e+03 pdb=" O HIS D 384 " -0.031 2.00e-02 2.50e+03 pdb=" N TYR D 385 " -0.027 2.00e-02 2.50e+03 ... (remaining 12177 not shown) Histogram of nonbonded interaction distances: 1.18 - 1.92: 1 1.92 - 2.67: 2252 2.67 - 3.41: 98789 3.41 - 4.16: 178881 4.16 - 4.90: 309820 Nonbonded interactions: 589743 Sorted by model distance: nonbonded pdb=" OH TYR A 613 " pdb=" O41 IHP A3001 " model vdw 1.176 2.440 nonbonded pdb=" OP2 G 6 75 " pdb="MG MG 6 202 " model vdw 2.032 2.170 nonbonded pdb=" CZ TYR A 613 " pdb=" O41 IHP A3001 " model vdw 2.033 3.260 nonbonded pdb=" NH2 ARG Q 140 " pdb="ZN ZN Q 202 " model vdw 2.154 2.310 nonbonded pdb=" CE2 TYR A 613 " pdb=" O42 IHP A3001 " model vdw 2.164 3.340 ... (remaining 589738 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 17.070 Check model and map are aligned: 0.820 Set scattering table: 0.530 Process input model: 176.050 Find NCS groups from input model: 1.710 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 203.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 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 : 0.011 0.143 74592 Z= 0.693 Angle : 1.315 14.347 102241 Z= 0.714 Chirality : 0.113 4.827 11356 Planarity : 0.009 0.157 12180 Dihedral : 15.314 175.208 29936 Min Nonbonded Distance : 1.176 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.31 % Allowed : 12.93 % Favored : 86.77 % Rotamer: Outliers : 1.26 % Allowed : 5.37 % Favored : 93.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.04 % Twisted Proline : 2.15 % Twisted General : 0.62 % 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: -4.84 (0.07), residues: 8146 helix: -3.20 (0.07), residues: 2798 sheet: -2.34 (0.15), residues: 960 loop : -3.52 (0.08), residues: 4388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.004 TRP B 549 HIS 0.027 0.003 HIS B 140 PHE 0.058 0.004 PHE A1192 TYR 0.062 0.005 TYR O 316 ARG 0.032 0.002 ARG A1748 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16292 Ramachandran restraints generated. 8146 Oldfield, 0 Emsley, 8146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16292 Ramachandran restraints generated. 8146 Oldfield, 0 Emsley, 8146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1507 residues out of total 7250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 1416 time to evaluate : 6.163 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: 3 612 TYR cc_start: 0.8335 (t80) cc_final: 0.8085 (t80) REVERT: 8 589 ASP cc_start: 0.7595 (t0) cc_final: 0.7378 (t0) REVERT: A 578 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8330 (pp) REVERT: A 599 MET cc_start: 0.8134 (tpp) cc_final: 0.7914 (tpt) REVERT: A 735 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8103 (mt) REVERT: A 914 LEU cc_start: 0.8800 (tp) cc_final: 0.8559 (tp) REVERT: A 1370 ARG cc_start: 0.7520 (mmt180) cc_final: 0.6702 (mtp180) REVERT: A 1732 LYS cc_start: 0.8405 (tppt) cc_final: 0.8137 (mmtm) REVERT: A 1781 ASP cc_start: 0.8278 (t0) cc_final: 0.8060 (t0) REVERT: A 1996 ASN cc_start: 0.7568 (t0) cc_final: 0.7302 (t0) REVERT: A 2279 TRP cc_start: 0.6672 (p-90) cc_final: 0.6115 (p-90) REVERT: B 134 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7708 (pp) REVERT: B 236 MET cc_start: 0.6903 (mtm) cc_final: 0.6666 (mtp) REVERT: C 116 TYR cc_start: 0.8319 (t80) cc_final: 0.7852 (t80) REVERT: C 214 ILE cc_start: 0.8791 (mm) cc_final: 0.8449 (mt) REVERT: D 185 MET cc_start: 0.5517 (tmm) cc_final: 0.4794 (tpt) REVERT: D 327 SER cc_start: 0.8246 (m) cc_final: 0.8016 (p) REVERT: D 351 ASP cc_start: 0.7635 (p0) cc_final: 0.7347 (p0) REVERT: E 184 ASN cc_start: 0.7688 (m-40) cc_final: 0.7458 (m-40) REVERT: S 18 TYR cc_start: 0.8201 (t80) cc_final: 0.7955 (t80) REVERT: Y 70 PHE cc_start: 0.7829 (OUTLIER) cc_final: 0.7594 (m-10) REVERT: u 453 MET cc_start: 0.4322 (mmm) cc_final: 0.4081 (mmt) REVERT: u 953 ASP cc_start: 0.7370 (m-30) cc_final: 0.7125 (m-30) REVERT: u 962 MET cc_start: 0.6776 (mtp) cc_final: 0.6499 (mtt) REVERT: u 1260 LYS cc_start: 0.8208 (ttpp) cc_final: 0.7958 (ptmm) REVERT: v 726 GLN cc_start: 0.7154 (mp10) cc_final: 0.6678 (mp10) REVERT: v 948 VAL cc_start: 0.8898 (OUTLIER) cc_final: 0.8650 (p) REVERT: x 44 MET cc_start: 0.8326 (ptp) cc_final: 0.8027 (ptm) outliers start: 91 outliers final: 22 residues processed: 1489 average time/residue: 0.7347 time to fit residues: 1806.7825 Evaluate side-chains 905 residues out of total 7250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 878 time to evaluate : 6.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1099 PHE Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1487 HIS Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1777 ILE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 385 TYR Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain Y residue 70 PHE Chi-restraints excluded: chain s residue 63 VAL Chi-restraints excluded: chain u residue 596 ILE Chi-restraints excluded: chain u residue 1065 LEU Chi-restraints excluded: chain v residue 278 LEU Chi-restraints excluded: chain v residue 948 VAL Chi-restraints excluded: chain z residue 20 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 707 optimal weight: 2.9990 chunk 635 optimal weight: 1.9990 chunk 352 optimal weight: 7.9990 chunk 216 optimal weight: 4.9990 chunk 428 optimal weight: 0.9980 chunk 339 optimal weight: 5.9990 chunk 656 optimal weight: 0.9990 chunk 254 optimal weight: 5.9990 chunk 399 optimal weight: 10.0000 chunk 488 optimal weight: 10.0000 chunk 760 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 5 HIS ** 7 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 483 GLN 8 496 ASN ** 8 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 587 HIS A 439 GLN A 495 GLN A 505 ASN A 563 GLN A 723 ASN A 834 HIS ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 873 ASN A 924 GLN A 994 ASN A1013 ASN A1023 ASN A1096 HIS A1293 ASN ** A1367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1476 GLN A1522 GLN ** A1543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1712 HIS A1728 GLN A1998 ASN B 280 HIS B 491 HIS B 583 ASN B 771 GLN B 890 HIS C 106 GLN ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 HIS C 283 ASN C 307 GLN D 350 HIS D 381 HIS ** D 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 109 GLN O 446 GLN P 120 ASN R 45 GLN R 196 ASN S 20 GLN V 134 GLN Y 97 ASN s 7 GLN s 88 HIS ** s 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 127 HIS s 156 HIS s 169 ASN t 141 GLN ** t 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 829 ASN u 832 GLN ** u 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 912 ASN u1209 ASN ** u1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u1277 GLN ** v 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 526 HIS v 885 ASN y 55 GLN ** z 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 93 ASN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 74592 Z= 0.382 Angle : 0.825 15.209 102241 Z= 0.426 Chirality : 0.050 0.879 11356 Planarity : 0.006 0.129 12180 Dihedral : 16.456 173.316 13299 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.29 % Favored : 87.58 % Rotamer: Outliers : 3.56 % Allowed : 10.62 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.04 % Twisted Proline : 0.96 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (0.08), residues: 8146 helix: -1.89 (0.08), residues: 2805 sheet: -2.10 (0.15), residues: 1003 loop : -3.17 (0.08), residues: 4338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 549 HIS 0.013 0.002 HIS B 140 PHE 0.038 0.002 PHE A1192 TYR 0.033 0.002 TYR B 817 ARG 0.012 0.001 ARG z 85 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16292 Ramachandran restraints generated. 8146 Oldfield, 0 Emsley, 8146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16292 Ramachandran restraints generated. 8146 Oldfield, 0 Emsley, 8146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1215 residues out of total 7250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 957 time to evaluate : 6.198 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: A 66 VAL cc_start: 0.8717 (OUTLIER) cc_final: 0.8459 (m) REVERT: A 599 MET cc_start: 0.8465 (tpp) cc_final: 0.8117 (tpt) REVERT: A 718 ARG cc_start: 0.8435 (mtt90) cc_final: 0.8185 (mtt90) REVERT: A 735 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8185 (mt) REVERT: A 1267 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8535 (tp) REVERT: A 1330 MET cc_start: 0.8771 (mmm) cc_final: 0.8469 (mmm) REVERT: A 1370 ARG cc_start: 0.7481 (mmt180) cc_final: 0.6644 (mtp180) REVERT: A 1405 LEU cc_start: 0.6988 (OUTLIER) cc_final: 0.6578 (tp) REVERT: A 1469 ASN cc_start: 0.9009 (OUTLIER) cc_final: 0.8614 (p0) REVERT: A 1513 MET cc_start: 0.6073 (pmm) cc_final: 0.5834 (pmm) REVERT: A 1732 LYS cc_start: 0.8418 (tppt) cc_final: 0.8095 (mmtm) REVERT: A 1996 ASN cc_start: 0.7536 (t0) cc_final: 0.7286 (t0) REVERT: B 116 MET cc_start: 0.5746 (mmp) cc_final: 0.4893 (mpp) REVERT: B 134 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7613 (pp) REVERT: B 465 MET cc_start: 0.6961 (mmm) cc_final: 0.6406 (mmm) REVERT: C 136 ASP cc_start: 0.6940 (p0) cc_final: 0.6655 (p0) REVERT: C 138 GLU cc_start: 0.8136 (mp0) cc_final: 0.7936 (mp0) REVERT: C 214 ILE cc_start: 0.8811 (mm) cc_final: 0.8557 (mt) REVERT: C 429 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7872 (pt) REVERT: D 185 MET cc_start: 0.5422 (tmm) cc_final: 0.4790 (tpt) REVERT: D 327 SER cc_start: 0.8212 (m) cc_final: 0.7882 (p) REVERT: D 400 PHE cc_start: 0.7408 (OUTLIER) cc_final: 0.6711 (t80) REVERT: D 474 GLU cc_start: 0.7596 (mp0) cc_final: 0.7276 (mp0) REVERT: E 108 ARG cc_start: 0.8377 (mtm110) cc_final: 0.8024 (mtm110) REVERT: L 18 ILE cc_start: 0.8537 (mt) cc_final: 0.8332 (mt) REVERT: L 37 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8104 (pp) REVERT: L 69 GLU cc_start: 0.6602 (pp20) cc_final: 0.6257 (pp20) REVERT: P 15 TRP cc_start: 0.7270 (t-100) cc_final: 0.7032 (t-100) REVERT: P 69 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7510 (mp0) REVERT: P 79 ASN cc_start: 0.8165 (t0) cc_final: 0.7853 (t0) REVERT: P 123 ARG cc_start: 0.6597 (tmt170) cc_final: 0.6385 (ttt-90) REVERT: V 62 ILE cc_start: 0.6439 (mt) cc_final: 0.6164 (mt) REVERT: s 4 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8365 (pt) REVERT: t 141 GLN cc_start: 0.7894 (mt0) cc_final: 0.7634 (mt0) REVERT: t 143 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.6514 (mp0) REVERT: t 205 TYR cc_start: 0.8880 (t80) cc_final: 0.8496 (t80) REVERT: u 962 MET cc_start: 0.6472 (mtp) cc_final: 0.6232 (mtt) REVERT: u 1260 LYS cc_start: 0.8220 (ttpp) cc_final: 0.7971 (ptmm) REVERT: v 948 VAL cc_start: 0.8901 (OUTLIER) cc_final: 0.8664 (p) REVERT: y 55 GLN cc_start: 0.8012 (tp-100) cc_final: 0.7738 (tp40) REVERT: z 37 ASP cc_start: 0.8089 (t0) cc_final: 0.7596 (t0) REVERT: z 93 ASN cc_start: 0.7193 (m-40) cc_final: 0.6957 (m110) outliers start: 258 outliers final: 144 residues processed: 1148 average time/residue: 0.6810 time to fit residues: 1340.1959 Evaluate side-chains 997 residues out of total 7250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 840 time to evaluate : 6.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 79 PHE Chi-restraints excluded: chain 8 residue 475 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 616 PHE Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 876 GLU Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 966 TRP Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 976 MET Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1099 PHE Chi-restraints excluded: chain A residue 1181 ASP Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1211 ASP Chi-restraints excluded: chain A residue 1235 GLU Chi-restraints excluded: chain A residue 1254 THR Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1286 ASP Chi-restraints excluded: chain A residue 1329 SER Chi-restraints excluded: chain A residue 1347 ASP Chi-restraints excluded: chain A residue 1397 ILE Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1469 ASN Chi-restraints excluded: chain A residue 1487 HIS Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1581 LEU Chi-restraints excluded: chain A residue 1608 THR Chi-restraints excluded: chain A residue 1664 ILE Chi-restraints excluded: chain A residue 1711 LEU Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1786 TYR Chi-restraints excluded: chain A residue 1804 ASN Chi-restraints excluded: chain A residue 1905 LEU Chi-restraints excluded: chain A residue 1957 ASP Chi-restraints excluded: chain A residue 1972 THR Chi-restraints excluded: chain A residue 2090 ILE Chi-restraints excluded: chain A residue 2159 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 179 TYR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 237 MET Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 385 TYR Chi-restraints excluded: chain D residue 395 ILE Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 410 SER Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 13 ASN Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain O residue 243 SER Chi-restraints excluded: chain O residue 263 SER Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 350 ILE Chi-restraints excluded: chain O residue 414 HIS Chi-restraints excluded: chain P residue 69 GLU Chi-restraints excluded: chain P residue 81 CYS Chi-restraints excluded: chain P residue 121 MET Chi-restraints excluded: chain P residue 136 MET Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 251 HIS Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain Y residue 70 PHE Chi-restraints excluded: chain s residue 2 SER Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 63 VAL Chi-restraints excluded: chain s residue 134 THR Chi-restraints excluded: chain s residue 141 MET Chi-restraints excluded: chain s residue 