Starting phenix.real_space_refine on Tue Mar 19 08:14:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c0f_7324/03_2024/6c0f_7324_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c0f_7324/03_2024/6c0f_7324.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c0f_7324/03_2024/6c0f_7324.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c0f_7324/03_2024/6c0f_7324.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c0f_7324/03_2024/6c0f_7324_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c0f_7324/03_2024/6c0f_7324_neut.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 1602 5.49 5 S 137 5.16 5 C 51832 2.51 5 N 16655 2.21 5 O 21513 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 49": "NH1" <-> "NH2" Residue "A ARG 275": "NH1" <-> "NH2" Residue "A ARG 288": "NH1" <-> "NH2" Residue "A ARG 350": "NH1" <-> "NH2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "C ARG 107": "NH1" <-> "NH2" Residue "C TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 246": "NH1" <-> "NH2" Residue "C ARG 326": "NH1" <-> "NH2" Residue "D ARG 18": "NH1" <-> "NH2" Residue "D PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 29": "NH1" <-> "NH2" Residue "D ARG 79": "NH1" <-> "NH2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D ARG 150": "NH1" <-> "NH2" Residue "E PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 30": "NH1" <-> "NH2" Residue "F ARG 88": "NH1" <-> "NH2" Residue "F ARG 100": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 57": "NH1" <-> "NH2" Residue "G ARG 68": "NH1" <-> "NH2" Residue "G PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 204": "NH1" <-> "NH2" Residue "I ARG 34": "NH1" <-> "NH2" Residue "I ARG 48": "NH1" <-> "NH2" Residue "I ARG 126": "NH1" <-> "NH2" Residue "I ARG 189": "NH1" <-> "NH2" Residue "I ARG 205": "NH1" <-> "NH2" Residue "I ARG 245": "NH1" <-> "NH2" Residue "I TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 34": "NH1" <-> "NH2" Residue "K ARG 170": "NH1" <-> "NH2" Residue "K ARG 240": "NH1" <-> "NH2" Residue "K ARG 277": "NH1" <-> "NH2" Residue "K ARG 285": "NH1" <-> "NH2" Residue "L ARG 42": "NH1" <-> "NH2" Residue "L ARG 49": "NH1" <-> "NH2" Residue "L ARG 73": "NH1" <-> "NH2" Residue "L PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 19": "NH1" <-> "NH2" Residue "M ARG 108": "NH1" <-> "NH2" Residue "N ARG 20": "NH1" <-> "NH2" Residue "N ARG 144": "NH1" <-> "NH2" Residue "N ARG 188": "NH1" <-> "NH2" Residue "O TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 18": "NH1" <-> "NH2" Residue "P ARG 56": "NH1" <-> "NH2" Residue "P ARG 126": "NH1" <-> "NH2" Residue "Q ARG 92": "NH1" <-> "NH2" Residue "S ARG 28": "NH1" <-> "NH2" Residue "S ARG 117": "NH1" <-> "NH2" Residue "V ARG 32": "NH1" <-> "NH2" Residue "V ARG 70": "NH1" <-> "NH2" Residue "V ARG 88": "NH1" <-> "NH2" Residue "W ARG 400": "NH1" <-> "NH2" Residue "W TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 121": "NH1" <-> "NH2" Residue "7 ARG 7": "NH1" <-> "NH2" Residue "7 ARG 11": "NH1" <-> "NH2" Residue "7 ARG 56": "NH1" <-> "NH2" Residue "7 ARG 172": "NH1" <-> "NH2" Residue "7 ARG 175": "NH1" <-> "NH2" Residue "7 ARG 221": "NH1" <-> "NH2" Residue "7 ARG 225": "NH1" <-> "NH2" Residue "b ARG 60": "NH1" <-> "NH2" Residue "b ARG 263": "NH1" <-> "NH2" Residue "b ARG 274": "NH1" <-> "NH2" Residue "b ARG 275": "NH1" <-> "NH2" Residue "e ARG 24": "NH1" <-> "NH2" Residue "e TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 48": "NH1" <-> "NH2" Residue "f ARG 60": "NH1" <-> "NH2" Residue "h TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 105": "NH1" <-> "NH2" Residue "h TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 99": "NH1" <-> "NH2" Residue "j ARG 56": "NH1" <-> "NH2" Residue "j ARG 63": "NH1" <-> "NH2" Residue "n ARG 13": "NH1" <-> "NH2" Residue "n ARG 18": "NH1" <-> "NH2" Residue "n ARG 23": "NH1" <-> "NH2" Residue "n ARG 34": "NH1" <-> "NH2" Residue "n ARG 88": "NH1" <-> "NH2" Residue "n ARG 92": "NH1" <-> "NH2" Residue "n ARG 104": "NH1" <-> "NH2" Residue "n ARG 109": "NH1" <-> "NH2" Residue "n ARG 369": "NH1" <-> "NH2" Residue "n ARG 414": "NH1" <-> "NH2" Residue "n ARG 424": "NH1" <-> "NH2" Residue "o ARG 97": "NH1" <-> "NH2" Residue "o ARG 121": "NH1" <-> "NH2" Residue "o ARG 182": "NH1" <-> "NH2" Residue "o ARG 207": "NH1" <-> "NH2" Residue "p ARG 71": "NH1" <-> "NH2" Residue "p ARG 80": "NH1" <-> "NH2" Residue "p ARG 112": "NH1" <-> "NH2" Residue "p ARG 135": "NH1" <-> "NH2" Residue "p PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 200": "NH1" <-> "NH2" Residue "p ARG 244": "NH1" <-> "NH2" Residue "p ARG 286": "NH1" <-> "NH2" Residue "p ARG 340": "NH1" <-> "NH2" Residue "p ARG 376": "NH1" <-> "NH2" Residue "s ARG 265": "NH1" <-> "NH2" Residue "s ARG 275": "NH1" <-> "NH2" Residue "s ARG 281": "NH1" <-> "NH2" Residue "s ARG 287": "NH1" <-> "NH2" Residue "s ARG 375": "NH1" <-> "NH2" Residue "s ARG 387": "NH1" <-> "NH2" Residue "t ARG 74": "NH1" <-> "NH2" Residue "t ARG 130": "NH1" <-> "NH2" Residue "t ARG 148": "NH1" <-> "NH2" Residue "t ARG 205": "NH1" <-> "NH2" Residue "t ARG 211": "NH1" <-> "NH2" Residue "t ARG 299": "NH1" <-> "NH2" Residue "u ARG 2": "NH1" <-> "NH2" Residue "u ARG 23": "NH1" <-> "NH2" Residue "u ARG 33": "NH1" <-> "NH2" Residue "u ARG 43": "NH1" <-> "NH2" Residue "u ARG 44": "NH1" <-> "NH2" Residue "u ARG 56": "NH1" <-> "NH2" Residue "u PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 75": "NH1" <-> "NH2" Residue "u ARG 105": "NH1" <-> "NH2" Residue "u ARG 113": "NH1" <-> "NH2" Residue "u ARG 122": "NH1" <-> "NH2" Residue "v ARG 62": "NH1" <-> "NH2" Residue "v ARG 126": "NH1" <-> "NH2" Residue "w ARG 187": "NH1" <-> "NH2" Residue "y TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 85": "NH1" <-> "NH2" Residue "y ARG 100": "NH1" <-> "NH2" Residue "y TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 223": "NH1" <-> "NH2" Residue "z ARG 15": "NH1" <-> "NH2" Residue "z ARG 60": "NH1" <-> "NH2" Residue "z ARG 115": "NH1" <-> "NH2" Residue "z ARG 117": "NH1" <-> "NH2" Residue "z ARG 127": "NH1" <-> "NH2" Residue "z ARG 235": "NH1" <-> "NH2" Residue "z ARG 247": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 91742 Number of models: 1 Model: "" Number of chains: 46 Chain: "1" Number of atoms: 29055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1357, 29055 Classifications: {'RNA': 1357} Modifications used: {'rna2p_pur': 128, 'rna2p_pyr': 87, 'rna3p_pur': 629, 'rna3p_pyr': 513} Link IDs: {'rna2p': 214, 'rna3p': 1142} Chain breaks: 13 Chain: "2" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3353 Classifications: {'RNA': 158} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 17, 'rna3p_pur': 61, 'rna3p_pyr': 63} Link IDs: {'rna2p': 33, 'rna3p': 124} Chain: "6" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1838 Classifications: {'RNA': 87} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 19, 'rna3p_pur': 32, 'rna3p_pyr': 28} Link IDs: {'rna2p': 26, 'rna3p': 60} Chain breaks: 1 Chain: "A" Number of atoms: 3126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3126 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 12, 'TRANS': 381} Chain breaks: 1 Chain: "B" Number of atoms: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2577 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 11, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2418 Classifications: {'peptide': 314} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 298} Chain breaks: 1 Chain: "D" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1578 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 6, 'TRANS': 183} Chain: "E" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1366 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 161} Chain: "F" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1941 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain: "G" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1453 Classifications: {'peptide': 187} Link IDs: {'CIS': 2, 'PTRANS': 8, 'TRANS': 176} Chain: "I" Number of atoms: 2429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2429 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 12, 'TRANS': 275} Chain: "K" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2099 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 10, 'TRANS': 249} Chain breaks: 1 Chain: "L" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 845 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "M" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 997 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "N" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1509 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 4, 'TRANS': 171} Chain breaks: 1 Chain: "O" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1451 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 176} Chain breaks: 1 Chain: "P" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 975 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain breaks: 2 Chain: "Q" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1015 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 7, 'TRANS': 124} Chain: "S" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1437 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "V" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 903 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "W" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 806 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 6, 'TRANS': 91} Chain: "Y" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 993 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "7" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1295 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain breaks: 1 Chain: "8" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 836 Classifications: {'peptide': 98} Link IDs: {'TRANS': 97} Chain: "b" Number of atoms: 1919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1919 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 228} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "e" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 914 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain breaks: 1 Chain: "f" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 850 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "h" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 969 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "i" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 665 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain: "j" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 575 Classifications: {'peptide': 72} Link IDs: {'PCIS': 1, 'TRANS': 70} Chain: "x" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 140 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'TRANS': 27} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'UNK:plan-1': 28} Unresolved non-hydrogen planarities: 28 Chain: "m" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 