156 HIS Chi-restraints excluded: chain t residue 143 GLU Chi-restraints excluded: chain u residue 414 VAL Chi-restraints excluded: chain u residue 447 GLN Chi-restraints excluded: chain u residue 454 LYS Chi-restraints excluded: chain u residue 477 LYS Chi-restraints excluded: chain u residue 565 ASP Chi-restraints excluded: chain u residue 596 ILE Chi-restraints excluded: chain u residue 632 PHE Chi-restraints excluded: chain u residue 801 VAL Chi-restraints excluded: chain u residue 827 ARG Chi-restraints excluded: chain u residue 873 GLU Chi-restraints excluded: chain u residue 1003 VAL Chi-restraints excluded: chain u residue 1029 GLU Chi-restraints excluded: chain u residue 1065 LEU Chi-restraints excluded: chain u residue 1128 VAL Chi-restraints excluded: chain v residue 55 THR Chi-restraints excluded: chain v residue 61 VAL Chi-restraints excluded: chain v residue 74 THR Chi-restraints excluded: chain v residue 278 LEU Chi-restraints excluded: chain v residue 379 LEU Chi-restraints excluded: chain v residue 478 PHE Chi-restraints excluded: chain v residue 665 ASN Chi-restraints excluded: chain v residue 689 THR Chi-restraints excluded: chain v residue 728 ARG Chi-restraints excluded: chain v residue 755 VAL Chi-restraints excluded: chain v residue 777 VAL Chi-restraints excluded: chain v residue 865 VAL Chi-restraints excluded: chain v residue 943 THR Chi-restraints excluded: chain v residue 948 VAL Chi-restraints excluded: chain v residue 988 ASN Chi-restraints excluded: chain v residue 1005 VAL Chi-restraints excluded: chain v residue 1048 ASP Chi-restraints excluded: chain x residue 6 THR Chi-restraints excluded: chain y residue 8 LEU Chi-restraints excluded: chain y residue 60 ILE Chi-restraints excluded: chain y residue 91 LEU Chi-restraints excluded: chain y residue 96 THR Chi-restraints excluded: chain z residue 102 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 422 optimal weight: 0.9990 chunk 236 optimal weight: 0.7980 chunk 633 optimal weight: 0.8980 chunk 518 optimal weight: 1.9990 chunk 209 optimal weight: 0.9990 chunk 762 optimal weight: 9.9990 chunk 823 optimal weight: 0.8980 chunk 678 optimal weight: 0.7980 chunk 756 optimal weight: 7.9990 chunk 259 optimal weight: 0.0970 chunk 611 optimal weight: 6.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 74 GLN 7 78 HIS A 57 GLN A 297 ASN A 333 HIS ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1450 GLN ** A1543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1860 GLN B 477 HIS ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 381 HIS ** D 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 455 GLN ** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 109 GLN P 120 ASN Q 99 ASN ** s 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 267 GLN t 304 ASN u 829 ASN ** u 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 941 ASN ** u1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 304 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 74592 Z= 0.196 Angle : 0.703 14.257 102241 Z= 0.363 Chirality : 0.045 0.488 11356 Planarity : 0.005 0.114 12180 Dihedral : 16.093 168.196 13291 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.26 % Favored : 88.67 % Rotamer: Outliers : 3.71 % Allowed : 12.40 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.04 % Twisted Proline : 0.72 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.09), residues: 8146 helix: -1.09 (0.09), residues: 2784 sheet: -1.83 (0.16), residues: 997 loop : -2.95 (0.09), residues: 4365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP O 313 HIS 0.016 0.001 HIS s 156 PHE 0.029 0.002 PHE A 166 TYR 0.027 0.002 TYR B 817 ARG 0.012 0.000 ARG C 148 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16292 Ramachandran restraints generated. 8146 Oldfield, 0 Emsley, 8146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16292 Ramachandran restraints generated. 8146 Oldfield, 0 Emsley, 8146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1271 residues out of total 7250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 1002 time to evaluate : 6.243 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: A 66 VAL cc_start: 0.8662 (OUTLIER) cc_final: 0.8392 (m) REVERT: A 735 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.8108 (mt) REVERT: A 1267 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8462 (tp) REVERT: A 1370 ARG cc_start: 0.7205 (mmt180) cc_final: 0.6419 (mtp180) REVERT: A 1405 LEU cc_start: 0.6946 (OUTLIER) cc_final: 0.6704 (tp) REVERT: A 1469 ASN cc_start: 0.8801 (OUTLIER) cc_final: 0.8566 (p0) REVERT: A 1732 LYS cc_start: 0.8372 (tppt) cc_final: 0.8115 (mmtm) REVERT: A 1960 THR cc_start: 0.9066 (OUTLIER) cc_final: 0.8758 (t) REVERT: A 1996 ASN cc_start: 0.7445 (t0) cc_final: 0.7173 (t0) REVERT: B 116 MET cc_start: 0.6058 (mmp) cc_final: 0.5319 (mpp) REVERT: B 134 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7514 (pp) REVERT: C 136 ASP cc_start: 0.7072 (p0) cc_final: 0.6802 (p0) REVERT: C 214 ILE cc_start: 0.8759 (mm) cc_final: 0.8507 (mt) REVERT: C 237 MET cc_start: 0.6595 (OUTLIER) cc_final: 0.6323 (ptp) REVERT: C 268 LEU cc_start: 0.5536 (OUTLIER) cc_final: 0.5270 (pt) REVERT: C 429 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7749 (pt) REVERT: D 185 MET cc_start: 0.5406 (tmm) cc_final: 0.4880 (tpt) REVERT: D 292 TYR cc_start: 0.8431 (m-10) cc_final: 0.8201 (m-10) REVERT: D 327 SER cc_start: 0.8090 (m) cc_final: 0.7837 (p) REVERT: E 104 MET cc_start: 0.6500 (mmt) cc_final: 0.6280 (mmm) REVERT: L 66 GLU cc_start: 0.5873 (mp0) cc_final: 0.5506 (mp0) REVERT: P 79 ASN cc_start: 0.8038 (t0) cc_final: 0.7789 (t0) REVERT: P 208 PRO cc_start: 0.5967 (Cg_endo) cc_final: 0.5571 (Cg_exo) REVERT: Y 96 LYS cc_start: 0.7452 (OUTLIER) cc_final: 0.7085 (ttmm) REVERT: t 141 GLN cc_start: 0.7821 (mt0) cc_final: 0.7452 (mt0) REVERT: t 152 ILE cc_start: 0.7232 (pt) cc_final: 0.7016 (pt) REVERT: t 205 TYR cc_start: 0.8827 (t80) cc_final: 0.8360 (t80) REVERT: u 839 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7400 (mm-30) REVERT: u 883 ASP cc_start: 0.7266 (t70) cc_final: 0.7026 (t0) REVERT: v 948 VAL cc_start: 0.8773 (OUTLIER) cc_final: 0.8528 (p) REVERT: y 55 GLN cc_start: 0.8060 (tp-100) cc_final: 0.7782 (tp40) outliers start: 269 outliers final: 138 residues processed: 1201 average time/residue: 0.7458 time to fit residues: 1542.5823 Evaluate side-chains 1007 residues out of total 7250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 857 time to evaluate : 6.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 475 VAL Chi-restraints excluded: chain 8 residue 487 LEU Chi-restraints excluded: chain 8 residue 586 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 616 PHE Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 876 GLU Chi-restraints excluded: chain A residue 966 TRP Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1099 PHE Chi-restraints excluded: chain A residue 1133 CYS Chi-restraints excluded: chain A residue 1235 GLU Chi-restraints excluded: chain A residue 1254 THR Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1329 SER Chi-restraints excluded: chain A residue 1347 ASP Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1397 ILE Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1469 ASN Chi-restraints excluded: chain A residue 1487 HIS Chi-restraints excluded: chain A residue 1519 THR Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1581 LEU Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1711 LEU Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1786 TYR Chi-restraints excluded: chain A residue 1804 ASN Chi-restraints excluded: chain A residue 1905 LEU Chi-restraints excluded: chain A residue 1938 LEU Chi-restraints excluded: chain A residue 1957 ASP Chi-restraints excluded: chain A residue 1960 THR Chi-restraints excluded: chain A residue 2090 ILE Chi-restraints excluded: chain A residue 2103 THR Chi-restraints excluded: chain A residue 2159 LEU Chi-restraints excluded: chain A residue 2200 MET Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain B residue 663 CYS Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 179 TYR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 237 MET Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 395 ILE Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 410 SER Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 13 ASN Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 78 MET Chi-restraints excluded: chain O residue 243 SER Chi-restraints excluded: chain O residue 269 LEU Chi-restraints excluded: chain O residue 350 ILE Chi-restraints excluded: chain O residue 411 MET Chi-restraints excluded: chain O residue 453 LYS Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 83 THR Chi-restraints excluded: chain P residue 116 TYR Chi-restraints excluded: chain P residue 121 MET Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 187 THR Chi-restraints excluded: chain P residue 251 HIS Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 49 ILE Chi-restraints excluded: chain Q residue 99 ASN Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 65 GLU Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 100 MET Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain Y residue 70 PHE Chi-restraints excluded: chain Y residue 96 LYS Chi-restraints excluded: chain s residue 63 VAL Chi-restraints excluded: chain s residue 141 MET Chi-restraints excluded: chain t residue 144 LEU Chi-restraints excluded: chain t residue 307 PHE Chi-restraints excluded: chain u residue 447 GLN Chi-restraints excluded: chain u residue 477 LYS Chi-restraints excluded: chain u residue 543 THR Chi-restraints excluded: chain u residue 596 ILE Chi-restraints excluded: chain u residue 632 PHE Chi-restraints excluded: chain u residue 801 VAL Chi-restraints excluded: chain u residue 827 ARG Chi-restraints excluded: chain u residue 873 GLU Chi-restraints excluded: chain u residue 935 THR Chi-restraints excluded: chain u residue 1065 LEU Chi-restraints excluded: chain u residue 1128 VAL Chi-restraints excluded: chain v residue 74 THR Chi-restraints excluded: chain v residue 278 LEU Chi-restraints excluded: chain v residue 364 LEU Chi-restraints excluded: chain v residue 475 ILE Chi-restraints excluded: chain v residue 549 VAL Chi-restraints excluded: chain v residue 728 ARG Chi-restraints excluded: chain v residue 736 TYR Chi-restraints excluded: chain v residue 759 THR Chi-restraints excluded: chain v residue 948 VAL Chi-restraints excluded: chain v residue 988 ASN Chi-restraints excluded: chain v residue 1005 VAL Chi-restraints excluded: chain v residue 1048 ASP Chi-restraints excluded: chain x residue 6 THR Chi-restraints excluded: chain y residue 91 LEU Chi-restraints excluded: chain y residue 96 THR Chi-restraints excluded: chain z residue 59 THR Chi-restraints excluded: chain z residue 62 VAL Chi-restraints excluded: chain z residue 88 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 753 optimal weight: 7.9990 chunk 573 optimal weight: 3.9990 chunk 395 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 363 optimal weight: 0.3980 chunk 511 optimal weight: 5.9990 chunk 765 optimal weight: 0.0870 chunk 810 optimal weight: 2.9990 chunk 399 optimal weight: 7.9990 chunk 725 optimal weight: 1.9990 chunk 218 optimal weight: 0.7980 overall best weight: 1.2562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1399 GLN ** A1543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 GLN ** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 99 ASN ** s 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 267 GLN t 289 HIS u 891 GLN ** u1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 553 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 74592 Z= 0.240 Angle : 0.696 14.678 102241 Z= 0.356 Chirality : 0.045 0.449 11356 Planarity : 0.005 0.103 12180 Dihedral : 15.875 169.590 13281 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.75 % Favored : 88.17 % Rotamer: Outliers : 4.15 % Allowed : 13.59 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.04 % Twisted Proline : 0.72 % Twisted General : 0.12 % 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: -2.87 (0.09), residues: 8146 helix: -0.73 (0.10), residues: 2781 sheet: -1.80 (0.16), residues: 995 loop : -2.82 (0.09), residues: 4370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A1637 HIS 0.010 0.001 HIS B 140 PHE 0.033 0.002 PHE A 166 TYR 0.028 0.002 TYR A 178 ARG 0.012 0.000 ARG z 85 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16292 Ramachandran restraints generated. 8146 Oldfield, 0 Emsley, 8146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16292 Ramachandran restraints generated. 