370 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'TRANS': 73} Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 222 Unresolved non-hydrogen dihedrals: 74 Planarities with less than four sites: {'UNK:plan-1': 74} Unresolved non-hydrogen planarities: 74 Chain: "n" Number of atoms: 2794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2794 Classifications: {'peptide': 341} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 320} Chain breaks: 3 Chain: "o" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1107 Classifications: {'peptide': 133} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 128} Chain: "p" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3486 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 21, 'TRANS': 415} Chain breaks: 1 Chain: "q" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 1409 Classifications: {'peptide': 285} Incomplete info: {'backbone_only': 16, 'truncation_to_alanine': 269} Link IDs: {'TRANS': 284} Chain breaks: 5 Unresolved non-hydrogen bonds: 586 Unresolved non-hydrogen angles: 887 Unresolved non-hydrogen dihedrals: 285 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'UNK:plan-1': 285} Unresolved non-hydrogen planarities: 285 Chain: "s" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1069 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 8, 'TRANS': 148} Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 73 Planarities with less than four sites: {'UNK:plan-1': 73} Unresolved non-hydrogen planarities: 73 Chain: "t" Number of atoms: 1965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1965 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 9, 'TRANS': 238} Chain breaks: 1 Chain: "u" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1088 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "v" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1795 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 11, 'TRANS': 213} Chain breaks: 1 Chain: "w" Number of atoms: 562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 562 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain: "y" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1709 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "z" Number of atoms: 2058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2058 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 7, 'TRANS': 235} Chain breaks: 1 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "u" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 42483 SG CYS D 15 194.310 105.763 129.296 1.00 48.84 S ATOM 42585 SG CYS D 28 194.871 107.518 126.205 1.00 48.96 S ATOM 42665 SG CYS D 38 194.712 104.487 125.925 1.00 41.05 S ATOM 42704 SG CYS D 43 197.337 105.725 127.106 1.00 41.34 S ATOM 71658 SG CYS j 19 130.007 90.737 174.531 1.00 76.24 S ATOM 71683 SG CYS j 22 132.452 91.435 171.901 1.00 80.69 S ATOM 71783 SG CYS j 34 131.110 88.059 172.311 1.00 77.17 S ATOM 71801 SG CYS j 37 133.332 89.398 174.734 1.00 76.14 S ATOM 84573 SG CYS u 6 57.787 76.209 82.607 1.00182.25 S ATOM 84600 SG CYS u 9 57.416 79.472 84.196 1.00191.89 S ATOM 84785 SG CYS u 32 60.398 78.631 82.871 1.00189.48 S ATOM 84817 SG CYS u 36 58.751 77.568 85.711 1.00178.40 S Time building chain proxies: 35.35, per 1000 atoms: 0.39 Number of scatterers: 91742 At special positions: 0 Unit cell: (269.1, 201.5, 323.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 137 16.00 P 1602 15.00 O 21513 8.00 N 16655 7.00 C 51832 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 37.36 Conformation dependent library (CDL) restraints added in 8.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 401 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 38 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 28 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 43 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 15 " pdb=" ZN j 101 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 37 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 34 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 22 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 19 " pdb=" ZN u 300 " pdb="ZN ZN u 300 " - pdb=" SG CYS u 36 " pdb="ZN ZN u 300 " - pdb=" SG CYS u 9 " pdb="ZN ZN u 300 " - pdb=" SG CYS u 32 " pdb="ZN ZN u 300 " - pdb=" SG CYS u 6 " Number of angles added : 18 13458 Ramachandran restraints generated. 6729 Oldfield, 0 Emsley, 6729 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13926 Finding SS restraints... Secondary structure from input PDB file: 253 helices and 73 sheets defined 45.2% alpha, 17.6% beta 501 base pairs and 845 stacking pairs defined. Time for finding SS restraints: 28.64 Creating SS restraints... Processing helix chain 'A' and resid 42 through 46 removed outlier: 4.005A pdb=" N TYR A 46 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 327 through 331 Processing helix chain 'B' and resid 111 through 119 removed outlier: 3.679A pdb=" N TYR B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 135 removed outlier: 3.645A pdb=" N ALA B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 154 Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 187 through 198 Processing helix chain 'B' and resid 204 through 208 Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'C' and resid 31 through 44 removed outlier: 3.682A pdb=" N SER C 41 " --> pdb=" O THR C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 132 removed outlier: 3.924A pdb=" N ALA C 130 " --> pdb=" O ILE C 126 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL C 131 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA C 132 " --> pdb=" O ALA C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 139 Processing helix chain 'C' and resid 153 through 159 Processing helix chain 'C' and resid 161 through 173 Processing helix chain 'C' and resid 174 through 184 Processing helix chain 'C' and resid 190 through 195 removed outlier: 3.775A pdb=" N LYS C 193 " --> pdb=" O GLY C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 219 Processing helix chain 'C' and resid 234 through 239 Processing helix chain 'C' and resid 240 through 243 Processing helix chain 'C' and resid 252 through 263 removed outlier: 4.259A pdb=" N ASP C 259 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN C 260 " --> pdb=" O THR C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 291 removed outlier: 3.670A pdb=" N ILE C 289 " --> pdb=" O ASP C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 299 Processing helix chain 'C' and resid 320 through 327 removed outlier: 3.524A pdb=" N LEU C 327 " --> pdb=" O VAL C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 338 removed outlier: 4.377A pdb=" N VAL C 333 " --> pdb=" O PRO C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 342 Processing helix chain 'D' and resid 3 through 13 Processing helix chain 'D' and resid 66 through 70 Processing helix chain 'D' and resid 85 through 97 Processing helix chain 'D' and resid 101 through 128 removed outlier: 3.614A pdb=" N ARG D 105 " --> pdb=" O SER D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 156 Processing helix chain 'D' and resid 157 through 173 removed outlier: 3.528A pdb=" N ALA D 161 " --> pdb=" O LYS D 157 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY D 173 " --> pdb=" O ARG D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 191 Processing helix chain 'E' and resid 68 through 73 Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.669A pdb=" N LYS E 100 " --> pdb=" O ASN E 97 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE E 101 " --> pdb=" O VAL E 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 97 through 101' Processing helix chain 'E' and resid 103 through 107 Processing helix chain 'E' and resid 112 through 122 removed outlier: 3.861A pdb=" N GLU E 118 " --> pdb=" O LYS E 114 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA E 119 " --> pdb=" O GLU E 115 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASN E 120 " --> pdb=" O LYS E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 150 removed outlier: 3.743A pdb=" N VAL E 135 " --> pdb=" O LYS E 131 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA E 144 " --> pdb=" O VAL E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 161 Processing helix chain 'F' and resid 9 through 73 removed outlier: 3.653A pdb=" N ALA F 35 " --> pdb=" O ALA F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 106 Processing helix chain 'F' and resid 120 through 131 Processing helix chain 'F' and resid 140 through 151 Processing helix chain 'F' and resid 165 through 174 removed outlier: 3.640A pdb=" N ILE F 169 " --> pdb=" O ASP F 165 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN F 172 " --> pdb=" O ILE F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 190 removed outlier: 3.509A pdb=" N LEU F 184 " --> pdb=" O SER F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 202 Processing helix chain 'F' and resid 234 through 244 removed outlier: 3.866A pdb=" N LYS F 238 " --> pdb=" O GLU F 234 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS F 241 " --> pdb=" O ASN F 237 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 62 Processing helix chain 'G' and resid 63 through 69 removed outlier: 3.728A pdb=" N ILE G 67 " --> pdb=" O LYS G 63 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 95 Processing helix chain 'G' and resid 101 through 119 Processing helix chain 'G' and resid 135 through 143 Processing helix chain 'G' and resid 159 through 163 Processing helix chain 'G' and resid 164 through 173 removed outlier: 4.659A pdb=" N ALA G 168 " --> pdb=" O VAL G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 189 removed outlier: 3.518A pdb=" N LEU G 189 " --> pdb=" O ARG G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 222 Processing helix chain 'G' and resid 226 through 231 removed outlier: 3.839A pdb=" N LYS G 231 " --> pdb=" O ASP G 227 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 44 Processing helix chain 'I' and resid 44 through 55 removed outlier: 4.317A pdb=" N ARG I 48 " --> pdb=" O ASN I 44 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU I 49 " --> pdb=" O PRO I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 84 Processing helix chain 'I' and resid 104 through 118 removed outlier: 3.862A pdb=" N TYR I 108 " --> pdb=" O LYS I 104 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU I 116 " --> pdb=" O ASN I 112 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE I 117 " --> pdb=" O ILE I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 131 through 142 Processing helix chain 'I' and resid 204 through 218 Processing helix chain 'I' and resid 283 through 288 Processing helix chain 'K' and resid 33 through 49 Processing helix chain 'K' and resid 70 through 76 Processing helix chain 'K' and resid 106 through 117 removed outlier: 4.026A pdb=" N THR K 116 " --> pdb=" O GLU K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 135 Processing helix chain 'K' and resid 136 through 148 removed outlier: 3.517A pdb=" N LEU K 140 " --> pdb=" O SER K 136 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN K 143 " --> pdb=" O ASP K 139 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER K 146 " --> pdb=" O ASP K 142 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU K 147 " --> pdb=" O GLN K 143 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 163 Processing helix chain 'K' and resid 166 through 176 removed outlier: 3.548A pdb=" N GLN K 176 " --> pdb=" O ALA K 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 188 removed outlier: 3.928A pdb=" N THR K 188 " --> pdb=" O ASP K 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 184 through 188' Processing helix chain 'K' and resid 190 through 195 removed outlier: 3.983A pdb=" N GLY K 195 " --> pdb=" O PRO K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 201 removed outlier: 3.506A pdb=" N TYR K 199 " --> pdb=" O GLY K 195 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS K 201 " --> pdb=" O LYS K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 218 through 232 removed outlier: 3.627A pdb=" N LYS K 227 " --> pdb=" O THR K 223 " (cutoff:3.500A) Processing helix chain 'K' and resid 255 through 274 Processing helix chain 'K' and resid 296 through 302 removed outlier: 4.162A pdb=" N GLU K 302 " --> pdb=" O LEU K 298 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 46 removed outlier: 3.755A pdb=" N LYS L 32 " --> pdb=" O GLN L 28 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL L 33 " --> pdb=" O ALA L 29 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA L 43 " --> pdb=" O ARG L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 84 removed outlier: 3.520A pdb=" N VAL L 80 " --> pdb=" O THR L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 91 Processing helix chain 'L' and resid 105 through 123 removed outlier: 3.520A pdb=" N ILE L 123 " --> pdb=" O TYR L 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 63 No H-bonds generated for 'chain 'M' and resid 61 through 63' Processing helix chain 'M' and resid 77 through 89 Processing helix chain 'M' and resid 89 through 96 Processing helix chain 'M' and resid 97 through 111 Processing helix chain 'M' and resid 113 through 135 Processing helix chain 'N' and resid 3 through 12 Processing helix chain 'N' and resid 16 through 33 removed outlier: 3.816A pdb=" N TRP N 28 " --> pdb=" O ARG N 24 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS N 33 " --> pdb=" O GLU N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 52 Processing helix chain 'N' and resid 97 through 110 removed outlier: 3.615A pdb=" N VAL N 106 " --> pdb=" O ALA N 102 " (cutoff:3.500A) Processing helix chain 'N' and resid 139 through 144 Processing helix chain 'N' and resid 148 through 157 Proline residue: N 154 - end of helix removed outlier: 3.591A pdb=" N LYS N 157 " --> pdb=" O PRO N 154 " (cutoff:3.500A) Processing helix chain 'N' and resid 165 through 173 Processing helix chain 'N' and resid 183 through 196 Processing helix chain 'O' and resid 16 through 29 removed outlier: 3.503A pdb=" N LEU O 28 " --> pdb=" O ALA O 24 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 39 No H-bonds generated for 'chain 'O' and resid 37 through 39' Processing helix chain 'O' and resid 46 through 59 removed outlier: 3.665A pdb=" N ASN O 50 " --> pdb=" O GLU O 46 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 88 removed outlier: 3.623A pdb=" N MET O 87 " --> pdb=" O ALA O 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 101 Processing helix chain 'O' and resid 111 through 115 Processing helix chain 'O' and resid 120 through 123 Processing helix chain 'O' and resid 124 through 129 Processing helix chain 'O' and resid 138 through 146 Processing helix chain 'O' and resid 149 through 186 Processing helix chain 'O' and resid 188 through 198 Processing helix chain 'P' and resid 25 through 37 removed outlier: 3.580A pdb=" N ILE P 36 " --> pdb=" O THR P 32 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN P 37 " --> pdb=" O ALA P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 53 Processing helix chain 'P' and resid 84 through 106 removed outlier: 3.534A pdb=" N VAL P 88 " --> pdb=" O PRO P 84 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE P 90 " --> pdb=" O LYS P 86 " (cutoff:3.500A) Processing helix chain 'Q' and resid 23 through 40 Processing helix chain 'Q' and resid 42 through 53 removed outlier: 4.445A pdb=" N LYS Q 46 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 72 Processing helix chain 'Q' and resid 107 through 117 Processing helix chain 'Q' and resid 124 through 131 Processing helix chain 'S' and resid 33 through 49 removed outlier: 3.895A pdb=" N LYS S 47 " --> pdb=" O TYR S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 98 through 115 removed outlier: 3.524A pdb=" N ALA S 102 " --> pdb=" O SER S 98 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG S 115 " --> pdb=" O ALA S 111 " (cutoff:3.500A) Processing helix chain 'S' and resid 137 through 142 Processing helix chain 'S' and resid 143 through 145 No H-bonds generated for 'chain 'S' and resid 143 through 145' Processing helix chain 'V' and resid 119 through 126 Processing helix chain 'V' and resid 126 through 132 Processing helix chain 'W' and resid 379 through 385 removed outlier: 3.537A pdb=" N LYS W 383 " --> pdb=" O PRO W 379 " (cutoff:3.500A) Processing helix chain 'W' and resid 398 through 404 Processing helix chain 'W' and resid 425 through 430 removed outlier: 3.847A pdb=" N ASN W 429 " --> pdb=" O ASP W 425 " (cutoff:3.500A) Processing helix chain 'W' and resid 448 through 466 removed outlier: 4.416A pdb=" N LYS W 452 " --> pdb=" O GLU W 448 " (cutoff:3.500A) Processing helix chain 'Y' and resid 11 through 21 removed outlier: 3.521A pdb=" N THR Y 21 " --> pdb=" O LYS Y 17 " (cutoff:3.500A) Processing helix chain 'Y' and resid 23 through 31 removed outlier: 3.915A pdb=" N VAL Y 29 " --> pdb=" O SER Y 25 " (cutoff:3.500A) Processing helix chain 'Y' and resid 36 through 44 Processing helix chain 'Y' and resid 75 through 78 Processing helix chain 'Y' and resid 100 through 102 No H-bonds generated for 'chain 'Y' and resid 100 through 102' Processing helix chain 'Y' and resid 112 through 122 Processing helix chain '7' and resid 3 through 12 Processing helix chain '7' and resid 33 through 40 Processing helix chain '7' and resid 45 through 54 Processing helix chain '7' and resid 157 through 168 Processing helix chain '7' and resid 178 through 192 Processing helix chain '7' and resid 196 through 201 removed outlier: 3.512A pdb=" N PHE 7 201 " --> pdb=" O LYS 7 197 " (cutoff:3.500A) Processing helix chain '7' and resid 213 through 226 Processing helix chain '8' and resid 297 through 314 removed outlier: 3.566A pdb=" N LYS 8 314 " --> pdb=" O LYS 8 310 " (cutoff:3.500A) Processing helix chain '8' and resid 315 through 337 Processing helix chain '8' and resid 343 through 393 removed outlier: 3.552A pdb=" N LEU 8 347 " --> pdb=" O ASP 8 343 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG 8 348 " --> pdb=" O GLU 8 344 " (cutoff:3.500A) Processing helix chain 'b' and resid 42 through 56 removed outlier: 4.141A pdb=" N LEU b 48 " --> pdb=" O ARG b 44 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ILE b 49 " --> pdb=" O HIS b 45 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN b 50 " --> pdb=" O ARG b 46 " (cutoff:3.500A) Processing helix chain 'b' and resid 71 through 82 removed outlier: 4.201A pdb=" N ASN b 75 " --> pdb=" O LEU b 71 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU b 76 " --> pdb=" O GLN b 72 " (cutoff:3.500A) Processing helix chain 'b' and resid 146 through 161 Processing helix chain 'b' and resid 244 through 276 removed outlier: 3.512A pdb=" N VAL b 248 " --> pdb=" O SER b 244 " (cutoff:3.500A) Processing helix chain 'b' and resid 285 through 290 Processing helix chain 'e' and resid 54 through 58 Processing helix chain 'e' and resid 78 through 83 Processing helix chain 'e' and resid 84 through 86 No H-bonds generated for 'chain 'e' and resid 84 through 86' Processing helix chain 'e' and resid 101 through 116 removed outlier: 3.727A pdb=" N VAL e 106 " --> pdb=" O ALA e 102 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL e 107 " --> pdb=" O LYS e 103 " (cutoff:3.500A) Processing helix chain 'f' and resid 37 through 44 removed outlier: 3.969A pdb=" N PHE f 43 " --> pdb=" O GLN f 39 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR f 44 " --> pdb=" O ASP f 40 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 11 removed outlier: 3.880A pdb=" N LEU h 9 " --> pdb=" O LYS h 5 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR h 11 " --> pdb=" O TYR h 7 " (cutoff:3.500A) Processing helix chain 'h' and resid 13 through 36 removed outlier: 3.556A pdb=" N VAL h 33 " --> pdb=" O ALA h 29 " (cutoff:3.500A) Processing helix chain 'h' and resid 41 through 70 removed outlier: 4.494A pdb=" N LYS h 45 " --> pdb=" O LEU h 41 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR h 46 " --> pdb=" O PRO h 42 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS h 49 " --> pdb=" O LYS h 45 " (cutoff:3.500A) Processing helix chain 'h' and resid 77 through 81 Processing helix chain 'h' and resid 94 through 99 Processing helix chain 'h' and resid 101 through 111 Processing helix chain 'i' and resid 27 through 31 Processing helix chain 'i' and resid 34 through 49 removed outlier: 3.582A pdb=" N GLU i 46 " --> pdb=" O SER i 42 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE i 47 " --> pdb=" O LEU i 43 " (cutoff:3.500A) Processing helix chain 'i' and resid 51 through 77 removed outlier: 3.647A pdb=" N ASP i 59 " --> pdb=" O ARG i 55 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N GLU i 66 " --> pdb=" O ARG i 62 " (cutoff:3.500A) removed outlier: 9.352A pdb=" N LYS i 67 " --> pdb=" O ASN i 63 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG i 68 " --> pdb=" O SER i 64 " (cutoff:3.500A) Processing helix chain 'i' and resid 80 through 98 Processing helix chain 'j' and resid 50 through 56 Processing helix chain 'j' and resid 66 through 68 No H-bonds generated for 'chain 'j' and resid 66 through 68' Processing helix chain 'j' and resid 69 through 77 removed outlier: 3.665A pdb=" N ARG j 73 " --> pdb=" O HIS j 69 " (cutoff:3.500A) Processing helix chain 'x' and resid 175 through 189 Processing helix chain 'm' and resid 197 through 208 Processing helix chain 'm' and resid 234 through 258 Processing helix chain 'm' and resid 261 through 269 Processing helix chain 'n' and resid 17 through 25 Processing helix chain 'n' and resid 28 through 40 Processing helix chain 'n' and resid 64 through 72 Processing helix chain 'n' and resid 74 through 96 Processing helix chain 'n' and resid 98 through 108 removed outlier: 3.592A pdb=" N ALA n 102 " --> pdb=" O GLU n 98 " (cutoff:3.500A) Processing helix chain 'n' and resid 114 through 120 Processing