8146 Oldfield, 0 Emsley, 8146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1218 residues out of total 7250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 301 poor density : 917 time to evaluate : 6.492 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: 1 49 GLU cc_start: 0.4787 (pm20) cc_final: 0.4581 (pm20) REVERT: 7 51 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7702 (pp) REVERT: A 66 VAL cc_start: 0.8695 (OUTLIER) cc_final: 0.8460 (m) REVERT: A 316 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7527 (p90) REVERT: A 735 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8128 (mt) REVERT: A 834 HIS cc_start: 0.7318 (OUTLIER) cc_final: 0.6944 (m-70) REVERT: A 1094 ARG cc_start: 0.7937 (mtp85) cc_final: 0.7725 (mtp85) REVERT: A 1136 ARG cc_start: 0.7934 (ttm110) cc_final: 0.7697 (tpp-160) REVERT: A 1208 THR cc_start: 0.5315 (OUTLIER) cc_final: 0.5013 (t) REVERT: A 1370 ARG cc_start: 0.7168 (mmt180) cc_final: 0.6477 (mtp180) REVERT: A 1405 LEU cc_start: 0.6406 (OUTLIER) cc_final: 0.6141 (tp) REVERT: A 1469 ASN cc_start: 0.8783 (OUTLIER) cc_final: 0.8564 (p0) REVERT: A 1960 THR cc_start: 0.9059 (OUTLIER) cc_final: 0.8801 (t) REVERT: A 2200 MET cc_start: 0.5338 (OUTLIER) cc_final: 0.4851 (tpp) REVERT: B 134 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7492 (pp) REVERT: C 214 ILE cc_start: 0.8775 (mm) cc_final: 0.8520 (mt) REVERT: C 268 LEU cc_start: 0.5509 (OUTLIER) cc_final: 0.5289 (pt) REVERT: C 429 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.7881 (pt) REVERT: D 185 MET cc_start: 0.5007 (tmm) cc_final: 0.4641 (tpt) REVERT: D 327 SER cc_start: 0.8111 (m) cc_final: 0.7874 (p) REVERT: D 400 PHE cc_start: 0.7203 (OUTLIER) cc_final: 0.6714 (t80) REVERT: L 37 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8152 (pp) REVERT: O 404 GLU cc_start: 0.6589 (OUTLIER) cc_final: 0.6296 (pm20) REVERT: P 79 ASN cc_start: 0.8116 (t0) cc_final: 0.7830 (t0) REVERT: P 208 PRO cc_start: 0.6066 (Cg_endo) cc_final: 0.5651 (Cg_exo) REVERT: Q 81 GLU cc_start: 0.6188 (tm-30) cc_final: 0.5778 (tm-30) REVERT: R 30 TYR cc_start: 0.6965 (m-80) cc_final: 0.6291 (m-80) REVERT: R 72 ARG cc_start: 0.6803 (OUTLIER) cc_final: 0.6497 (ppp-140) REVERT: V 53 PHE cc_start: 0.4891 (t80) cc_final: 0.3443 (m-80) REVERT: t 152 ILE cc_start: 0.7120 (pt) cc_final: 0.6900 (pt) REVERT: t 205 TYR cc_start: 0.8833 (t80) cc_final: 0.8425 (t80) REVERT: u 495 ARG cc_start: 0.6487 (OUTLIER) cc_final: 0.6278 (ppt170) REVERT: u 860 GLU cc_start: 0.7327 (mp0) cc_final: 0.7082 (mp0) REVERT: v 948 VAL cc_start: 0.8761 (OUTLIER) cc_final: 0.8503 (p) REVERT: y 55 GLN cc_start: 0.8130 (tp-100) cc_final: 0.7835 (tp40) outliers start: 301 outliers final: 193 residues processed: 1135 average time/residue: 0.7336 time to fit residues: 1449.1834 Evaluate side-chains 1046 residues out of total 7250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 834 time to evaluate : 6.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 48 THR Chi-restraints excluded: chain 1 residue 68 VAL Chi-restraints excluded: chain 1 residue 79 PHE Chi-restraints excluded: chain 1 residue 90 THR Chi-restraints excluded: chain 7 residue 16 VAL Chi-restraints excluded: chain 7 residue 51 LEU Chi-restraints excluded: chain 7 residue 70 LEU Chi-restraints excluded: chain 8 residue 461 THR Chi-restraints excluded: chain 8 residue 475 VAL Chi-restraints excluded: chain 8 residue 586 ILE Chi-restraints excluded: chain 8 residue 587 HIS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 834 HIS Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 966 TRP Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1099 PHE Chi-restraints excluded: chain A residue 1133 CYS Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1211 ASP Chi-restraints excluded: chain A residue 1235 GLU Chi-restraints excluded: chain A residue 1254 THR Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1286 ASP Chi-restraints excluded: chain A residue 1329 SER Chi-restraints excluded: chain A residue 1347 ASP Chi-restraints excluded: chain A residue 1351 THR Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1469 ASN Chi-restraints excluded: chain A residue 1487 HIS Chi-restraints excluded: chain A residue 1519 THR Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1548 TYR Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1608 THR Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1711 LEU Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1748 ARG Chi-restraints excluded: chain A residue 1786 TYR Chi-restraints excluded: chain A residue 1804 ASN Chi-restraints excluded: chain A residue 1905 LEU Chi-restraints excluded: chain A residue 1938 LEU Chi-restraints excluded: chain A residue 1957 ASP Chi-restraints excluded: chain A residue 1960 THR Chi-restraints excluded: chain A residue 1972 THR Chi-restraints excluded: chain A residue 2014 MET Chi-restraints excluded: chain A residue 2090 ILE Chi-restraints excluded: chain A residue 2103 THR Chi-restraints excluded: chain A residue 2159 LEU Chi-restraints excluded: chain A residue 2200 MET Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain B residue 663 CYS Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 179 TYR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 395 ILE Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 410 SER Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 489 TYR Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 13 ASN Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 78 MET Chi-restraints excluded: chain O residue 242 ILE Chi-restraints excluded: chain O residue 243 SER Chi-restraints excluded: chain O residue 269 LEU Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 350 ILE Chi-restraints excluded: chain O residue 370 VAL Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 404 GLU Chi-restraints excluded: chain O residue 411 MET Chi-restraints excluded: chain O residue 453 LYS Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 63 MET Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 81 CYS Chi-restraints excluded: chain P residue 83 THR Chi-restraints excluded: chain P residue 121 MET Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 187 THR Chi-restraints excluded: chain P residue 251 HIS Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 49 ILE Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 72 ARG Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 100 MET Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain Y residue 70 PHE Chi-restraints excluded: chain s residue 27 GLU Chi-restraints excluded: chain s residue 63 VAL Chi-restraints excluded: chain s residue 141 MET Chi-restraints excluded: chain s residue 156 HIS Chi-restraints excluded: chain s residue 174 ILE Chi-restraints excluded: chain t residue 307 PHE Chi-restraints excluded: chain u residue 447 GLN Chi-restraints excluded: chain u residue 454 LYS Chi-restraints excluded: chain u residue 477 LYS Chi-restraints excluded: chain u residue 495 ARG Chi-restraints excluded: chain u residue 543 THR Chi-restraints excluded: chain u residue 565 ASP Chi-restraints excluded: chain u residue 596 ILE Chi-restraints excluded: chain u residue 624 VAL Chi-restraints excluded: chain u residue 632 PHE Chi-restraints excluded: chain u residue 801 VAL Chi-restraints excluded: chain u residue 827 ARG Chi-restraints excluded: chain u residue 873 GLU Chi-restraints excluded: chain u residue 891 GLN Chi-restraints excluded: chain u residue 935 THR Chi-restraints excluded: chain u residue 1003 VAL Chi-restraints excluded: chain u residue 1065 LEU Chi-restraints excluded: chain u residue 1110 VAL Chi-restraints excluded: chain u residue 1124 SER Chi-restraints excluded: chain u residue 1128 VAL Chi-restraints excluded: chain v residue 61 VAL Chi-restraints excluded: chain v residue 74 THR Chi-restraints excluded: chain v residue 181 MET Chi-restraints excluded: chain v residue 278 LEU Chi-restraints excluded: chain v residue 325 ILE Chi-restraints excluded: chain v residue 364 LEU Chi-restraints excluded: chain v residue 403 SER Chi-restraints excluded: chain v residue 475 ILE Chi-restraints excluded: chain v residue 516 LEU Chi-restraints excluded: chain v residue 614 VAL Chi-restraints excluded: chain v residue 665 ASN Chi-restraints excluded: chain v residue 736 TYR Chi-restraints excluded: chain v residue 759 THR Chi-restraints excluded: chain v residue 865 VAL Chi-restraints excluded: chain v residue 914 ILE Chi-restraints excluded: chain v residue 930 LEU Chi-restraints excluded: chain v residue 943 THR Chi-restraints excluded: chain v residue 948 VAL Chi-restraints excluded: chain v residue 988 ASN Chi-restraints excluded: chain v residue 1005 VAL Chi-restraints excluded: chain v residue 1048 ASP Chi-restraints excluded: chain x residue 6 THR Chi-restraints excluded: chain y residue 8 LEU Chi-restraints excluded: chain y residue 60 ILE Chi-restraints excluded: chain y residue 67 SER Chi-restraints excluded: chain y residue 91 LEU Chi-restraints excluded: chain y residue 96 THR Chi-restraints excluded: chain z residue 17 VAL Chi-restraints excluded: chain z residue 59 THR Chi-restraints excluded: chain z residue 62 VAL Chi-restraints excluded: chain z residue 63 VAL Chi-restraints excluded: chain z residue 88 VAL Chi-restraints excluded: chain z residue 102 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 674 optimal weight: 0.9980 chunk 459 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 603 optimal weight: 6.9990 chunk 334 optimal weight: 9.9990 chunk 691 optimal weight: 0.0980 chunk 559 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 413 optimal weight: 0.6980 chunk 727 optimal weight: 2.9990 chunk 204 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 78 HIS A 788 GLN ** A 793 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1982 GLN A1996 ASN ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 GLN ** D 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 244 ASN ** O 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 141 GLN t 304 ASN u 901 GLN ** u1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 104 GLN ** v 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 34 ASN y 50 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 74592 Z= 0.185 Angle : 0.665 14.691 102241 Z= 0.339 Chirality : 0.044 0.397 11356 Planarity : 0.005 0.093 12180 Dihedral : 15.740 169.347 13279 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.95 % Favored : 88.99 % Rotamer: Outliers : 4.11 % Allowed : 14.47 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.04 % Twisted Proline : 0.72 % Twisted General : 0.12 % 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: -2.62 (0.09), residues: 8146 helix: -0.45 (0.10), residues: 2777 sheet: -1.66 (0.16), residues: 982 loop : -2.73 (0.09), residues: 4387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP L 63 HIS 0.009 0.001 HIS B 140 PHE 0.032 0.001 PHE A 166 TYR 0.025 0.001 TYR B 66 ARG 0.009 0.000 ARG V 55 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16292 Ramachandran restraints generated. 8146 Oldfield, 0 Emsley, 8146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16292 Ramachandran restraints generated. 8146 Oldfield, 0 Emsley, 8146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1218 residues out of total 7250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 298 poor density : 920 time to evaluate : 6.297 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: 7 51 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7826 (pp) REVERT: A 45 TYR cc_start: 0.5817 (p90) cc_final: 0.5529 (p90) REVERT: A 66 VAL cc_start: 0.8706 (OUTLIER) cc_final: 0.8487 (m) REVERT: A 234 MET cc_start: 0.7260 (ttp) cc_final: 0.7027 (ttp) REVERT: A 316 PHE cc_start: 0.8020 (OUTLIER) cc_final: 0.7574 (p90) REVERT: A 1022 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8205 (mtp) REVERT: A 1208 THR cc_start: 0.5323 (OUTLIER) cc_final: 0.5011 (t) REVERT: A 1311 PHE cc_start: 0.8518 (OUTLIER) cc_final: 0.8091 (m-80) REVERT: A 1370 ARG cc_start: 0.7136 (mmt180) cc_final: 0.6467 (mtp180) REVERT: A 1405 LEU cc_start: 0.6468 (OUTLIER) cc_final: 0.6265 (tp) REVERT: A 1487 HIS cc_start: 0.6140 (OUTLIER) cc_final: 0.5722 (p90) REVERT: A 1745 GLU cc_start: 0.7425 (pp20) cc_final: 0.7177 (pp20) REVERT: A 1960 THR cc_start: 0.9068 (OUTLIER) cc_final: 0.8760 (t) REVERT: A 2200 MET cc_start: 0.5409 (OUTLIER) cc_final: 0.4882 (tpp) REVERT: B 116 MET cc_start: 0.5375 (mmm) cc_final: 0.4909 (mpp) REVERT: B 134 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7574 (pp) REVERT: B 641 MET cc_start: 0.8092 (mmm) cc_final: 0.7766 (mmt) REVERT: C 214 ILE cc_start: 0.8741 (mm) cc_final: 0.8504 (mt) REVERT: C 268 LEU cc_start: 0.5457 (OUTLIER) cc_final: 0.5212 (pt) REVERT: C 429 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.7785 (pt) REVERT: D 185 MET cc_start: 0.5291 (tmm) cc_final: 0.4852 (tpt) REVERT: D 292 TYR cc_start: 0.8353 (m-10) cc_final: 0.8144 (m-10) REVERT: E 127 GLN cc_start: 0.8197 (tm-30) cc_final: 0.7966 (tm-30) REVERT: L 37 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8107 (pp) REVERT: O 411 MET cc_start: 0.2682 (OUTLIER) cc_final: 0.0818 (tpt) REVERT: P 79 ASN cc_start: 0.8043 (t0) cc_final: 0.7699 (t0) REVERT: P 208 PRO cc_start: 0.6084 (Cg_endo) cc_final: 0.5697 (Cg_exo) REVERT: Q 81 GLU cc_start: 0.6194 (tm-30) cc_final: 0.5915 (tm-30) REVERT: R 30 TYR cc_start: 0.7112 (m-10) cc_final: 0.6888 (m-80) REVERT: R 72 ARG cc_start: 0.6766 (OUTLIER) cc_final: 0.6433 (ppp-140) REVERT: Y 90 THR cc_start: 0.8222 (p) cc_final: 0.7975 (p) REVERT: t 141 GLN cc_start: 0.7798 (mt0) cc_final: 0.7517 (mt0) REVERT: t 205 TYR cc_start: 0.8808 (t80) cc_final: 0.8360 (t80) REVERT: u 477 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7856 (mtmm) REVERT: u 979 TYR cc_start: 0.8098 (t80) cc_final: 0.7873 (t80) REVERT: v 948 VAL cc_start: 0.8628 (OUTLIER) cc_final: 0.8361 (p) REVERT: y 50 ASN cc_start: 0.7778 (OUTLIER) cc_final: 0.7469 (t0) outliers start: 298 outliers final: 192 residues processed: 1131 average time/residue: 0.6791 time to fit residues: 1324.5050 Evaluate side-chains 1057 residues out of total 7250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 846 time to evaluate : 6.