helix chain 'n' and resid 124 through 145 removed outlier: 4.769A pdb=" N ASP n 133 " --> pdb=" O ILE n 129 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ASP n 134 " --> pdb=" O ARG n 130 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA n 135 " --> pdb=" O ASP n 131 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASN n 137 " --> pdb=" O ASP n 133 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET n 138 " --> pdb=" O ASP n 134 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU n 139 " --> pdb=" O ALA n 135 " (cutoff:3.500A) Processing helix chain 'n' and resid 152 through 174 removed outlier: 3.506A pdb=" N LYS n 172 " --> pdb=" O ALA n 168 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU n 173 " --> pdb=" O TYR n 169 " (cutoff:3.500A) Processing helix chain 'n' and resid 214 through 240 removed outlier: 4.378A pdb=" N MET n 218 " --> pdb=" O ASP n 214 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N THR n 220 " --> pdb=" O ARG n 216 " (cutoff:3.500A) Processing helix chain 'n' and resid 249 through 256 Processing helix chain 'n' and resid 258 through 262 Processing helix chain 'n' and resid 372 through 384 removed outlier: 4.029A pdb=" N LEU n 376 " --> pdb=" O PRO n 372 " (cutoff:3.500A) Processing helix chain 'n' and resid 389 through 394 Processing helix chain 'n' and resid 429 through 439 removed outlier: 3.650A pdb=" N ASN n 437 " --> pdb=" O PHE n 433 " (cutoff:3.500A) Processing helix chain 'o' and resid 103 through 112 Processing helix chain 'o' and resid 141 through 151 Processing helix chain 'o' and resid 192 through 215 removed outlier: 4.581A pdb=" N GLY o 215 " --> pdb=" O LEU o 211 " (cutoff:3.500A) Processing helix chain 'p' and resid 50 through 60 Processing helix chain 'p' and resid 66 through 79 Proline residue: p 74 - end of helix Processing helix chain 'p' and resid 91 through 108 removed outlier: 3.583A pdb=" N PHE p 96 " --> pdb=" O LYS p 92 " (cutoff:3.500A) Proline residue: p 99 - end of helix Processing helix chain 'p' and resid 123 through 141 removed outlier: 4.597A pdb=" N GLU p 136 " --> pdb=" O GLY p 132 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU p 137 " --> pdb=" O VAL p 133 " (cutoff:3.500A) Processing helix chain 'p' and resid 153 through 164 Processing helix chain 'p' and resid 171 through 182 removed outlier: 3.664A pdb=" N LEU p 175 " --> pdb=" O THR p 171 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU p 176 " --> pdb=" O PRO p 172 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP p 177 " --> pdb=" O GLY p 173 " (cutoff:3.500A) Processing helix chain 'p' and resid 197 through 205 Processing helix chain 'p' and resid 206 through 217 Processing helix chain 'p' and resid 232 through 243 Processing helix chain 'p' and resid 275 through 287 Processing helix chain 'p' and resid 298 through 312 Processing helix chain 'p' and resid 324 through 339 Processing helix chain 'p' and resid 347 through 352 Processing helix chain 'p' and resid 369 through 384 Processing helix chain 'p' and resid 398 through 409 removed outlier: 4.056A pdb=" N LEU p 402 " --> pdb=" O GLU p 398 " (cutoff:3.500A) Processing helix chain 'p' and resid 425 through 436 Processing helix chain 'p' and resid 436 through 456 Processing helix chain 'p' and resid 464 through 468 Processing helix chain 'p' and resid 469 through 478 Processing helix chain 's' and resid 269 through 285 Processing helix chain 's' and resid 290 through 308 removed outlier: 4.009A pdb=" N UNK s 303 " --> pdb=" O UNK s 299 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N UNK s 306 " --> pdb=" O UNK s 302 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N UNK s 308 " --> pdb=" O UNK s 304 " (cutoff:3.500A) Processing helix chain 's' and resid 344 through 350 Processing helix chain 's' and resid 350 through 357 Processing helix chain 's' and resid 358 through 366 removed outlier: 4.403A pdb=" N UNK s 364 " --> pdb=" O UNK s 360 " (cutoff:3.500A) Processing helix chain 's' and resid 380 through 395 removed outlier: 4.653A pdb=" N ILE s 384 " --> pdb=" O TYR s 380 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG s 385 " --> pdb=" O GLY s 381 " (cutoff:3.500A) Processing helix chain 't' and resid 59 through 87 removed outlier: 3.534A pdb=" N THR t 65 " --> pdb=" O ILE t 61 " (cutoff:3.500A) Processing helix chain 't' and resid 156 through 166 Processing helix chain 't' and resid 183 through 191 removed outlier: 3.973A pdb=" N LEU t 187 " --> pdb=" O VAL t 183 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS t 188 " --> pdb=" O TYR t 184 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL t 189 " --> pdb=" O PRO t 185 " (cutoff:3.500A) Processing helix chain 't' and resid 200 through 211 Processing helix chain 't' and resid 231 through 239 Processing helix chain 't' and resid 247 through 257 Processing helix chain 't' and resid 261 through 268 Processing helix chain 't' and resid 281 through 299 removed outlier: 3.601A pdb=" N ARG t 285 " --> pdb=" O GLY t 281 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU t 286 " --> pdb=" O SER t 282 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG t 287 " --> pdb=" O LEU t 283 " (cutoff:3.500A) Processing helix chain 't' and resid 313 through 322 removed outlier: 3.786A pdb=" N ALA t 319 " --> pdb=" O ASP t 315 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS t 320 " --> pdb=" O SER t 316 " (cutoff:3.500A) Processing helix chain 'u' and resid 33 through 42 Processing helix chain 'u' and resid 52 through 60 Processing helix chain 'u' and resid 66 through 72 removed outlier: 3.583A pdb=" N THR u 70 " --> pdb=" O SER u 67 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE u 71 " --> pdb=" O THR u 68 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA u 72 " --> pdb=" O LEU u 69 " (cutoff:3.500A) Processing helix chain 'u' and resid 82 through 109 removed outlier: 3.720A pdb=" N VAL u 86 " --> pdb=" O ASN u 82 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA u 87 " --> pdb=" O ARG u 83 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR u 88 " --> pdb=" O GLU u 84 " (cutoff:3.500A) Processing helix chain 'u' and resid 113 through 124 removed outlier: 3.687A pdb=" N GLU u 117 " --> pdb=" O ARG u 113 " (cutoff:3.500A) Processing helix chain 'v' and resid 31 through 37 Processing helix chain 'v' and resid 37 through 51 removed outlier: 3.621A pdb=" N ASN v 41 " --> pdb=" O ASN v 37 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN v 42 " --> pdb=" O HIS v 38 " (cutoff:3.500A) Processing helix chain 'v' and resid 70 through 75 removed outlier: 4.145A pdb=" N CYS v 74 " --> pdb=" O PHE v 70 " (cutoff:3.500A) Processing helix chain 'v' and resid 76 through 78 No H-bonds generated for 'chain 'v' and resid 76 through 78' Processing helix chain 'v' and resid 116 through 124 Processing helix chain 'v' and resid 132 through 136 removed outlier: 3.776A pdb=" N VAL v 135 " --> pdb=" O ASN v 132 " (cutoff:3.500A) Processing helix chain 'v' and resid 156 through 173 removed outlier: 3.935A pdb=" N PHE v 173 " --> pdb=" O PHE v 169 " (cutoff:3.500A) Processing helix chain 'w' and resid 175 through 215 removed outlier: 3.611A pdb=" N LYS w 182 " --> pdb=" O LYS w 178 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY w 193 " --> pdb=" O ILE w 189 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA w 194 " --> pdb=" O ALA w 190 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN w 215 " --> pdb=" O GLU w 211 " (cutoff:3.500A) Processing helix chain 'w' and resid 225 through 243 Processing helix chain 'y' and resid 32 through 42 Processing helix chain 'y' and resid 77 through 88 Processing helix chain 'y' and resid 122 through 133 removed outlier: 3.868A pdb=" N SER y 130 " --> pdb=" O GLU y 126 " (cutoff:3.500A) Processing helix chain 'y' and resid 166 through 178 removed outlier: 4.046A pdb=" N LEU y 176 " --> pdb=" O GLU y 172 " (cutoff:3.500A) Processing helix chain 'y' and resid 192 through 196 Processing helix chain 'y' and resid 211 through 222 Processing helix chain 'z' and resid 2 through 11 Processing helix chain 'z' and resid 14 through 29 removed outlier: 3.570A pdb=" N ARG z 18 " --> pdb=" O ASN z 14 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS z 27 " --> pdb=" O GLU z 23 " (cutoff:3.500A) Processing helix chain 'z' and resid 31 through 37 removed outlier: 3.699A pdb=" N LYS z 35 " --> pdb=" O ALA z 31 " (cutoff:3.500A) Processing helix chain 'z' and resid 38 through 55 removed outlier: 3.725A pdb=" N PHE z 42 " --> pdb=" O LYS z 38 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE z 55 " --> pdb=" O TYR z 51 " (cutoff:3.500A) Processing helix chain 'z' and resid 58 through 76 removed outlier: 3.607A pdb=" N HIS z 73 " --> pdb=" O LEU z 69 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N TYR z 76 " --> pdb=" O LEU z 72 " (cutoff:3.500A) Processing helix chain 'z' and resid 78 through 85 removed outlier: 3.846A pdb=" N ASN z 82 " --> pdb=" O ASP z 78 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER z 83 " --> pdb=" O PRO z 79 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA z 85 " --> pdb=" O ASP z 81 " (cutoff:3.500A) Processing helix chain 'z' and resid 89 through 110 Processing helix chain 'z' and resid 111 through 113 No H-bonds generated for 'chain 'z' and resid 111 through 113' Processing helix chain 'z' and resid 117 through 139 removed outlier: 4.072A pdb=" N TYR z 121 " --> pdb=" O ARG z 117 " (cutoff:3.500A) Processing helix chain 'z' and resid 142 through 152 Processing helix chain 'z' and resid 157 through 161 removed outlier: 4.113A pdb=" N GLY z 161 " --> pdb=" O PRO z 158 " (cutoff:3.500A) Processing helix chain 'z' and resid 167 through 186 removed outlier: 5.045A pdb=" N LEU z 178 " --> pdb=" O VAL z 174 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ASP z 179 " --> pdb=" O ASP z 175 " (cutoff:3.500A) Processing helix chain 'z' and resid 198 through 211 Processing helix chain 'z' and resid 213 through 227 removed outlier: 3.794A pdb=" N VAL z 217 " --> pdb=" O PRO z 213 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA z 219 " --> pdb=" O ALA z 215 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE z 220 " --> pdb=" O ASP z 216 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE z 221 " --> pdb=" O VAL z 217 " (cutoff:3.500A) Processing helix chain 'z' and resid 231 through 242 Processing helix chain 'z' and resid 245 through 251 removed outlier: 4.198A pdb=" N VAL z 249 " --> pdb=" O ASP z 245 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 38 removed outlier: 4.299A pdb=" N PHE A 406 " --> pdb=" O SER A 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 53 removed outlier: 3.593A pdb=" N GLU A 57 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL A 67 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER A 113 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU A 69 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 