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 7 residue 16 VAL Chi-restraints excluded: chain 7 residue 51 LEU Chi-restraints excluded: chain 7 residue 70 LEU Chi-restraints excluded: chain 8 residue 461 THR Chi-restraints excluded: chain 8 residue 475 VAL Chi-restraints excluded: chain 8 residue 487 LEU Chi-restraints excluded: chain 8 residue 586 ILE Chi-restraints excluded: chain 8 residue 587 HIS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 923 ASP Chi-restraints excluded: chain A residue 966 TRP Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1099 PHE Chi-restraints excluded: chain A residue 1133 CYS Chi-restraints excluded: chain A residue 1177 VAL Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1235 GLU Chi-restraints excluded: chain A residue 1254 THR Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1311 PHE Chi-restraints excluded: chain A residue 1329 SER Chi-restraints excluded: chain A residue 1347 ASP Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1487 HIS Chi-restraints excluded: chain A residue 1494 TYR Chi-restraints excluded: chain A residue 1519 THR Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1548 TYR Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1560 ILE Chi-restraints excluded: chain A residue 1594 CYS Chi-restraints excluded: chain A residue 1608 THR Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1711 LEU Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1786 TYR Chi-restraints excluded: chain A residue 1804 ASN Chi-restraints excluded: chain A residue 1905 LEU Chi-restraints excluded: chain A residue 1938 LEU Chi-restraints excluded: chain A residue 1957 ASP Chi-restraints excluded: chain A residue 1960 THR Chi-restraints excluded: chain A residue 2014 MET Chi-restraints excluded: chain A residue 2090 ILE Chi-restraints excluded: chain A residue 2103 THR Chi-restraints excluded: chain A residue 2111 LEU Chi-restraints excluded: chain A residue 2200 MET Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain B residue 663 CYS Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 179 TYR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 395 ILE Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 410 SER Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 489 TYR Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 13 ASN Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 68 GLU Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 78 MET Chi-restraints excluded: chain O residue 243 SER Chi-restraints excluded: chain O residue 269 LEU Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 347 HIS Chi-restraints excluded: chain O residue 350 ILE Chi-restraints excluded: chain O residue 370 VAL Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 391 TYR Chi-restraints excluded: chain O residue 411 MET Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 83 THR Chi-restraints excluded: chain P residue 121 MET Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 251 HIS Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 49 ILE Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 72 ARG Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain S residue 2 TYR Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 100 MET Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain V residue 149 SER Chi-restraints excluded: chain Y residue 45 LEU Chi-restraints excluded: chain Y residue 70 PHE Chi-restraints excluded: chain s residue 2 SER Chi-restraints excluded: chain s residue 27 GLU Chi-restraints excluded: chain s residue 63 VAL Chi-restraints excluded: chain s residue 141 MET Chi-restraints excluded: chain s residue 174 ILE Chi-restraints excluded: chain t residue 144 LEU Chi-restraints excluded: chain t residue 275 THR Chi-restraints excluded: chain t residue 281 PHE Chi-restraints excluded: chain t residue 307 PHE Chi-restraints excluded: chain u residue 415 LEU Chi-restraints excluded: chain u residue 447 GLN Chi-restraints excluded: chain u residue 454 LYS Chi-restraints excluded: chain u residue 477 LYS Chi-restraints excluded: chain u residue 543 THR Chi-restraints excluded: chain u residue 596 ILE Chi-restraints excluded: chain u residue 632 PHE Chi-restraints excluded: chain u residue 641 ILE Chi-restraints excluded: chain u residue 801 VAL Chi-restraints excluded: chain u residue 827 ARG Chi-restraints excluded: chain u residue 873 GLU Chi-restraints excluded: chain u residue 935 THR Chi-restraints excluded: chain u residue 974 LEU Chi-restraints excluded: chain u residue 1003 VAL Chi-restraints excluded: chain u residue 1065 LEU Chi-restraints excluded: chain u residue 1128 VAL Chi-restraints excluded: chain u residue 1303 ILE Chi-restraints excluded: chain v residue 61 VAL Chi-restraints excluded: chain v residue 74 THR Chi-restraints excluded: chain v residue 175 VAL Chi-restraints excluded: chain v residue 278 LEU Chi-restraints excluded: chain v residue 325 ILE Chi-restraints excluded: chain v residue 364 LEU Chi-restraints excluded: chain v residue 403 SER Chi-restraints excluded: chain v residue 475 ILE Chi-restraints excluded: chain v residue 508 CYS Chi-restraints excluded: chain v residue 605 LEU Chi-restraints excluded: chain v residue 614 VAL Chi-restraints excluded: chain v residue 664 LEU Chi-restraints excluded: chain v residue 665 ASN Chi-restraints excluded: chain v residue 736 TYR Chi-restraints excluded: chain v residue 759 THR Chi-restraints excluded: chain v residue 930 LEU Chi-restraints excluded: chain v residue 948 VAL Chi-restraints excluded: chain v residue 988 ASN Chi-restraints excluded: chain v residue 1005 VAL Chi-restraints excluded: chain v residue 1048 ASP Chi-restraints excluded: chain v residue 1185 MET Chi-restraints excluded: chain y residue 50 ASN Chi-restraints excluded: chain y residue 67 SER Chi-restraints excluded: chain y residue 91 LEU Chi-restraints excluded: chain y residue 96 THR Chi-restraints excluded: chain z residue 17 VAL Chi-restraints excluded: chain z residue 59 THR Chi-restraints excluded: chain z residue 62 VAL Chi-restraints excluded: chain z residue 63 VAL Chi-restraints excluded: chain z residue 88 VAL Chi-restraints excluded: chain z residue 102 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 272 optimal weight: 10.0000 chunk 729 optimal weight: 1.9990 chunk 160 optimal weight: 0.7980 chunk 475 optimal weight: 6.9990 chunk 199 optimal weight: 7.9990 chunk 810 optimal weight: 0.0020 chunk 673 optimal weight: 0.9990 chunk 375 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 268 optimal weight: 4.9990 chunk 425 optimal weight: 4.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 506 GLN A 601 GLN A 792 HIS ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1543 ASN ** A1710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1996 ASN B 306 ASN ** B 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 GLN ** D 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 38 HIS ** s 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 891 GLN ** u1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 74592 Z= 0.202 Angle : 0.663 14.794 102241 Z= 0.337 Chirality : 0.044 0.395 11356 Planarity : 0.005 0.084 12180 Dihedral : 15.626 170.133 13276 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.16 % Favored : 88.78 % Rotamer: Outliers : 4.18 % Allowed : 14.82 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.04 % Twisted Proline : 0.48 % Twisted General : 0.09 % 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: -2.47 (0.09), residues: 8146 helix: -0.30 (0.10), residues: 2799 sheet: -1.59 (0.16), residues: 988 loop : -2.66 (0.09), residues: 4359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP L 63 HIS 0.009 0.001 HIS B 140 PHE 0.034 0.001 PHE A 166 TYR 0.025 0.001 TYR t 297 ARG 0.009 0.000 ARG R 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16292 Ramachandran restraints generated. 8146 Oldfield, 0 Emsley, 8146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16292 Ramachandran restraints generated. 8146 Oldfield, 0 Emsley, 8146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1190 residues out of total 7250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 303 poor density : 887 time to evaluate : 6.221 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: 3 518 MET cc_start: 0.6388 (ttt) cc_final: 0.5845 (tpt) REVERT: 7 51 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7879 (pp) REVERT: A 45 TYR cc_start: 0.5852 (p90) cc_final: 0.5578 (p90) REVERT: A 316 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7567 (p90) REVERT: A 834 HIS cc_start: 0.7172 (OUTLIER) cc_final: 0.6702 (m-70) REVERT: A 1022 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8172 (mtp) REVERT: A 1208 THR cc_start: 0.5432 (OUTLIER) cc_final: 0.5140 (t) REVERT: A 1311 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.8095 (m-80) REVERT: A 1370 ARG cc_start: 0.7165 (mmt180) cc_final: 0.6468 (mtp180) REVERT: A 1405 LEU cc_start: 0.6410 (OUTLIER) cc_final: 0.6152 (tt) REVERT: A 1487 HIS cc_start: 0.6039 (OUTLIER) cc_final: 0.5633 (p90) REVERT: A 1960 THR cc_start: 0.9132 (OUTLIER) cc_final: 0.8840 (t) REVERT: A 2090 ILE cc_start: 0.6070 (OUTLIER) cc_final: 0.5251 (tp) REVERT: A 2200 MET cc_start: 0.5382 (OUTLIER) cc_final: 0.4832 (tpp) REVERT: B 116 MET cc_start: 0.5474 (mmm) cc_final: 0.4898 (mpp) REVERT: B 134 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7594 (pp) REVERT: B 588 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8564 (mt) REVERT: B 641 MET cc_start: 0.8055 (mmm) cc_final: 0.7751 (mmt) REVERT: B 668 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6854 (pm20) REVERT: C 136 ASP cc_start: 0.6885 (p0) cc_final: 0.6674 (p0) REVERT: C 214 ILE cc_start: 0.8762 (mm) cc_final: 0.8490 (mt) REVERT: C 429 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7851 (pt) REVERT: D 185 MET cc_start: 0.5205 (tmm) cc_final: 0.4778 (tpt) REVERT: D 292 TYR cc_start: 0.8409 (m-10) cc_final: 0.8209 (m-10) REVERT: E 127 GLN cc_start: 0.8237 (tm-30) cc_final: 0.7912 (tm-30) REVERT: L 37 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8128 (pp) REVERT: O 411 MET cc_start: 0.2657 (OUTLIER) cc_final: 0.0880 (tpt) REVERT: P 79 ASN cc_start: 0.7991 (t0) cc_final: 0.7746 (t0) REVERT: P 208 PRO cc_start: 0.6114 (Cg_endo) cc_final: 0.5718 (Cg_exo) REVERT: R 30 TYR cc_start: 0.7000 (m-10) cc_final: 0.6521 (m-80) REVERT: R 72 ARG cc_start: 0.6810 (OUTLIER) cc_final: 0.6496 (ppp-140) REVERT: Y 70 PHE cc_start: 0.8264 (OUTLIER) cc_final: 0.7958 (t80) REVERT: t 205 TYR cc_start: 0.8814 (t80) cc_final: 0.8335 (t80) REVERT: u 477 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7830 (mtmm) REVERT: v 478 PHE cc_start: 0.5904 (p90) cc_final: 0.5688 (p90) REVERT: v 948 VAL cc_start: 0.8670 (OUTLIER) cc_final: 0.8408 (p) REVERT: v 1062 THR cc_start: 0.7555 (OUTLIER) cc_final: 0.7235 (t) REVERT: y 50 ASN cc_start: 0.7901 (OUTLIER) cc_final: 0.6743 (t0) REVERT: y 55 GLN cc_start: 0.7843 (tp40) cc_final: 0.7588 (tp40) outliers start: 303 outliers final: 210 residues processed: 1107 average time/residue: 0.6763 time to fit residues: 1293.8824 Evaluate side-chains 1066 residues out of total 7250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 833 time to evaluate : 6.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 40 LEU Chi-restraints excluded: chain 1 residue 79 PHE Chi-restraints excluded: chain 3 residue 547 ASN Chi-restraints excluded: chain 7 residue 16 VAL Chi-restraints excluded: chain 7 residue 51 LEU Chi-restraints excluded: chain 7 residue 70 LEU Chi-restraints excluded: chain 8 residue 461 THR Chi-restraints excluded: chain 8 residue 475 VAL Chi-restraints excluded: chain 8 residue 487 LEU Chi-restraints excluded: chain 8 residue 586 ILE Chi-restraints excluded: chain 8 residue 587 HIS Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 834 HIS Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 923 ASP Chi-restraints excluded: chain A residue 966 TRP Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1097 ILE Chi-restraints excluded: chain A residue 1099 PHE Chi-restraints excluded: chain A residue 1133 CYS Chi-restraints excluded: chain A residue 1177 VAL Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1211 ASP Chi-restraints excluded: chain A residue 1235 GLU Chi-restraints excluded: chain A residue 1254 THR Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1311 PHE Chi-restraints excluded: chain A residue 1329 SER Chi-restraints excluded: chain A residue 1347 ASP Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1487 HIS Chi-restraints excluded: chain A residue 1519 THR Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1548 TYR Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1560 ILE Chi-restraints excluded: chain A residue 1594 CYS Chi-restraints excluded: chain A residue 1608 THR Chi-restraints excluded: chain A residue 1683 LYS Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1711 LEU Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1786 TYR Chi-restraints excluded: chain A residue 1804 ASN Chi-restraints excluded: chain A residue 1891 LEU Chi-restraints excluded: chain A residue 1905 LEU Chi-restraints excluded: chain A residue 1938 LEU Chi-restraints excluded: chain A residue 1957 ASP Chi-restraints excluded: chain A residue 1960 THR Chi-restraints excluded: chain A residue 2014 MET Chi-restraints excluded: chain A residue 2090 ILE Chi-restraints excluded: chain A residue 2103 THR Chi-restraints excluded: chain A residue 2111 LEU Chi-restraints excluded: chain A residue 2200 MET Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 476 CYS Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain B residue 663 CYS Chi-restraints excluded: chain B residue 668 GLU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 179 TYR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 395 ILE Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 410 SER Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 489 TYR Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 13 ASN Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 78 MET Chi-restraints excluded: chain O residue 242 ILE Chi-restraints excluded: chain O residue 243 SER Chi-restraints excluded: chain O residue 269 LEU Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 347 HIS Chi-restraints excluded: chain O residue 350 ILE Chi-restraints excluded: chain O residue 370 VAL Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 391 TYR Chi-restraints excluded: chain O residue 411 MET Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 83 THR Chi-restraints excluded: chain P residue 121 MET Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 187 THR Chi-restraints excluded: chain P residue 203 TYR Chi-restraints excluded: chain P residue 251 HIS Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 49 ILE Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 72 ARG Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain S residue 2 TYR Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 93 THR Chi-restraints excluded: chain V residue 100 MET Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain V residue 133 CYS Chi-restraints excluded: chain V residue 149 SER Chi-restraints excluded: chain Y residue 45 LEU Chi-restraints excluded: chain Y residue 70 PHE Chi-restraints excluded: chain s residue 2 SER Chi-restraints excluded: chain s residue 27 GLU Chi-restraints excluded: chain s residue 63 VAL Chi-restraints excluded: chain s residue 141 MET Chi-restraints excluded: chain s residue 174 ILE Chi-restraints excluded: chain s residue 175 ILE Chi-restraints excluded: chain t residue 144 LEU Chi-restraints excluded: chain t residue 275 THR Chi-restraints excluded: chain t residue 281 PHE Chi-restraints excluded: chain t residue 307 PHE Chi-restraints excluded: chain u residue 447 GLN Chi-restraints excluded: chain u residue 454 LYS Chi-restraints excluded: chain u residue 477 LYS Chi-restraints excluded: chain u residue 543 THR Chi-restraints excluded: chain u residue 596 ILE Chi-restraints excluded: chain u residue 624 VAL Chi-restraints excluded: chain u residue 632 PHE Chi-restraints excluded: chain u residue 801 VAL Chi-restraints excluded: chain u residue 827 ARG Chi-restraints excluded: chain u residue 873 GLU Chi-restraints excluded: chain u residue 891 GLN Chi-restraints excluded: chain u residue 935 THR Chi-restraints excluded: chain u residue 974 LEU Chi-restraints excluded: chain u residue 1003 VAL Chi-restraints excluded: chain u residue 1065 LEU Chi-restraints excluded: chain u residue 1110 VAL Chi-restraints excluded: chain u residue 1128 VAL Chi-restraints excluded: chain u residue 1303 ILE Chi-restraints excluded: chain v residue 61 VAL Chi-restraints excluded: chain v residue 74 THR Chi-restraints excluded: chain v residue 181 MET Chi-restraints excluded: chain v residue 278 LEU Chi-restraints excluded: chain v residue 325 ILE Chi-restraints excluded: chain v residue 364 LEU Chi-restraints excluded: chain v residue 403 SER Chi-restraints excluded: chain v residue 475 ILE Chi-restraints excluded: chain v residue 508 CYS Chi-restraints excluded: chain v residue 516 LEU Chi-restraints excluded: chain v residue 605 LEU Chi-restraints excluded: chain v residue 614 VAL Chi-restraints excluded: chain v residue 736 TYR Chi-restraints excluded: chain v residue 759 THR Chi-restraints excluded: chain v residue 930 LEU Chi-restraints excluded: chain v residue 948 VAL Chi-restraints excluded: chain v residue 988 ASN Chi-restraints excluded: chain v residue 1005 VAL Chi-restraints excluded: chain v residue 1048 ASP Chi-restraints excluded: chain v residue 1062 THR Chi-restraints excluded: chain v residue 1185 MET Chi-restraints excluded: chain x residue 6 THR Chi-restraints excluded: chain x residue 68 LEU Chi-restraints excluded: chain y residue 8 LEU Chi-restraints excluded: chain y residue 50 ASN Chi-restraints excluded: chain y residue 60 ILE Chi-restraints excluded: chain y residue 67 SER Chi-restraints excluded: chain y residue 91 LEU Chi-restraints excluded: chain y residue 96 THR Chi-restraints excluded: chain z residue 17 VAL Chi-restraints excluded: chain z residue 59 THR Chi-restraints excluded: chain z residue 62 VAL Chi-restraints excluded: chain z residue 63 VAL Chi-restraints excluded: chain z residue 88 VAL Chi-restraints excluded: chain z residue 102 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 781 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 461 optimal weight: 2.9990 chunk 592 optimal weight: 6.9990 chunk 458 optimal weight: 0.0980 chunk 682 optimal weight: 4.9990 chunk 452 optimal weight: 6.9990 chunk 807 optimal weight: 3.9990 chunk 505 optimal weight: 2.9990 chunk 492 optimal weight: 0.3980 chunk 372 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 659 GLN A 788 GLN A 792 HIS A 793 ASN ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1982 GLN A1996 ASN ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 141 GLN u 832 GLN u 891 GLN ** u1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 74592 Z= 0.258 Angle : 0.683 14.812 102241 Z= 0.347 Chirality : 0.045 0.395 11356 Planarity : 0.005 0.083 12180 Dihedral : 15.597 170.371 13276 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.51 % Favored : 88.41 % Rotamer: Outliers : 4.44 % Allowed : 15.15 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.04 % Twisted Proline : 0.24 % Twisted General : 0.12 % 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: -2.40 (0.09), residues: 8146 helix: -0.24 (0.10), residues: 2796 sheet: -1.67 (0.16), residues: 996 loop : -2.59 (0.09), residues: 4354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP O 336 HIS 0.008 0.001 HIS A 691 PHE 0.033 0.002 PHE A 166 TYR 0.026 0.002 TYR A 178 ARG 0.009 0.000 ARG v 532 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16292 Ramachandran restraints generated. 8146 Oldfield, 0 Emsley, 8146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16292 Ramachandran restraints generated. 8146 Oldfield, 0 Emsley, 8146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1173 residues out of total 7250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 322 poor density : 851 time to evaluate : 6.256 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: 7 51 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7894 (pp) REVERT: A 45 TYR cc_start: 0.5844 (p90) cc_final: 0.5584 (p90) REVERT: A 316 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7587 (p90) REVERT: A 406 TRP cc_start: 0.8471 (m100) cc_final: 0.8228 (m100) REVERT: A 834 HIS cc_start: 0.7325 (OUTLIER) cc_final: 0.6904 (m-70) REVERT: A 1022 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.7679 (mtp) REVERT: A 1311 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.8147 (m-80) REVERT: A 1370 ARG cc_start: 0.7242 (mmt180) cc_final: 0.6407 (mtp180) REVERT: A 1405 LEU cc_start: 0.6457 (OUTLIER) cc_final: 0.6042 (tt) REVERT: A 1467 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8840 (pp) REVERT: A 1894 GLN cc_start: 0.6796 (tp40) cc_final: 0.6583 (tp-100) REVERT: A 1960 THR cc_start: 0.9127 (OUTLIER) cc_final: 0.8831 (t) REVERT: A 2090 ILE cc_start: 0.6103 (OUTLIER) cc_final: 0.5278 (tp) REVERT: A 2200 MET cc_start: 0.5457 (OUTLIER) cc_final: 0.4897 (tpp) REVERT: B 116 MET cc_start: 0.5589 (mmm) cc_final: 0.5033 (mpp) REVERT: B 134 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7624 (pp) REVERT: B 160 ARG cc_start: 0.4514 (OUTLIER) cc_final: 0.4185 (ptp-170) REVERT: B 381 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8059 (mp) REVERT: B 588 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8711 (mt) REVERT: C 214 ILE cc_start: 0.8752 (mm) cc_final: 0.8491 (mt) REVERT: C 429 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8001 (pt) REVERT: D 185 MET cc_start: 0.5109 (tmm) cc_final: 0.4710 (tpt) REVERT: D 400 PHE cc_start: 0.7124 (OUTLIER) cc_final: 0.6645 (t80) REVERT: D 474 GLU cc_start: 0.7411 (mp0) cc_final: 0.7198 (mp0) REVERT: E 108 ARG cc_start: 0.8319 (mtm110) cc_final: 0.8054 (mtm110) REVERT: E 127 GLN cc_start: 0.8255 (tm-30) cc_final: 0.7964 (tm-30) REVERT: L 37 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8163 (pp) REVERT: O 411 MET cc_start: 0.2734 (OUTLIER) cc_final: 0.0822 (tpt) REVERT: P 79 ASN cc_start: 0.8062 (t0) cc_final: 0.7788 (t0) REVERT: P 208 PRO cc_start: 0.6182 (Cg_endo) cc_final: 0.5787 (Cg_exo) REVERT: R 72 ARG cc_start: 0.6848 (OUTLIER) cc_final: 0.6495 (ppp-140) REVERT: Y 40 MET cc_start: 0.7314 (mmm) cc_final: 0.6680 (mmp) REVERT: Y 70 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.8057 (t80) REVERT: t 141 GLN cc_start: 0.7765 (mt0) cc_final: 0.7564 (mt0) REVERT: u 770 MET cc_start: 0.6887 (mtm) cc_final: 0.6676 (mtm) REVERT: v 948 VAL cc_start: 0.8714 (OUTLIER) cc_final: 0.8457 (p) REVERT: x 73 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8405 (tt) outliers start: 322 outliers final: 231 residues processed: 1085 average time/residue: 0.6832 time to fit residues: 1280.9647 Evaluate side-chains 1069 residues out of total 7250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 816 time to evaluate : 6.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 40 LEU Chi-restraints excluded: chain 1 residue 48 THR Chi-restraints excluded: chain 1 residue 54 CYS Chi-restraints excluded: chain 1 residue 79 PHE Chi-restraints excluded: chain 1 residue 90 THR Chi-restraints excluded: chain 3 residue 547 ASN Chi-restraints excluded: chain 7 residue 16 VAL Chi-restraints excluded: chain 7 residue 51 LEU Chi-restraints excluded: chain 7 residue 70 LEU Chi-restraints excluded: chain 8 residue 461 THR Chi-restraints excluded: chain 8 residue 475 VAL Chi-restraints excluded: chain 8 residue 487 LEU Chi-restraints excluded: chain 8 residue 586 ILE Chi-restraints excluded: chain 8 residue 587 HIS Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 834 HIS Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 876 GLU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 923 ASP Chi-restraints excluded: chain A residue 966 TRP Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1097 ILE Chi-restraints excluded: chain A residue 1099 PHE Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1133 CYS Chi-restraints excluded: chain A residue 1177 VAL Chi-restraints excluded: chain A residue 1211 ASP Chi-restraints excluded: chain A residue 1235 GLU Chi-restraints excluded: chain A residue 1254 THR Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1286 ASP Chi-restraints excluded: chain A residue 1311 PHE Chi-restraints excluded: chain A residue 1329 SER Chi-restraints excluded: chain A residue 1347 ASP Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1406 GLU Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1519 THR Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1548 TYR Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1560 ILE Chi-restraints excluded: chain A residue 1594 CYS Chi-restraints excluded: chain A residue 1608 THR Chi-restraints excluded: chain A residue 1683 LYS Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1711 LEU Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1786 TYR Chi-restraints excluded: chain A residue 1804 ASN Chi-restraints excluded: chain A residue 1938 LEU Chi-restraints excluded: chain A residue 1957 ASP Chi-restraints excluded: chain A residue 1960 THR Chi-restraints excluded: chain A residue 2014 MET Chi-restraints excluded: chain A residue 2090 ILE Chi-restraints excluded: chain A residue 2111 LEU Chi-restraints excluded: chain A residue 2200 MET Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 160 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain B residue 663 CYS Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 179 TYR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 385 TYR Chi-restraints excluded: chain D residue 395 ILE Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 410 SER Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 489 TYR Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 13 ASN Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 49 ARG Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 78 MET Chi-restraints excluded: chain O residue 242 ILE Chi-restraints excluded: chain O residue 243 SER Chi-restraints excluded: chain O residue 269 LEU Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 347 HIS Chi-restraints excluded: chain O residue 350 ILE Chi-restraints excluded: chain O residue 370 VAL Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 391 TYR Chi-restraints excluded: chain O residue 411 MET Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 63 MET Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 83 THR Chi-restraints excluded: chain P residue 121 MET Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 187 THR Chi-restraints excluded: chain P residue 203 TYR Chi-restraints excluded: chain P residue 251 HIS Chi-restraints excluded: chain P residue 276 THR Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 49 ILE Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 72 ARG Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain S residue 2 TYR Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 93 THR Chi-restraints excluded: chain V residue 100 MET Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain V residue 133 CYS Chi-restraints excluded: chain V residue 149 SER Chi-restraints excluded: chain Y residue 43 VAL Chi-restraints excluded: chain Y residue 45 LEU Chi-restraints excluded: chain Y residue 70 PHE Chi-restraints excluded: chain Y residue 77 VAL Chi-restraints excluded: chain s residue 2 SER Chi-restraints excluded: chain s residue 27 GLU Chi-restraints excluded: chain s residue 63 VAL Chi-restraints excluded: chain s residue 89 SER Chi-restraints excluded: chain s residue 141 MET Chi-restraints excluded: chain s residue 174 ILE Chi-restraints excluded: chain s residue 175 ILE Chi-restraints excluded: chain t residue 144 LEU Chi-restraints excluded: chain t residue 202 CYS Chi-restraints excluded: chain t residue 265 CYS Chi-restraints