145 removed outlier: 3.714A pdb=" N THR A 142 " --> pdb=" O ALA A 158 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS A 144 " --> pdb=" O VAL A 156 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LEU A 164 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER A 180 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE A 166 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 189 through 192 removed outlier: 3.864A pdb=" N PHE A 189 " --> pdb=" O GLY A 208 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY A 208 " --> pdb=" O PHE A 189 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N TYR A 203 " --> pdb=" O GLU A 218 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU A 218 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE A 205 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU A 216 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N TYR A 207 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE A 214 " --> pdb=" O TYR A 207 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ILE A 214 " --> pdb=" O GLU A 231 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLU A 231 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU A 216 " --> pdb=" O ILE A 229 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 248 through 253 removed outlier: 6.569A pdb=" N ILE A 273 " --> pdb=" O MET A 249 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU A 251 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA A 271 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N PHE A 253 " --> pdb=" O GLN A 269 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N GLN A 269 " --> pdb=" O PHE A 253 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N HIS A 278 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA A 292 " --> pdb=" O LYS A 281 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 303 through 308 removed outlier: 6.367A pdb=" N THR A 336 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N MET A 306 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE A 334 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY A 353 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 366 through 370 removed outlier: 6.459A pdb=" N VAL A 384 " --> pdb=" O LYS A 397 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS A 397 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE A 386 " --> pdb=" O LEU A 395 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 355 through 359 removed outlier: 4.754A pdb=" N SER B 355 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP B 59 " --> pdb=" O SER B 355 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL B 57 " --> pdb=" O LYS B 357 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ILE B 359 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N THR B 55 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ILE B 335 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N VAL B 220 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ALA B 217 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ILE B 278 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ALA B 219 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N THR B 276 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N LYS B 281 " --> pdb=" O LYS B 325 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N MET B 323 " --> pdb=" O TYR B 283 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL B 285 " --> pdb=" O PHE B 321 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE B 321 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG B 70 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY B 52 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ASP B 80 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LYS B 50 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 98 through 106 removed outlier: 5.098A pdb=" N LEU B 99 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N THR B 95 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N SER B 101 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL B 93 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR B 103 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY B 91 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N VAL B 86 " --> pdb=" O HIS B 163 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N HIS B 163 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 98 through 106 removed outlier: 5.098A pdb=" N LEU B 99 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N THR B 95 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N SER B 101 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL B 93 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR B 103 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY B 91 " --> pdb=" O THR B 103 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 5 through 9 removed outlier: 5.939A pdb=" N ASN C 18 " --> pdb=" O VAL C 8 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 150 through 152 removed outlier: 4.266A pdb=" N LEU C 150 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LEU C 206 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N THR C 251 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL C 208 " --> pdb=" O THR C 251 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL C 207 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 186 through 187 Processing sheet with id=AB5, first strand: chain 'D' and resid 18 through 20 Processing sheet with id=AB6, first strand: chain 'D' and resid 50 through 55 Processing sheet with id=AB7, first strand: chain 'D' and resid 133 through 135 removed outlier: 3.667A pdb=" N HIS D 133 " --> pdb=" O GLU e 129 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 77 through 80 removed outlier: 3.593A pdb=" N LYS E 56 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N SER E 66 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N TYR E 54 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR E 38 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N VAL E 39 " --> pdb=" O THR E 87 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 205 through 206 removed outlier: 4.570A pdb=" N SER F 113 " --> pdb=" O ARG F 88 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 153 through 154 Processing sheet with id=AC2, first strand: chain 'G' and resid 177 through 180 removed outlier: 6.060A pdb=" N VAL G 151 " --> pdb=" O ALA G 178 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL G 180 " --> pdb=" O VAL G 151 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ILE G 153 " --> pdb=" O VAL G 180 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 121 through 125 removed outlier: 4.162A pdb=" N THR I 99 " --> pdb=" O VAL I 124 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE I 147 " --> pdb=" O PHE I 162 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE I 162 " --> pdb=" O ILE I 147 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE I 149 " --> pdb=" O LEU I 160 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU I 160 " --> pdb=" O ILE I 149 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASN I 151 " --> pdb=" O THR I 158 " (cutoff:3.500A) removed outlier: 12.272A pdb=" N LYS I 156 " --> pdb=" O SER I 177 " (cutoff:3.500A) removed outlier: 10.222A pdb=" N SER I 177 " --> pdb=" O LYS I 156 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N THR I 158 " --> pdb=" O LEU I 175 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR I 170 " --> pdb=" O LEU I 270 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU I 270 " --> pdb=" O THR I 170 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TYR I 172 " --> pdb=" O LYS I 268 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR I 264 " --> pdb=" O SER I 176 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N PHE I 178 " --> pdb=" O GLN I 262 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLN I 262 " --> pdb=" O PHE I 178 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 121 through 125 removed outlier: 4.162A pdb=" N THR I 99 " --> pdb=" O VAL I 124 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE I 147 " --> pdb=" O PHE I 162 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE I 162 " --> pdb=" O ILE I 147 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE I 149 " --> pdb=" O LEU I 160 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU I 160 " --> pdb=" O ILE I 149 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASN I 151 " --> pdb=" O THR I 158 " (cutoff:3.500A) removed outlier: 12.272A pdb=" N LYS I 156 " --> pdb=" O SER I 177 " (cutoff:3.500A) removed outlier: 10.222A pdb=" N SER I 177 " --> pdb=" O LYS I 156 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N THR I 158 " --> pdb=" O LEU I 175 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR I 170 " --> pdb=" O LEU I 270 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU I 270 " --> pdb=" O THR I 170 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TYR I 172 " --> pdb=" O LYS I 268 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR I 264 " --> pdb=" O SER I 176 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N PHE I 178 " --> pdb=" O GLN I 262 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLN I 262 " --> pdb=" O PHE I 178 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N LYS I 268 " --> pdb=" O GLU I 281 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLU I 281 " --> pdb=" O LYS I 268 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU I 270 " --> pdb=" O GLU I 279 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 247 through 248 Processing sheet with id=AC6, first strand: chain 'K' and resid 243 through 250 removed outlier: 6.222A pdb=" N GLN K 79 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ARG K 277 " --> pdb=" O TYR K 293 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N TYR K 293 " --> pdb=" O ARG K 277 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE K 279 " --> pdb=" O LEU K 291 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 100 through 101 Processing sheet with id=AC8, first strand: chain 'K' and resid 153 through 156 removed outlier: 6.297A pdb=" N VAL K 123 " --> pdb=" O GLU K 153 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ILE K 155 " --> pdb=" O VAL K 123 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU K 125 " --> pdb=" O ILE K 155 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 23 through 24 removed outlier: 6.620A pdb=" N LYS L 23 " --> pdb=" O LEU N 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'L' and resid 57 through 59 Processing sheet with id=AD2, first strand: chain 'L' and resid 124 through 126 removed outlier: 4.438A pdb=" N LYS h 115 " --> pdb=" O PHE L 126 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 53 through 59 removed outlier: 4.207A pdb=" N GLY M 48 " --> pdb=" O PRO M 54 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ASP M 47 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ILE