excluded: chain t residue 281 PHE Chi-restraints excluded: chain t residue 307 PHE Chi-restraints excluded: chain u residue 415 LEU Chi-restraints excluded: chain u residue 447 GLN Chi-restraints excluded: chain u residue 454 LYS Chi-restraints excluded: chain u residue 477 LYS Chi-restraints excluded: chain u residue 540 MET Chi-restraints excluded: chain u residue 543 THR Chi-restraints excluded: chain u residue 565 ASP Chi-restraints excluded: chain u residue 596 ILE Chi-restraints excluded: chain u residue 624 VAL Chi-restraints excluded: chain u residue 632 PHE Chi-restraints excluded: chain u residue 827 ARG Chi-restraints excluded: chain u residue 873 GLU Chi-restraints excluded: chain u residue 891 GLN Chi-restraints excluded: chain u residue 935 THR Chi-restraints excluded: chain u residue 974 LEU Chi-restraints excluded: chain u residue 1065 LEU Chi-restraints excluded: chain u residue 1110 VAL Chi-restraints excluded: chain u residue 1128 VAL Chi-restraints excluded: chain u residue 1303 ILE Chi-restraints excluded: chain v residue 61 VAL Chi-restraints excluded: chain v residue 74 THR Chi-restraints excluded: chain v residue 88 VAL Chi-restraints excluded: chain v residue 116 VAL Chi-restraints excluded: chain v residue 181 MET Chi-restraints excluded: chain v residue 278 LEU Chi-restraints excluded: chain v residue 325 ILE Chi-restraints excluded: chain v residue 364 LEU Chi-restraints excluded: chain v residue 402 ASP Chi-restraints excluded: chain v residue 403 SER Chi-restraints excluded: chain v residue 475 ILE Chi-restraints excluded: chain v residue 508 CYS Chi-restraints excluded: chain v residue 516 LEU Chi-restraints excluded: chain v residue 614 VAL Chi-restraints excluded: chain v residue 665 ASN Chi-restraints excluded: chain v residue 736 TYR Chi-restraints excluded: chain v residue 759 THR Chi-restraints excluded: chain v residue 914 ILE Chi-restraints excluded: chain v residue 930 LEU Chi-restraints excluded: chain v residue 943 THR Chi-restraints excluded: chain v residue 948 VAL Chi-restraints excluded: chain v residue 988 ASN Chi-restraints excluded: chain v residue 1005 VAL Chi-restraints excluded: chain v residue 1048 ASP Chi-restraints excluded: chain v residue 1062 THR Chi-restraints excluded: chain x residue 6 THR Chi-restraints excluded: chain x residue 8 HIS Chi-restraints excluded: chain x residue 27 THR Chi-restraints excluded: chain x residue 68 LEU Chi-restraints excluded: chain x residue 73 LEU Chi-restraints excluded: chain y residue 8 LEU Chi-restraints excluded: chain y residue 60 ILE Chi-restraints excluded: chain y residue 67 SER Chi-restraints excluded: chain y residue 91 LEU Chi-restraints excluded: chain y residue 96 THR Chi-restraints excluded: chain z residue 17 VAL Chi-restraints excluded: chain z residue 59 THR Chi-restraints excluded: chain z residue 62 VAL Chi-restraints excluded: chain z residue 63 VAL Chi-restraints excluded: chain z residue 88 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 499 optimal weight: 0.9980 chunk 322 optimal weight: 0.7980 chunk 482 optimal weight: 3.9990 chunk 243 optimal weight: 0.4980 chunk 158 optimal weight: 0.3980 chunk 156 optimal weight: 0.7980 chunk 513 optimal weight: 2.9990 chunk 550 optimal weight: 9.9990 chunk 399 optimal weight: 0.0870 chunk 75 optimal weight: 0.9980 chunk 634 optimal weight: 4.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 509 GLN ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 788 GLN A 792 HIS ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1528 GLN ** A1710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1996 ASN ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 GLN ** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 119 GLN ** P 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 95 GLN ** s 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 820 GLN u 832 GLN u 891 GLN ** u1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 50 ASN ** z 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 74592 Z= 0.172 Angle : 0.659 14.927 102241 Z= 0.333 Chirality : 0.043 0.369 11356 Planarity : 0.005 0.085 12180 Dihedral : 15.501 170.994 13274 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.67 % Favored : 89.30 % Rotamer: Outliers : 3.68 % Allowed : 16.26 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.25 (0.09), residues: 8146 helix: -0.08 (0.10), residues: 2792 sheet: -1.56 (0.16), residues: 984 loop : -2.53 (0.09), residues: 4370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.001 TRP O 336 HIS 0.021 0.001 HIS A1487 PHE 0.040 0.001 PHE A 166 TYR 0.027 0.001 TYR t 297 ARG 0.012 0.000 ARG z 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16292 Ramachandran restraints generated. 8146 Oldfield, 0 Emsley, 8146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16292 Ramachandran restraints generated. 8146 Oldfield, 0 Emsley, 8146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1152 residues out of total 7250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 885 time to evaluate : 6.348 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: 7 51 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7781 (pp) REVERT: A 45 TYR cc_start: 0.5830 (p90) cc_final: 0.5589 (p90) REVERT: A 316 PHE cc_start: 0.8027 (OUTLIER) cc_final: 0.7551 (p90) REVERT: A 406 TRP cc_start: 0.8442 (m100) cc_final: 0.8200 (m100) REVERT: A 834 HIS cc_start: 0.7149 (OUTLIER) cc_final: 0.6721 (m-70) REVERT: A 1022 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.7843 (mtp) REVERT: A 1094 ARG cc_start: 0.7744 (mtp85) cc_final: 0.7475 (mmt-90) REVERT: A 1208 THR cc_start: 0.5270 (OUTLIER) cc_final: 0.4968 (t) REVERT: A 1311 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.8084 (m-80) REVERT: A 1370 ARG cc_start: 0.7130 (mmt180) cc_final: 0.6426 (mtp180) REVERT: A 1405 LEU cc_start: 0.6127 (OUTLIER) cc_final: 0.5854 (tt) REVERT: A 1745 GLU cc_start: 0.7603 (pp20) cc_final: 0.7197 (pp20) REVERT: A 1894 GLN cc_start: 0.6716 (tp40) cc_final: 0.6512 (tp-100) REVERT: A 1960 THR cc_start: 0.9100 (OUTLIER) cc_final: 0.8845 (t) REVERT: A 1967 ILE cc_start: 0.8222 (pp) cc_final: 0.7669 (pt) REVERT: A 2090 ILE cc_start: 0.6143 (OUTLIER) cc_final: 0.5414 (tp) REVERT: A 2200 MET cc_start: 0.5717 (OUTLIER) cc_final: 0.5136 (tpp) REVERT: B 116 MET cc_start: 0.5727 (mmm) cc_final: 0.5246 (mpp) REVERT: B 134 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7548 (pp) REVERT: B 160 ARG cc_start: 0.4550 (OUTLIER) cc_final: 0.4217 (ptp-170) REVERT: B 381 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8023 (mp) REVERT: B 433 MET cc_start: 0.7426 (ttp) cc_final: 0.6818 (ttm) REVERT: B 588 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8658 (mt) REVERT: B 668 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6832 (pm20) REVERT: C 214 ILE cc_start: 0.8612 (mm) cc_final: 0.8344 (mt) REVERT: C 429 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7782 (pt) REVERT: D 185 MET cc_start: 0.5003 (tmm) cc_final: 0.4395 (tpt) REVERT: D 292 TYR cc_start: 0.8464 (m-10) cc_final: 0.8219 (m-10) REVERT: E 108 ARG cc_start: 0.8275 (mtm110) cc_final: 0.8068 (mtm110) REVERT: E 127 GLN cc_start: 0.8246 (tm-30) cc_final: 0.7958 (tm-30) REVERT: L 37 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8148 (pp) REVERT: O 287 MET cc_start: 0.7787 (OUTLIER) cc_final: 0.7527 (mtp) REVERT: O 411 MET cc_start: 0.2838 (OUTLIER) cc_final: 0.0942 (tpt) REVERT: P 79 ASN cc_start: 0.8007 (t0) cc_final: 0.7743 (t0) REVERT: P 208 PRO cc_start: 0.6185 (Cg_endo) cc_final: 0.5790 (Cg_exo) REVERT: R 30 TYR cc_start: 0.6092 (m-80) cc_final: 0.5787 (t80) REVERT: R 72 ARG cc_start: 0.6807 (OUTLIER) cc_final: 0.6485 (ppp-140) REVERT: Y 40 MET cc_start: 0.7369 (mmm) cc_final: 0.6877 (mmp) REVERT: u 477 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7641 (mtmm) REVERT: u 1133 MET cc_start: 0.8684 (mtp) cc_final: 0.8429 (mtp) REVERT: u 1235 GLU cc_start: 0.6937 (tp30) cc_final: 0.6725 (tp30) REVERT: v 131 MET cc_start: 0.8433 (ttm) cc_final: 0.8099 (ttt) REVERT: v 321 MET cc_start: 0.5844 (mmp) cc_final: 0.5464 (mmp) REVERT: v 736 TYR cc_start: 0.7697 (OUTLIER) cc_final: 0.7067 (t80) REVERT: v 948 VAL cc_start: 0.8659 (OUTLIER) cc_final: 0.8406 (p) REVERT: y 50 ASN cc_start: 0.7788 (OUTLIER) cc_final: 0.7341 (t0) REVERT: y 55 GLN cc_start: 0.7996 (tp40) cc_final: 0.7778 (tp40) outliers start: 267 outliers final: 190 residues processed: 1081 average time/residue: 0.6839 time to fit residues: 1274.1040 Evaluate side-chains 1051 residues out of total 7250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 837 time to evaluate : 6.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 40 LEU Chi-restraints excluded: chain 1 residue 54 CYS Chi-restraints excluded: chain 3 residue 547 ASN Chi-restraints excluded: chain 7 residue 16 VAL Chi-restraints excluded: chain 7 residue 51 LEU Chi-restraints excluded: chain 7 residue 70 LEU Chi-restraints excluded: chain 8 residue 461 THR Chi-restraints excluded: chain 8 residue 475 VAL Chi-restraints excluded: chain 8 residue 487 LEU Chi-restraints excluded: chain 8 residue 586 ILE Chi-restraints excluded: chain 8 residue 587 HIS Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 834 HIS Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 876 GLU Chi-restraints excluded: chain A residue 923 ASP Chi-restraints excluded: chain A residue 966 TRP Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain A residue 1097 ILE Chi-restraints excluded: chain A residue 1099 PHE Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1133 CYS Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1211 ASP Chi-restraints excluded: chain A residue 1254 THR Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1311 PHE Chi-restraints excluded: chain A residue 1329 SER Chi-restraints excluded: chain A residue 1347 ASP Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1406 GLU Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1560 ILE Chi-restraints excluded: chain A residue 1581 LEU Chi-restraints excluded: chain A residue 1608 THR Chi-restraints excluded: chain A residue 1664 ILE Chi-restraints excluded: chain A residue 1683 LYS Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1711 LEU Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1786 TYR Chi-restraints excluded: chain A residue 1905 LEU Chi-restraints excluded: chain A residue 1938 LEU Chi-restraints excluded: chain A residue 1957 ASP Chi-restraints excluded: chain A residue 1960 THR Chi-restraints excluded: chain A residue 1971 LEU Chi-restraints excluded: chain A residue 2014 MET Chi-restraints excluded: chain A residue 2090 ILE Chi-restraints excluded: chain A residue 2200 MET Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 160 ARG Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain B residue 663 CYS Chi-restraints excluded: chain B residue 668 GLU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 179 TYR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 395 ILE Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 489 TYR Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 13 ASN Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 49 ARG Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 78 MET Chi-restraints excluded: chain O residue 269 LEU Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 287 MET Chi-restraints excluded: chain O residue 347 HIS Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 411 MET Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 63 MET Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 81 CYS Chi-restraints excluded: chain P residue 83 THR Chi-restraints excluded: chain P residue 116 TYR Chi-restraints excluded: chain P residue 121 MET Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 203 TYR Chi-restraints excluded: chain P residue 251 HIS Chi-restraints excluded: chain P residue 276 THR Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 97 TYR Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 72 ARG Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain S residue 2 TYR Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 93 THR Chi-restraints excluded: chain V residue 100 MET Chi-restraints excluded: chain V residue 149 SER Chi-restraints excluded: chain Y residue 45 LEU Chi-restraints excluded: chain Y residue 96 LYS Chi-restraints excluded: chain s residue 2 SER Chi-restraints excluded: chain s residue 27 GLU Chi-restraints excluded: chain s residue 141 MET Chi-restraints excluded: chain s residue 152 ASP Chi-restraints excluded: chain s residue 174 ILE Chi-restraints excluded: chain s residue 175 ILE Chi-restraints excluded: chain t residue 144 LEU Chi-restraints excluded: chain t residue 202 CYS Chi-restraints excluded: chain t residue 307 PHE Chi-restraints excluded: chain u residue 415 LEU Chi-restraints excluded: chain u residue 447 GLN Chi-restraints excluded: chain u residue 454 LYS Chi-restraints excluded: chain u residue 464 LEU Chi-restraints excluded: chain u residue 477 LYS Chi-restraints excluded: chain u residue 543 THR Chi-restraints excluded: chain u residue 596 ILE Chi-restraints excluded: chain u residue 632 PHE Chi-restraints excluded: chain u residue 827 ARG Chi-restraints excluded: chain u residue 873 GLU Chi-restraints excluded: chain u residue 935 THR Chi-restraints excluded: chain u residue 974 LEU Chi-restraints excluded: chain u residue 1065 LEU Chi-restraints excluded: chain u residue 1128 VAL Chi-restraints excluded: chain u residue 1303 ILE Chi-restraints excluded: chain v residue 61 VAL Chi-restraints excluded: chain v residue 74 THR Chi-restraints excluded: chain v residue 88 VAL Chi-restraints excluded: chain v residue 98 MET Chi-restraints excluded: chain v residue 278 LEU Chi-restraints excluded: chain v residue 325 ILE Chi-restraints excluded: chain v residue 364 LEU Chi-restraints excluded: chain v residue 475 ILE Chi-restraints excluded: chain v residue 484 VAL Chi-restraints excluded: chain v residue 508 CYS Chi-restraints excluded: chain v residue 516 LEU Chi-restraints excluded: chain v residue 664 LEU Chi-restraints excluded: chain v residue 736 TYR Chi-restraints excluded: chain v residue 930 LEU Chi-restraints excluded: chain v residue 943 THR Chi-restraints excluded: chain v residue 948 VAL Chi-restraints excluded: chain v residue 988 ASN Chi-restraints excluded: chain v residue 1005 VAL Chi-restraints excluded: chain v residue 1048 ASP Chi-restraints excluded: chain v residue 1062 THR Chi-restraints excluded: chain x residue 6 THR Chi-restraints excluded: chain x residue 8 HIS Chi-restraints excluded: chain x residue 68 LEU Chi-restraints excluded: chain y residue 8 LEU Chi-restraints excluded: chain y residue 50 ASN Chi-restraints excluded: chain y residue 91 LEU Chi-restraints excluded: chain y residue 94 SER Chi-restraints excluded: chain y residue 96 THR Chi-restraints excluded: chain z residue 17 VAL Chi-restraints excluded: chain z residue 62 VAL Chi-restraints excluded: chain z residue 63 VAL Chi-restraints excluded: chain z residue 88 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 734 optimal weight: 5.9990 chunk 773 optimal weight: 2.9990 chunk 705 optimal weight: 0.2980 chunk 752 optimal weight: 10.0000 chunk 453 optimal weight: 8.9990 chunk 327 optimal weight: 0.9990 chunk 591 optimal weight: 0.7980 chunk 230 optimal weight: 4.9990 chunk 680 optimal weight: 3.9990 chunk 711 optimal weight: 1.9990 chunk 750 optimal weight: 10.0000 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 509 GLN A 160 HIS A 505 ASN ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1996 ASN ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 GLN ** D 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 141 GLN u 832 GLN u1252 GLN ** u1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 58 ASN ** z 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 109 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 74592 Z= 0.254 Angle : 0.691 14.916 102241 Z= 0.348 Chirality : 0.045 0.384 11356 Planarity : 0.005 0.084 12180 Dihedral : 15.484 171.162 13271 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.26 % Favored : 88.69 % Rotamer: Outliers : 3.61 % Allowed : 16.61 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.23 (0.09), residues: 8146 helix: -0.09 (0.10), residues: 2800 sheet: -1.58 (0.16), residues: 1001 loop : -2.49 (0.09), residues: 4345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP O 336 HIS 0.032 0.001 HIS A1487 PHE 0.035 0.001 PHE A 166 TYR 0.039 0.002 TYR O 391 ARG 0.016 0.000 ARG z 85 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16292 Ramachandran restraints generated. 8146 Oldfield, 0 Emsley, 8146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16292 Ramachandran restraints generated. 8146 Oldfield, 0 Emsley, 8146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1094 residues out of total 7250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 832 time to evaluate : 6.259 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: 7 51 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7911 (pp) REVERT: A 45 TYR cc_start: 0.5897 (p90) cc_final: 0.5652 (p90) REVERT: A 316 PHE cc_start: 0.8141 (OUTLIER) cc_final: 0.7514 (p90) REVERT: A 834 HIS cc_start: 0.7312 (OUTLIER) cc_final: 0.6930 (m-70) REVERT: A 1022 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.7882 (mtp) REVERT: A 1208 THR cc_start: 0.5494 (OUTLIER) cc_final: 0.5219 (t) REVERT: A 1311 PHE cc_start: 0.8574 (OUTLIER) cc_final: 0.8211 (m-80) REVERT: A 1370 ARG cc_start: 0.7256 (mmt180) cc_final: 0.6437 (mtp180) REVERT: A 1405 LEU cc_start: 0.6287 (OUTLIER) cc_final: 0.5996 (tt) REVERT: A 1467 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8904 (pp) REVERT: A 1894 GLN cc_start: 0.6799 (tp40) cc_final: 0.6599 (tp-100) REVERT: A 1960 THR cc_start: 0.9137 (OUTLIER) cc_final: 0.8849 (t) REVERT: A 2090 ILE cc_start: 0.6170 (OUTLIER) cc_final: 0.5426 (tp) REVERT: A 2200 MET cc_start: 0.5880 (OUTLIER) cc_final: 0.5364 (tpp) REVERT: B 134 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7437 (pp) REVERT: B 160 ARG cc_start: 0.4566 (OUTLIER) cc_final: 0.4171 (ptp-170) REVERT: B 381 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.7986 (mp) REVERT: B 433 MET cc_start: 0.7508 (ttp) cc_final: 0.6831 (ttm) REVERT: B 668 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6878 (pm20) REVERT: C 214 ILE cc_start: 0.8640 (mm) cc_final: 0.8369 (mt) REVERT: C 429 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.7851 (pp) REVERT: D 185 MET cc_start: 0.4821 (tmm) cc_final: 0.4221 (tpt) REVERT: D 292 TYR cc_start: 0.8513 (m-10) cc_final: 0.8290 (m-10) REVERT: E 127 GLN cc_start: 0.8255 (tm-30) cc_final: 0.7975 (tm-30) REVERT: L 37 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8180 (pp) REVERT: O 287 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7619 (mtp) REVERT: O 411 MET cc_start: 0.2859 (OUTLIER) cc_final: 0.0817 (tpt) REVERT: P 79 ASN cc_start: 0.8061 (t0) cc_final: 0.7793 (t0) REVERT: P 208 PRO cc_start: 0.6264 (Cg_endo) cc_final: 0.5874 (Cg_exo) REVERT: P 227 GLU cc_start: 0.1571 (OUTLIER) cc_final: 0.1042 (pt0) REVERT: R 72 ARG cc_start: 0.6835 (OUTLIER) cc_final: 0.6479 (ppp-140) REVERT: Y 40 MET cc_start: 0.7448 (mmm) cc_final: 0.6957 (mmp) REVERT: t 141 GLN cc_start: 0.7729 (mt0) cc_final: 0.7526 (mt0) REVERT: v 736 TYR cc_start: 0.7884 (OUTLIER) cc_final: 0.7236 (t80) REVERT: v 948 VAL cc_start: 0.8704 (OUTLIER) cc_final: 0.8463 (p) REVERT: y 55 GLN cc_start: 0.7705 (tp40) cc_final: 0.7445 (tp40) REVERT: z 46 ARG cc_start: 0.6593 (mmm160) cc_final: 0.6368 (mmm160) outliers start: 262 outliers final: 209 residues processed: 1026 average time/residue: 0.6797 time to fit residues: 1205.1636 Evaluate side-chains 1041 residues out of total 7250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 809 time to evaluate : 6.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 40 LEU Chi-restraints excluded: chain 1 residue 54 CYS Chi-restraints excluded: chain 3 residue 547 ASN Chi-restraints excluded: chain 7 residue 16 VAL Chi-restraints excluded: chain 7 residue 51 LEU Chi-restraints excluded: chain 7 residue 70 LEU Chi-restraints excluded: chain 8 residue 461 THR Chi-restraints excluded: chain 8 residue 475 VAL Chi-restraints excluded: chain 8 residue 487 LEU Chi-restraints excluded: chain 8 residue 586 ILE Chi-restraints excluded: chain 8 residue 587 HIS Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 834 HIS Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 876 GLU Chi-restraints excluded: chain A residue 923 ASP Chi-restraints excluded: chain A residue 966 TRP Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain A residue 1099 PHE Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1133 CYS Chi-restraints excluded: chain A residue 1177 VAL Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1211 ASP Chi-restraints excluded: chain A residue 1254 THR Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1311 PHE Chi-restraints excluded: chain A residue 1329 SER Chi-restraints excluded: chain A residue 1347 ASP Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1406 GLU Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1548 TYR Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1581 LEU Chi-restraints excluded: chain A residue 1608 THR Chi-restraints excluded: chain A residue 1664 ILE Chi-restraints excluded: chain A residue 1683 LYS Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1711 LEU Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1786 TYR Chi-restraints excluded: chain A residue 1905 LEU Chi-restraints excluded: chain A residue 1938 LEU Chi-restraints excluded: chain A residue 1957 ASP Chi-restraints excluded: chain A residue 1960 THR Chi-restraints excluded: chain A residue 1971 LEU Chi-restraints excluded: chain A residue 2014 MET Chi-restraints excluded: chain A residue 2090 ILE Chi-restraints excluded: chain A residue 2111 LEU Chi-restraints excluded: chain A residue 2200 MET Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 160 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain B residue 663 CYS Chi-restraints excluded: chain B residue 668 GLU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 179 TYR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 395 ILE Chi-restraints excluded: chain D residue 410 SER Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 489 TYR Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 13 ASN Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 49 ARG Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 78 MET Chi-restraints excluded: chain O residue 242 ILE Chi-restraints excluded: chain O residue 269 LEU Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 287 MET Chi-restraints excluded: chain O residue 347 HIS Chi-restraints excluded: chain O residue 370 VAL Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 411 MET Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 63 MET Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 81 CYS Chi-restraints excluded: chain P residue 83 THR Chi-restraints excluded: chain P residue 116 TYR Chi-restraints excluded: chain P residue 121 MET Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 187 THR Chi-restraints excluded: chain P residue 203 TYR Chi-restraints excluded: chain P residue 227 GLU Chi-restraints excluded: chain P residue 251 HIS Chi-restraints excluded: chain P residue 276 THR Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 49 ILE Chi-restraints excluded: chain Q residue 97 TYR Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 72 ARG Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain S residue 2 TYR Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 93 THR Chi-restraints excluded: chain V residue 133 CYS Chi-restraints excluded: chain Y residue 45 LEU Chi-restraints excluded: chain s residue 2 SER Chi-restraints excluded: chain s residue 27 GLU Chi-restraints excluded: chain s residue 141 MET Chi-restraints excluded: chain s residue 152 ASP Chi-restraints excluded: chain s residue 174 ILE Chi-restraints excluded: chain s residue 175 ILE Chi-restraints excluded: chain t residue 144 LEU Chi-restraints excluded: chain t residue 202 CYS Chi-restraints excluded: chain t residue 265 CYS Chi-restraints excluded: chain t residue 307 PHE Chi-restraints excluded: chain u residue 415 LEU Chi-restraints excluded: chain u residue 447 GLN Chi-restraints excluded: chain u residue 454 LYS Chi-restraints excluded: chain u residue 464 LEU Chi-restraints excluded: chain u residue 477 LYS Chi-restraints excluded: chain u residue 540 MET Chi-restraints excluded: chain u residue 543 THR Chi-restraints excluded: chain u residue 565 ASP Chi-restraints excluded: chain u residue 596 ILE Chi-restraints excluded: chain u residue 624 VAL Chi-restraints excluded: chain u residue 632 PHE Chi-restraints excluded: chain u residue 641 ILE Chi-restraints excluded: chain u residue 827 ARG Chi-restraints excluded: chain u residue 873 GLU Chi-restraints excluded: chain u residue 935 THR Chi-restraints excluded: chain u residue 974 LEU Chi-restraints excluded: chain u residue 1065 LEU Chi-restraints excluded: chain u residue 1128 VAL Chi-restraints excluded: chain u residue 1154 LEU Chi-restraints excluded: chain u residue 1303 ILE Chi-restraints excluded: chain v residue 61 VAL Chi-restraints excluded: chain v residue 74 THR Chi-restraints excluded: chain v residue 88 VAL Chi-restraints excluded: chain v residue 98 MET Chi-restraints excluded: chain v residue 278 LEU Chi-restraints excluded: chain v residue 325 ILE Chi-restraints excluded: chain v residue 364 LEU Chi-restraints excluded: chain v residue 475 ILE Chi-restraints excluded: chain v residue 484 VAL Chi-restraints excluded: chain v residue 508 CYS Chi-restraints excluded: chain v residue 516 LEU Chi-restraints excluded: chain v residue 614 VAL Chi-restraints excluded: chain v residue 664 LEU Chi-restraints excluded: chain v residue 736 TYR Chi-restraints excluded: chain v residue 759 THR Chi-restraints excluded: chain v residue 865 VAL Chi-restraints excluded: chain v residue 930 LEU Chi-restraints excluded: chain v residue 943 THR Chi-restraints excluded: chain v residue 948 VAL Chi-restraints excluded: chain v residue 988 ASN Chi-restraints excluded: chain v residue 1005 VAL Chi-restraints excluded: chain v residue 1048 ASP Chi-restraints excluded: chain v residue 1062 THR Chi-restraints excluded: chain x residue 6 THR Chi-restraints excluded: chain x residue 8 HIS Chi-restraints excluded: chain x residue 68 LEU Chi-restraints excluded: chain y residue 8 LEU Chi-restraints excluded: chain y residue 91 LEU Chi-restraints excluded: chain y residue 94 SER Chi-restraints excluded: chain y residue 96 THR Chi-restraints excluded: chain z residue 17 VAL Chi-restraints excluded: chain z residue 59 THR Chi-restraints excluded: chain z residue 62 VAL Chi-restraints excluded: chain z residue 63 VAL Chi-restraints excluded: chain z residue 88 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 494 optimal weight: 0.6980 chunk 795 optimal weight: 0.7980 chunk 485 optimal weight: 8.9990 chunk 377 optimal weight: 5.9990 chunk 553 optimal weight: 8.9990 chunk 834 optimal weight: 6.9990 chunk 768 optimal weight: 0.9980 chunk 664 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 513 optimal weight: 5.9990 chunk 407 optimal weight: 3.