M 35 " --> pdb=" O ASP M 47 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ARG M 19 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N VAL M 20 " --> pdb=" O THR M 66 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 36 through 39 removed outlier: 4.566A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N TYR N 127 " --> pdb=" O ASN N 122 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ASN N 122 " --> pdb=" O TYR N 127 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N TYR N 129 " --> pdb=" O TRP N 120 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N TRP N 120 " --> pdb=" O TYR N 129 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLU N 131 " --> pdb=" O SER N 118 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N SER N 118 " --> pdb=" O GLU N 131 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE N 133 " --> pdb=" O LEU N 116 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 6 through 10 Processing sheet with id=AD6, first strand: chain 'O' and resid 14 through 15 removed outlier: 5.715A pdb=" N HIS O 14 " --> pdb=" O ASN O 42 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N SER O 44 " --> pdb=" O HIS O 14 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'P' and resid 14 through 22 removed outlier: 5.041A pdb=" N SER P 144 " --> pdb=" O TYR P 21 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N HIS P 145 " --> pdb=" O VAL P 119 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL P 119 " --> pdb=" O HIS P 145 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLU P 147 " --> pdb=" O ILE P 117 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ILE P 117 " --> pdb=" O GLU P 147 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL P 149 " --> pdb=" O SER P 115 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'P' and resid 58 through 59 Processing sheet with id=AD9, first strand: chain 'Q' and resid 62 through 63 removed outlier: 6.294A pdb=" N VAL Q 81 " --> pdb=" O ALA Q 102 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N LEU Q 104 " --> pdb=" O VAL Q 81 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N VAL Q 83 " --> pdb=" O LEU Q 104 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N PHE Q 106 " --> pdb=" O VAL Q 83 " (cutoff:3.500A) removed outlier: 11.232A pdb=" N GLY Q 85 " --> pdb=" O PHE Q 106 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL Q 101 " --> pdb=" O ILE Q 122 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Q' and resid 62 through 63 Processing sheet with id=AE2, first strand: chain 'S' and resid 25 through 31 removed outlier: 7.324A pdb=" N GLU S 6 " --> pdb=" O GLN S 63 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLN S 63 " --> pdb=" O GLU S 6 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLN S 8 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE S 61 " --> pdb=" O GLN S 8 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE S 10 " --> pdb=" O VAL S 59 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'S' and resid 86 through 96 removed outlier: 3.641A pdb=" N TYR S 81 " --> pdb=" O HIS S 88 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASN S 74 " --> pdb=" O ILE S 129 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ARG S 80 " --> pdb=" O ILE S 123 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ILE S 123 " --> pdb=" O ARG S 80 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'V' and resid 21 through 25 removed outlier: 3.779A pdb=" N ALA V 21 " --> pdb=" O ILE V 36 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N MET V 59 " --> pdb=" O ILE V 37 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL V 39 " --> pdb=" O MET V 57 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N MET V 57 " --> pdb=" O VAL V 39 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ALA V 99 " --> pdb=" O VAL V 79 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N GLY V 100 " --> pdb=" O ILE V 22 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ASN V 24 " --> pdb=" O GLY V 100 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE V 102 " --> pdb=" O ASN V 24 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'V' and resid 85 through 86 removed outlier: 3.540A pdb=" N LEU V 93 " --> pdb=" O TRP V 85 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N PHE V 92 " --> pdb=" O MET u 20 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N VAL u 22 " --> pdb=" O PHE V 92 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TYR V 94 " --> pdb=" O VAL u 22 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'V' and resid 114 through 118 removed outlier: 5.554A pdb=" N SER V 133 " --> pdb=" O ILE V 114 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N GLY V 116 " --> pdb=" O SER V 133 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL V 135 " --> pdb=" O GLY V 116 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'W' and resid 435 through 436 Processing sheet with id=AE8, first strand: chain 'Y' and resid 32 through 34 Processing sheet with id=AE9, first strand: chain 'Y' and resid 94 through 99 removed outlier: 6.839A pdb=" N VAL Y 85 " --> pdb=" O ILE Y 97 " (cutoff:3.500A) removed outlier: 9.932A pdb=" N LEU Y 99 " --> pdb=" O ASP Y 83 " (cutoff:3.500A) removed outlier: 10.558A pdb=" N ASP Y 83 " --> pdb=" O LEU Y 99 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA Y 79 " --> pdb=" O VAL Y 73 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N VAL Y 73 " --> pdb=" O ALA Y 79 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLN Y 81 " --> pdb=" O SER Y 71 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N LYS Y 69 " --> pdb=" O ASP Y 83 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N VAL Y 85 " --> pdb=" O GLU Y 67 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N GLU Y 67 " --> pdb=" O VAL Y 85 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LEU Y 57 " --> pdb=" O ILE Y 106 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ILE Y 106 " --> pdb=" O LEU Y 57 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'b' and resid 33 through 37 removed outlier: 6.036A pdb=" N LEU b 34 " --> pdb=" O LEU b 87 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N PHE b 89 " --> pdb=" O LEU b 34 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE b 36 " --> pdb=" O PHE b 89 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ALA b 91 " --> pdb=" O ILE b 36 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N LEU b 97 " --> pdb=" O ILE b 114 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU b 101 " --> pdb=" O ILE b 110 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE b 110 " --> pdb=" O LEU b 101 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N THR b 109 " --> pdb=" O ILE b 226 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE b 226 " --> pdb=" O THR b 109 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LYS b 111 " --> pdb=" O ILE b 224 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU b 117 " --> pdb=" O ARG b 218 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ARG b 218 " --> pdb=" O LEU b 117 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'b' and resid 213 through 214 removed outlier: 3.838A pdb=" N VAL b 213 " --> pdb=" O GLU b 192 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 218 through 227 current: chain 'b' and resid 136 through 139 Processing sheet with id=AF3, first strand: chain 'e' and resid 72 through 76 removed outlier: 6.143A pdb=" N LYS e 72 " --> pdb=" O ALA e 93 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLU e 95 " --> pdb=" O LYS e 72 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N PHE e 74 " --> pdb=" O GLU e 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'f' and resid 8 through 18 removed outlier: 9.821A pdb=" N VAL f 9 " --> pdb=" O ILE f 32 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ILE f 32 " --> pdb=" O VAL f 9 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N GLY f 11 " --> pdb=" O ILE f 30 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ILE f 30 " --> pdb=" O GLY f 11 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N HIS f 13 " --> pdb=" O SER f 28 " (cutoff:3.500A) removed outlier: 9.772A pdb=" N SER f 28 " --> pdb=" O HIS f 13 " (cutoff:3.500A) removed outlier: 10.538A pdb=" N SER f 15 " --> pdb=" O ASN f 26 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N ASN f 26 " --> pdb=" O SER f 15 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N ASN f 26 " --> pdb=" O PHE f 85 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N PHE f 85 " --> pdb=" O ASN f 26 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL f 80 " --> pdb=" O HIS f 75 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG f 73 " --> pdb=" O ARG f 82 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N THR f 84 " --> pdb=" O VAL f 71 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N VAL f 71 " --> pdb=" O THR f 84 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG f 48 " --> pdb=" O PHE f 101 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N VAL f 52 " --> pdb=" O SER f 97 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N SER f 97 " --> pdb=" O VAL f 52 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA f 96 " --> pdb=" O HIS f 13 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'j' and resid 16 through 17 Processing sheet with id=AF6, first strand: chain 'n' and resid 187 through 191 Processing sheet with id=AF7, first strand: chain 'n' and resid 365 through 367 Processing sheet with id=AF8, first strand: chain 'o' and resid 117 through 124 removed outlier: 4.758A pdb=" N LEU o 117 " --> pdb=" O GLU o 138 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLU o 138 " --> pdb=" O LEU o 117 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU o 119 " --> pdb=" O PHE o 136 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N PHE o 136 " --> pdb=" O GLU o 119 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ARG o 121 " --> pdb=" O TYR o 134 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N TYR o 134 " --> pdb=" O ARG o 121 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA o 123 " --> pdb=" O ARG o 132 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE o 139 " --> pdb=" O GLY o 91 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N GLY o 91 " --> pdb=" O PHE o 139 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ILE o 92 " --> pdb=" O LEU o 167 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN o 163 " --> pdb=" O SER o 96 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'p' and resid 146 through 148 removed outlier: 3.602A pdb=" N ILE p 169 " --> pdb=" O GLY p 146 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE p 117 " --> pdb=" O LEU p 168 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ALA p 170 " --> pdb=" O ILE p 117 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N VAL p 119 " --> pdb=" O ALA p 170 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU p 193 " --> pdb=" O MET p 225 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N PHE p 227 " --> pdb=" O LEU p 193 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE p 195 " --> pdb=" O PHE p 227 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE p 250 " --> pdb=" O LEU p 83 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'p' and resid 316 through 319 removed outlier: 3.662A pdb=" N THR p 346 " --> pdb=" O LEU p 319 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N GLN p 266 " --> pdb=" O ASN p 413 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'q' and resid 97 through 102 removed outlier: 6.585A pdb=" N UNK q 423 " --> pdb=" O UNK q 99 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N UNK q 101 " --> pdb=" O UNK q 421 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N UNK q 421 " --> pdb=" O UNK q 101 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'q' and resid 109 through 113 removed outlier: 3.634A pdb=" N UNK q 113 " --> pdb=" O UNK q 120 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N UNK q 120 " --> pdb=" O UNK q 113 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N UNK q 128 " --> pdb=" O UNK q 141 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N UNK q 141 " --> pdb=" O UNK q 128 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N UNK q 130 " --> pdb=" O UNK q 139 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'q' and resid 149 through 154 removed outlier: 6.779A pdb=" N UNK q 179 " --> pdb=" O UNK q 150 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N UNK q 152 " --> pdb=" O UNK q 177 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N UNK q 177 " --> pdb=" O UNK q 152 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N UNK q 154 " --> pdb=" O UNK q 175 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N UNK q 175 " --> pdb=" O UNK q 154 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N UNK q 189 " --> pdb=" O UNK q 195 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N UNK q 195 " --> pdb=" O UNK q 189 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'q' and resid 206 through 211 removed outlier: 6.744A pdb=" N UNK q 221 " --> pdb=" O UNK q 207 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N UNK q 209 " --> pdb=" O UNK q 219 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N UNK q 219 " --> pdb=" O UNK q 209 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'q' and resid 251 through 257 removed outlier: 6.885A pdb=" N UNK q 265 " --> pdb=" O UNK q 252 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N UNK q 254 " --> pdb=" O UNK q 263 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N UNK q 263 " --> pdb=" O UNK q 254 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N UNK q 256 " --> pdb=" O UNK q 261 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N UNK q 261 " --> pdb=" O UNK q 256 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N UNK q 266 " --> pdb=" O UNK q 270 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N UNK q 270 " --> pdb=" O UNK q 266 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N UNK q 275 " --> pdb=" O UNK q 281 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N UNK q 281 " --> pdb=" O UNK q 275 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'q' and resid 294 through 297 removed outlier: 3.883A pdb=" N UNK q 294 " --> pdb=" O UNK q 311 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N UNK q 311 " --> pdb=" O UNK q 294 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N UNK q 296 " --> pdb=" O UNK q 309 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N UNK q 317 " --> pdb=" O UNK q 349 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N UNK q 349 " --> pdb=" O UNK q 317 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N UNK q 319 " --> pdb=" O UNK q 347 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'q' and resid 361 through 362 removed outlier: 6.206A pdb=" N UNK q 380 " --> pdb=" O UNK q 393 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N UNK q 393 " --> pdb=" O UNK q 380 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N UNK q 382 " --> pdb=" O UNK q 391 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N UNK q 389 " --> pdb=" O UNK q 384 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 't' and resid 130 through 134 Processing sheet with id=AH1, first strand: chain 't' and resid 174 through 179 Processing sheet with id=AH2, first strand: chain 't' and resid 213 through 215 Processing sheet with id=AH3, first strand: chain 'u' and resid 4 through 5 Processing sheet with id=AH4, first strand: chain 'v' and resid 28 through 29 removed outlier: 6.278A pdb=" N VAL v 94 " --> pdb=" O VAL v 111 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS v 341 " --> pdb=" O THR v 108 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N GLN v 110 " --> pdb=" O LEU v 339 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N LEU v 339 " --> pdb=" O GLN v 110 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N LEU v 112 " --> pdb=" O LEU v 337 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LEU v 337 " --> pdb=" O LEU v 112 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'v' and resid 142 through 144 removed outlier: 3.815A pdb=" N LYS v 194 " --> pdb=" O ASN v 144 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP v 195 " --> pdb=" O GLU v 200 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU v 200 " --> pdb=" O ASP v 195 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA v 325 " --> pdb=" O ARG v 211 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'y' and resid 3 through 4 removed outlier: 6.195A pdb=" N THR y 3 " --> pdb=" O THR y 206 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'y' and resid 17 through 19 removed outlier: 6.618A pdb=" N CYS y 24 " --> pdb=" O VAL y 49 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'y' and resid 64 through 65 Processing sheet with id=AH9, first strand: chain 'y' and resid 109 through 110 Processing sheet with id=AI1, first strand: chain 'y' and resid 152 through 154 removed outlier: 3.607A pdb=" N VAL y 182 " --> pdb=" O GLY y 159 " (cutoff:3.500A) 2520 hydrogen bonds defined for protein. 7254 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1236 hydrogen bonds 1970 hydrogen bond angles 0 basepair planarities 501 basepair parallelities 845 stacking parallelities Total time for adding SS restraints: 58.35 Time building geometry restraints manager: 40.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 18171 1.33 - 1.46: 37292 1.46 - 1.60: 39730 1.60 - 1.73: 1356 1.73 - 1.87: 227 Bond restraints: 96776 Sorted by residual: bond pdb=" CA UNK q 314 " pdb=" C UNK q 314 " ideal model delta sigma weight residual 1.525 1.598 -0.073 2.10e-02 2.27e+03 1.22e+01 bond pdb=" CA ARG B 37 " pdb=" C ARG B 37 " ideal model delta sigma weight residual 1.523 1.474 0.049 1.48e-02 4.57e+03 1.09e+01 bond pdb=" C LEU Y 99 " pdb=" N HIS Y 100 " ideal model delta sigma weight residual 1.332 1.290 0.043 1.40e-02 5.10e+03 9.31e+00 bond pdb=" C LYS G 128 " pdb=" N PRO G 129 " ideal model delta sigma weight residual 1.334 1.301 0.033 1.11e-02 8.12e+03 8.89e+00 bond pdb=" CG LEU b 99 " pdb=" CD2 LEU b 99 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.79e+00 ... (remaining 96771 not shown) Histogram of bond angle deviations from ideal: 96.81 - 105.08: 8242 105.08 - 113.35: 58261 113.35 - 121.63: 49527 121.63 - 129.90: 21194 129.90 - 138.17: 1157 Bond angle restraints: 138381 Sorted by residual: angle pdb=" C ARG S 13 " pdb=" N LEU S 14 " pdb=" CA LEU S 14 " ideal model delta sigma weight residual 121.80 138.17 -16.37 2.44e+00 1.68e-01 4.50e+01 angle pdb=" C GLY G 119 " pdb=" N LYS G 120 " pdb=" CA LYS G 120 " ideal model delta sigma weight residual 121.70 133.24 -11.54 1.80e+00 3.09e-01 4.11e+01 angle pdb=" C ASN G 145 " pdb=" N LYS G 146 " pdb=" CA LYS G 146 " ideal model delta sigma weight residual 121.70 132.56 -10.86 1.80e+00 3.09e-01 3.64e+01 angle pdb=" C ASN F 157 " pdb=" N LYS F 158 " pdb=" CA LYS F 158 " ideal model delta sigma weight residual 121.54 132.70 -11.16 1.91e+00 2.74e-01 3.42e+01 angle pdb=" C LYS A 265 " pdb=" N LEU A 266 " pdb=" CA LEU A 266 " ideal model delta sigma weight residual 121.54 132.39 -10.85 1.91e+00 2.74e-01 3.22e+01 ... (remaining 138376 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 56365 35.88 - 71.77: 4104 71.77 - 107.65: 432 107.65 - 143.53: 22 143.53 - 179.42: 40 Dihedral angle restraints: 60963 sinusoidal: 39561 harmonic: 21402 Sorted by residual: dihedral pdb=" CA ALA A 185 " pdb=" C ALA A 185 " pdb=" N PRO A 186 " pdb=" CA PRO A 186 " ideal model delta harmonic sigma weight residual -180.00 -115.10 -64.90 0 5.00e+00 4.00e-02 1.68e+02 dihedral pdb=" C5' U 13351 " pdb=" C4' U 13351 " pdb=" C3' U 13351 " pdb=" O3' U 13351 " ideal model delta sinusoidal sigma weight residual 147.00 71.64 75.36 1 8.00e+00 1.56e-02 1.12e+02 dihedral pdb=" CA SER S 83 " pdb=" C SER S 83 " pdb=" N ARG S 84 " pdb=" CA ARG S 84 " ideal model delta harmonic sigma weight residual -180.00 -128.07 -51.93 0 5.00e+00 4.00e-02 1.08e+02 ... (remaining 60960 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 15968 0.103 - 0.205: 829 0.205 - 0.308: 71 0.308 - 0.411: 8 0.411 - 0.514: 1 Chirality restraints: 16877 Sorted by residual: chirality pdb=" C3' U 13351 " pdb=" C4' U 13351 " pdb=" O3' U 13351 " pdb=" C2' U 13351 " both_signs ideal model delta sigma weight residual False -2.74 -2.23 -0.51 2.00e-01 2.50e+01 6.60e+00 chirality pdb=" CB ILE p 194 " pdb=" CA ILE p 194 " pdb=" CG1 ILE p 194 " pdb=" CG2 ILE p 194 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CB VAL G 190 " pdb=" CA VAL G 190 " pdb=" CG1 VAL G 190 " pdb=" CG2 VAL G 190 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.41e+00 ... (remaining 16874 not shown) Planarity restraints: 11636 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 1 406 " -0.085 2.00e-02 2.50e+03 3.80e-02 4.33e+01 pdb=" N9 G 1 406 " 0.095 2.00e-02 2.50e+03 pdb=" C8 G 1 406 " 0.005 2.00e-02 2.50e+03 pdb=" N7 G 1 406 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G 1 406 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G 1 406 " -0.013 2.00e-02 2.50e+03 pdb=" O6 G 1 406 " -0.018 2.00e-02 2.50e+03 pdb=" N1 G 1 406 " -0.010 2.00e-02 2.50e+03 pdb=" C2 G 1 406 " -0.006 2.00e-02 2.50e+03 pdb=" N2 G 1 406 " 0.018 2.00e-02 2.50e+03 pdb=" N3 G 1 406 " 0.009 2.00e-02 2.50e+03 pdb=" C4 G 1 406 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 185 " 0.071 5.00e-02 4.00e+02 1.07e-01 1.82e+01 pdb=" N PRO A 186 " -0.185 5.00e-02 4.00e+02 pdb=" CA PRO A 186 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO A 186 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G 2 39 " -0.057 2.00e-02 2.50e+03 2.35e-02 1.66e+01 pdb=" N9 G 2 39 " 0.053 2.00e-02 2.50e+03 pdb=" C8 G 2 39 " 0.006 2.00e-02 2.50e+03 pdb=" N7 G 2 39 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G 2 39 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G 2 39 " -0.008 2.00e-02 2.50e+03 pdb=" O6 G 2 39 " -0.015 2.00e-02 2.50e+03 pdb=" N1 G 2 39 " -0.006 2.00e-02 2.50e+03 pdb=" C2 G 2 39 " 0.007 2.00e-02 2.50e+03 pdb=" N2 G 2 39 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G 2 39 " 0.013 2.00e-02 2.50e+03 pdb=" C4 G 2 39 " 0.007 2.00e-02 2.50e+03 ... (remaining 11633 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 1137 2.57 - 3.15: 70333 3.15 - 3.73: 175825 3.73 - 4.32: 230676 4.32 - 4.90: 329202 Nonbonded interactions: 807173 Sorted by model distance: nonbonded pdb=" OE2 GLU A 57 " pdb=" NZ LYS A 169 " model vdw 1.985 2.520 nonbonded pdb=" NH1 ARG v 334 " pdb=" OE2 GLU w 183 " model vdw 1.985 2.520 nonbonded pdb=" OE2 GLU G 144 " pdb=" OH TYR N 6 " model vdw 2.007 2.440 nonbonded pdb=" OP2 A 1 438 " pdb=" NZ LYS I 104 " model vdw 2.023 2.520 nonbonded pdb=" O2' A 1 533 " pdb=" OP2 G 1 535 " model vdw 2.027 2.440 ... (remaining 807168 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.260 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: 0.060 Extract box with map and model: 24.780 Check model and map are aligned: 0.980 Set scattering table: 0.610 Process input model: 246.820 Find NCS groups from input model: 2.610 Set up NCS constraints: 0.290 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:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 284.