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 ASN A 723 ASN A 788 GLN ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 994 ASN ** A1359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1996 ASN B 502 HIS ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN ** O 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 251 HIS ** P 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 796 ASN ** z 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 74592 Z= 0.357 Angle : 0.748 14.900 102241 Z= 0.379 Chirality : 0.047 0.411 11356 Planarity : 0.005 0.089 12180 Dihedral : 15.596 172.871 13271 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.41 % Favored : 87.52 % Rotamer: Outliers : 3.67 % Allowed : 16.71 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.36 (0.09), residues: 8146 helix: -0.26 (0.10), residues: 2802 sheet: -1.69 (0.16), residues: 1008 loop : -2.52 (0.09), residues: 4336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP O 336 HIS 0.029 0.001 HIS A1487 PHE 0.036 0.002 PHE A 166 TYR 0.038 0.002 TYR O 391 ARG 0.010 0.001 ARG t 154 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16292 Ramachandran restraints generated. 8146 Oldfield, 0 Emsley, 8146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16292 Ramachandran restraints generated. 8146 Oldfield, 0 Emsley, 8146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1082 residues out of total 7250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 816 time to evaluate : 6.839 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: 7 51 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7930 (pp) REVERT: A 45 TYR cc_start: 0.5881 (p90) cc_final: 0.5646 (p90) REVERT: A 316 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.7364 (p90) REVERT: A 320 TYR cc_start: 0.7081 (m-80) cc_final: 0.6821 (m-80) REVERT: A 834 HIS cc_start: 0.7473 (OUTLIER) cc_final: 0.7121 (m-70) REVERT: A 1022 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.7977 (mtp) REVERT: A 1208 THR cc_start: 0.5458 (OUTLIER) cc_final: 0.5189 (t) REVERT: A 1311 PHE cc_start: 0.8607 (OUTLIER) cc_final: 0.8282 (m-80) REVERT: A 1370 ARG cc_start: 0.7411 (mmt180) cc_final: 0.6278 (mtp180) REVERT: A 1405 LEU cc_start: 0.6673 (OUTLIER) cc_final: 0.6125 (tt) REVERT: A 1467 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8921 (pp) REVERT: A 1960 THR cc_start: 0.9178 (OUTLIER) cc_final: 0.8864 (t) REVERT: A 2090 ILE cc_start: 0.6238 (OUTLIER) cc_final: 0.5474 (tp) REVERT: A 2200 MET cc_start: 0.5961 (OUTLIER) cc_final: 0.5457 (tpp) REVERT: B 116 MET cc_start: 0.4761 (mmm) cc_final: 0.4071 (tmm) REVERT: B 134 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7497 (pp) REVERT: B 160 ARG cc_start: 0.4952 (OUTLIER) cc_final: 0.4397 (ptp-170) REVERT: B 381 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8101 (mp) REVERT: B 433 MET cc_start: 0.7554 (ttp) cc_final: 0.6845 (ttm) REVERT: C 163 MET cc_start: 0.3640 (tpt) cc_final: 0.3283 (mmt) REVERT: C 214 ILE cc_start: 0.8908 (mm) cc_final: 0.8629 (mt) REVERT: C 325 ARG cc_start: 0.6379 (tpm170) cc_final: 0.6062 (tpp-160) REVERT: C 429 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.7851 (pp) REVERT: E 127 GLN cc_start: 0.8278 (tm-30) cc_final: 0.8031 (tm-30) REVERT: L 37 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8160 (pp) REVERT: O 287 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7598 (mtp) REVERT: O 411 MET cc_start: 0.2997 (OUTLIER) cc_final: 0.0627 (tpt) REVERT: P 79 ASN cc_start: 0.8085 (t0) cc_final: 0.7819 (t0) REVERT: P 208 PRO cc_start: 0.6331 (Cg_endo) cc_final: 0.6040 (Cg_exo) REVERT: P 227 GLU cc_start: 0.1689 (OUTLIER) cc_final: 0.1095 (pt0) REVERT: R 72 ARG cc_start: 0.6848 (OUTLIER) cc_final: 0.6576 (ppp-140) REVERT: V 63 GLN cc_start: 0.7326 (tt0) cc_final: 0.7110 (tt0) REVERT: Y 40 MET cc_start: 0.7474 (mmm) cc_final: 0.7015 (mmp) REVERT: u 447 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.6148 (mp10) REVERT: u 477 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7581 (mtmm) REVERT: u 757 MET cc_start: 0.7783 (mtp) cc_final: 0.7246 (mtm) REVERT: u 1009 MET cc_start: 0.7099 (ptm) cc_final: 0.6689 (ptm) REVERT: v 736 TYR cc_start: 0.7858 (OUTLIER) cc_final: 0.7372 (t80) REVERT: v 948 VAL cc_start: 0.8739 (OUTLIER) cc_final: 0.8512 (p) REVERT: y 55 GLN cc_start: 0.8005 (tp40) cc_final: 0.7788 (tp40) outliers start: 266 outliers final: 215 residues processed: 1015 average time/residue: 0.6834 time to fit residues: 1197.0237 Evaluate side-chains 1029 residues out of total 7250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 790 time to evaluate : 6.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 40 LEU Chi-restraints excluded: chain 1 residue 48 THR Chi-restraints excluded: chain 1 residue 54 CYS Chi-restraints excluded: chain 3 residue 547 ASN Chi-restraints excluded: chain 7 residue 16 VAL Chi-restraints excluded: chain 7 residue 51 LEU Chi-restraints excluded: chain 7 residue 70 LEU Chi-restraints excluded: chain 8 residue 461 THR Chi-restraints excluded: chain 8 residue 475 VAL Chi-restraints excluded: chain 8 residue 487 LEU Chi-restraints excluded: chain 8 residue 586 ILE Chi-restraints excluded: chain 8 residue 587 HIS Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 834 HIS Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 876 GLU Chi-restraints excluded: chain A residue 923 ASP Chi-restraints excluded: chain A residue 966 TRP Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain A residue 1099 PHE Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1133 CYS Chi-restraints excluded: chain A residue 1177 VAL Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1211 ASP Chi-restraints excluded: chain A residue 1235 GLU Chi-restraints excluded: chain A residue 1254 THR Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1311 PHE Chi-restraints excluded: chain A residue 1329 SER Chi-restraints excluded: chain A residue 1347 ASP Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1405 LEU Chi-restraints excluded: chain A residue 1406 GLU Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1548 TYR Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1581 LEU Chi-restraints excluded: chain A residue 1594 CYS Chi-restraints excluded: chain A residue 1608 THR Chi-restraints excluded: chain A residue 1683 LYS Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1711 LEU Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain A residue 1755 SER Chi-restraints excluded: chain A residue 1786 TYR Chi-restraints excluded: chain A residue 1804 ASN Chi-restraints excluded: chain A residue 1905 LEU Chi-restraints excluded: chain A residue 1915 VAL Chi-restraints excluded: chain A residue 1938 LEU Chi-restraints excluded: chain A residue 1957 ASP Chi-restraints excluded: chain A residue 1960 THR Chi-restraints excluded: chain A residue 2014 MET Chi-restraints excluded: chain A residue 2090 ILE Chi-restraints excluded: chain A residue 2200 MET Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 160 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain B residue 663 CYS Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 857 VAL Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain B residue 957 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 179 TYR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 385 TYR Chi-restraints excluded: chain D residue 395 ILE Chi-restraints excluded: chain D residue 410 SER Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 489 TYR Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 13 ASN Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 49 ARG Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 78 MET Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain O residue 242 ILE Chi-restraints excluded: chain O residue 243 SER Chi-restraints excluded: chain O residue 269 LEU Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 287 MET Chi-restraints excluded: chain O residue 347 HIS Chi-restraints excluded: chain O residue 370 VAL Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 411 MET Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 63 MET Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 81 CYS Chi-restraints excluded: chain P residue 83 THR Chi-restraints excluded: chain P residue 116 TYR Chi-restraints excluded: chain P residue 121 MET Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 187 THR Chi-restraints excluded: chain P residue 203 TYR Chi-restraints excluded: chain P residue 227 GLU Chi-restraints excluded: chain P residue 251 HIS Chi-restraints excluded: chain P residue 276 THR Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 49 ILE Chi-restraints excluded: chain Q residue 97 TYR Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 72 ARG Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 214 THR Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 84 ASP Chi-restraints excluded: chain V residue 133 CYS Chi-restraints excluded: chain s residue 2 SER Chi-restraints excluded: chain s residue 27 GLU Chi-restraints excluded: chain s residue 89 SER Chi-restraints excluded: chain s residue 141 MET Chi-restraints excluded: chain s residue 174 ILE Chi-restraints excluded: chain s residue 175 ILE Chi-restraints excluded: chain t residue 144 LEU Chi-restraints excluded: chain t residue 202 CYS Chi-restraints excluded: chain t residue 265 CYS Chi-restraints excluded: chain t residue 307 PHE Chi-restraints excluded: chain u residue 415 LEU Chi-restraints excluded: chain u residue 447 GLN Chi-restraints excluded: chain u residue 454 LYS Chi-restraints excluded: chain u residue 464 LEU Chi-restraints excluded: chain u residue 467 LEU Chi-restraints excluded: chain u residue 477 LYS Chi-restraints excluded: chain u residue 540 MET Chi-restraints excluded: chain u residue 543 THR Chi-restraints excluded: chain u residue 565 ASP Chi-restraints excluded: chain u residue 596 ILE Chi-restraints excluded: chain u residue 624 VAL Chi-restraints excluded: chain u residue 632 PHE Chi-restraints excluded: chain u residue 827 ARG Chi-restraints excluded: chain u residue 873 GLU Chi-restraints excluded: chain u residue 935 THR Chi-restraints excluded: chain u residue 974 LEU Chi-restraints excluded: chain u residue 1003 VAL Chi-restraints excluded: chain u residue 1065 LEU Chi-restraints excluded: chain u residue 1128 VAL Chi-restraints excluded: chain u residue 1303 ILE Chi-restraints excluded: chain v residue 61 VAL Chi-restraints excluded: chain v residue 74 THR Chi-restraints excluded: chain v residue 278 LEU Chi-restraints excluded: chain v residue 325 ILE Chi-restraints excluded: chain v residue 364 LEU Chi-restraints excluded: chain v residue 402 ASP Chi-restraints excluded: chain v residue 403 SER Chi-restraints excluded: chain v residue 475 ILE Chi-restraints excluded: chain v residue 484 VAL Chi-restraints excluded: chain v residue 508 CYS Chi-restraints excluded: chain v residue 516 LEU Chi-restraints excluded: chain v residue 577 TYR Chi-restraints excluded: chain v residue 614 VAL Chi-restraints excluded: chain v residue 664 LEU Chi-restraints excluded: chain v residue 736 TYR Chi-restraints excluded: chain v residue 759 THR Chi-restraints excluded: chain v residue 865 VAL Chi-restraints excluded: chain v residue 930 LEU Chi-restraints excluded: chain v residue 943 THR Chi-restraints excluded: chain v residue 948 VAL Chi-restraints excluded: chain v residue 988 ASN Chi-restraints excluded: chain v residue 1005 VAL Chi-restraints excluded: chain v residue 1048 ASP Chi-restraints excluded: chain v residue 1062 THR Chi-restraints excluded: chain x residue 6 THR Chi-restraints excluded: chain x residue 8 HIS Chi-restraints excluded: chain x residue 27 THR Chi-restraints excluded: chain x residue 68 LEU Chi-restraints excluded: chain y residue 8 LEU Chi-restraints excluded: chain y residue 91 LEU Chi-restraints excluded: chain y residue 96 THR Chi-restraints excluded: chain z residue 17 VAL Chi-restraints excluded: chain z residue 62 VAL Chi-restraints excluded: chain z residue 63 VAL Chi-restraints excluded: chain z residue 88 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 528 optimal weight: 4.9990 chunk 708 optimal weight: 0.9980 chunk 203 optimal weight: 2.9990 chunk 612 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 184 optimal weight: 0.6980 chunk 665 optimal weight: 0.9980 chunk 278 optimal weight: 7.9990 chunk 683 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 122 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 788 GLN A 858 GLN ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 994 ASN A1013 ASN ** A1359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1996 ASN ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 251 HIS ** P 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 832 GLN u 942 ASN ** u1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.137935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.106944 restraints weight = 151901.444| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.46 r_work: 0.3430 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 74592 Z= 0.208 Angle : 0.689 15.114 102241 Z= 0.348 Chirality : 0.044 0.387 11356 Planarity : 0.005 0.085 12180 Dihedral : 15.510 170.975 13271 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.21 % Favored : 88.74 % Rotamer: Outliers : 3.37 % Allowed : 17.33 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.22 (0.09), residues: 8146 helix: -0.10 (0.10), residues: 2795 sheet: -1.61 (0.16), residues: 995 loop : -2.46 (0.09), residues: 4356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.002 TRP O 336 HIS 0.024 0.001 HIS A1487 PHE 0.037 0.001 PHE A 166 TYR 0.035 0.002 TYR O 391 ARG 0.012 0.000 ARG E 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20782.84 seconds wall clock time: 364 minutes 21.35 seconds (21861.35 seconds total)