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 96776 Z= 0.407 Angle : 1.027 16.373 138381 Z= 0.551 Chirality : 0.052 0.514 16877 Planarity : 0.007 0.107 11636 Dihedral : 20.567 179.418 47037 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.17 % Favored : 94.75 % Rotamer: Outliers : 0.28 % Allowed : 3.55 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.06 % Twisted Proline : 0.74 % 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: -2.72 (0.08), residues: 6729 helix: -1.82 (0.08), residues: 2612 sheet: -1.13 (0.16), residues: 928 loop : -1.91 (0.09), residues: 3189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.004 TRP A 247 HIS 0.019 0.003 HIS C 243 PHE 0.042 0.004 PHE K 259 TYR 0.047 0.003 TYR N 6 ARG 0.017 0.001 ARG E 22 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13458 Ramachandran restraints generated. 6729 Oldfield, 0 Emsley, 6729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13458 Ramachandran restraints generated. 6729 Oldfield, 0 Emsley, 6729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1843 residues out of total 5975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 1826 time to evaluate : 5.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.8165 (mmm) cc_final: 0.7797 (tpp) REVERT: A 306 MET cc_start: 0.8169 (tmt) cc_final: 0.7822 (tmm) REVERT: C 34 ILE cc_start: 0.9267 (mt) cc_final: 0.8797 (tt) REVERT: C 45 ASN cc_start: 0.8300 (m-40) cc_final: 0.7818 (m110) REVERT: C 234 ASN cc_start: 0.8997 (t0) cc_final: 0.8639 (t0) REVERT: D 134 TYR cc_start: 0.8758 (m-80) cc_final: 0.8553 (m-10) REVERT: D 168 ASP cc_start: 0.8168 (m-30) cc_final: 0.6682 (m-30) REVERT: D 182 VAL cc_start: 0.8244 (t) cc_final: 0.7841 (t) REVERT: F 123 THR cc_start: 0.8862 (p) cc_final: 0.8618 (p) REVERT: G 57 ARG cc_start: 0.8593 (ttp80) cc_final: 0.8292 (ptt90) REVERT: G 89 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7493 (mm-30) REVERT: G 130 TYR cc_start: 0.8106 (m-10) cc_final: 0.7811 (m-80) REVERT: G 227 ASP cc_start: 0.8209 (p0) cc_final: 0.7514 (p0) REVERT: I 26 LYS cc_start: 0.9027 (tttt) cc_final: 0.8796 (ttmt) REVERT: K 81 ILE cc_start: 0.8337 (mt) cc_final: 0.8110 (mt) REVERT: K 179 LEU cc_start: 0.8396 (tp) cc_final: 0.8183 (tp) REVERT: K 229 VAL cc_start: 0.9112 (t) cc_final: 0.8763 (m) REVERT: L 37 ASN cc_start: 0.8511 (m-40) cc_final: 0.8266 (m-40) REVERT: L 52 ASP cc_start: 0.8425 (p0) cc_final: 0.7717 (p0) REVERT: L 124 ILE cc_start: 0.7952 (pp) cc_final: 0.7626 (pt) REVERT: M 47 ASP cc_start: 0.7892 (t0) cc_final: 0.7621 (t0) REVERT: N 46 ASP cc_start: 0.7902 (p0) cc_final: 0.7701 (p0) REVERT: N 152 CYS cc_start: 0.8653 (m) cc_final: 0.8393 (m) REVERT: P 31 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7563 (mm-30) REVERT: P 58 ILE cc_start: 0.9112 (mm) cc_final: 0.8871 (mm) REVERT: P 94 LEU cc_start: 0.9269 (mp) cc_final: 0.9037 (mt) REVERT: P 107 LEU cc_start: 0.8597 (mp) cc_final: 0.7709 (mt) REVERT: P 118 GLN cc_start: 0.8303 (tt0) cc_final: 0.8016 (tt0) REVERT: P 145 HIS cc_start: 0.8178 (m-70) cc_final: 0.7944 (m170) REVERT: P 151 THR cc_start: 0.9321 (m) cc_final: 0.8968 (p) REVERT: V 24 ASN cc_start: 0.7252 (m-40) cc_final: 0.6823 (m-40) REVERT: V 32 ARG cc_start: 0.7687 (mmt90) cc_final: 0.7274 (mmt90) REVERT: Y 7 ASP cc_start: 0.7747 (m-30) cc_final: 0.6581 (m-30) REVERT: Y 78 PHE cc_start: 0.9202 (m-80) cc_final: 0.8895 (m-10) REVERT: 7 181 GLU cc_start: 0.7719 (pp20) cc_final: 0.7221 (pp20) REVERT: 8 301 LEU cc_start: 0.9247 (tt) cc_final: 0.9031 (tt) REVERT: 8 329 GLN cc_start: 0.8681 (mt0) cc_final: 0.8220 (mm-40) REVERT: 8 333 LEU cc_start: 0.8959 (mt) cc_final: 0.8482 (mt) REVERT: 8 334 GLN cc_start: 0.8915 (mt0) cc_final: 0.8618 (mm-40) REVERT: 8 340 ILE cc_start: 0.8353 (mt) cc_final: 0.7008 (mm) REVERT: 8 346 LEU cc_start: 0.8438 (mt) cc_final: 0.8115 (mp) REVERT: 8 357 GLN cc_start: 0.9064 (mt0) cc_final: 0.8649 (mt0) REVERT: 8 371 VAL cc_start: 0.9037 (t) cc_final: 0.8426 (p) REVERT: 8 379 ARG cc_start: 0.8708 (mmm-85) cc_final: 0.8110 (tpt90) REVERT: 8 382 ARG cc_start: 0.8076 (mtt180) cc_final: 0.6445 (tpp-160) REVERT: b 98 TYR cc_start: 0.7829 (m-10) cc_final: 0.6989 (m-10) REVERT: b 99 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8249 (tt) REVERT: b 113 TYR cc_start: 0.8614 (t80) cc_final: 0.7827 (t80) REVERT: b 149 TYR cc_start: 0.8264 (m-10) cc_final: 0.8023 (m-10) REVERT: e 78 ASN cc_start: 0.8645 (p0) cc_final: 0.8432 (p0) REVERT: f 18 ARG cc_start: 0.8070 (ptm160) cc_final: 0.7840 (ptm-80) REVERT: f 24 ASN cc_start: 0.8708 (t0) cc_final: 0.8433 (t0) REVERT: f 103 TYR cc_start: 0.8818 (p90) cc_final: 0.8533 (p90) REVERT: h 58 ILE cc_start: 0.8519 (mt) cc_final: 0.8042 (tp) REVERT: h 102 GLU cc_start: 0.7356 (tm-30) cc_final: 0.7154 (tp30) REVERT: j 21 ARG cc_start: 0.8575 (ttm170) cc_final: 0.7464 (ttm-80) REVERT: j 49 TRP cc_start: 0.7265 (p-90) cc_final: 0.4903 (t60) REVERT: n 36 CYS cc_start: 0.8368 (m) cc_final: 0.8074 (m) REVERT: n 69 GLN cc_start: 0.8927 (mt0) cc_final: 0.8606 (mm-40) REVERT: n 165 GLN cc_start: 0.8125 (mt0) cc_final: 0.7917 (mt0) REVERT: o 149 GLN cc_start: 0.7608 (tm-30) cc_final: 0.7190 (pp30) REVERT: p 102 GLU cc_start: 0.7547 (mt-10) cc_final: 0.6798 (mt-10) REVERT: p 162 MET cc_start: 0.8518 (mmt) cc_final: 0.8307 (mmp) REVERT: p 217 LEU cc_start: 0.8850 (mt) cc_final: 0.8639 (mt) REVERT: p 343 LEU cc_start: 0.8428 (tp) cc_final: 0.7880 (tt) REVERT: s 388 PHE cc_start: 0.8764 (t80) cc_final: 0.8394 (t80) REVERT: s 392 LEU cc_start: 0.8862 (mm) cc_final: 0.8336 (mt) REVERT: t 155 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8173 (mt) REVERT: t 168 LEU cc_start: 0.7973 (mt) cc_final: 0.7662 (mt) REVERT: t 254 ILE cc_start: 0.8813 (mt) cc_final: 0.8533 (mm) REVERT: u 7 HIS cc_start: 0.7342 (t70) cc_final: 0.7134 (t-170) REVERT: u 15 PRO cc_start: 0.7820 (Cg_exo) cc_final: 0.7617 (Cg_endo) REVERT: u 37 HIS cc_start: 0.8483 (t70) cc_final: 0.8149 (t70) REVERT: u 40 PHE cc_start: 0.8248 (t80) cc_final: 0.7375 (t80) REVERT: u 93 MET cc_start: 0.6623 (mtm) cc_final: 0.5606 (mtp) REVERT: v 206 TYR cc_start: 0.5726 (m-80) cc_final: 0.4234 (m-80) REVERT: w 186 LEU cc_start: 0.8413 (pp) cc_final: 0.8125 (pp) REVERT: w 191 GLN cc_start: 0.7137 (tt0) cc_final: 0.6931 (tp40) REVERT: w 231 GLU cc_start: 0.9305 (mt-10) cc_final: 0.9091 (mt-10) REVERT: w 232 VAL cc_start: 0.9296 (t) cc_final: 0.8986 (p) outliers start: 17 outliers final: 3 residues processed: 1838 average time/residue: 0.9579 time to fit residues: 2919.7698 Evaluate side-chains 958 residues out of total 5975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 953 time to evaluate : 5.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 80 VAL Chi-restraints excluded: chain b residue 99 LEU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain j residue 67 LEU Chi-restraints excluded: chain t residue 155 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 857 random chunks: chunk 723 optimal weight: 50.0000 chunk 649 optimal weight: 3.9990 chunk 360 optimal weight: 2.9990 chunk 221 optimal weight: 10.0000 chunk 438 optimal weight: 0.9990 chunk 347 optimal weight: 0.9990 chunk 671 optimal weight: 1.9990 chunk 259 optimal weight: 0.9990 chunk 408 optimal weight: 1.9990 chunk 499 optimal weight: 30.0000 chunk 778 optimal weight: 5.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 GLN A 332 ASN ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 GLN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 ASN C 116 ASN C 221 ASN ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 GLN ** D 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 GLN ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 ASN F 172 ASN ** F 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 GLN G 95 ASN G 137 ASN G 138 HIS ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 ASN ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 ASN I 164 HIS I 203 GLN I 228 GLN ** I 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 GLN K 200 ASN ** K 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 GLN N 37 HIS N 175 ASN N 194 GLN N 195 ASN O 50 ASN P 28 ASN P 45 GLN P 92 GLN P 97 ASN ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 78 ASN S 46 GLN S 74 ASN S 89 ASN W 384 ASN Y 120 GLN 7 29 ASN 7 31 GLN ** 7 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 49 ASN ** 7 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 210 GLN 8 319 GLN ** b 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 75 ASN b 118 HIS b 158 HIS b 254 GLN e 31 ASN e 52 GLN f 42 GLN h 108 GLN i 91 ASN ** i 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 48 ASN n 73 HIS n 160 GLN ** n 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 100 HIS ** o 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 69 GLN ** p 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 141 HIS p 153 ASN p 156 GLN ** p 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 325 GLN p 330 ASN p 413 ASN p 441 GLN t 92 HIS ** t 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 45 ASN u 82 ASN u 115 ASN v 81 HIS v 137 ASN v 171 ASN ** v 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 221 ASN ** y 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 178 GLN ** z 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 43 ASN z 132 GLN Total number of N/Q/H flips: 74 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 96776 Z= 0.205 Angle : 0.676 12.722 138381 Z= 0.346 Chirality : 0.038 0.277 16877 Planarity : 0.005 0.084 11636 Dihedral : 23.111 179.514 32812 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.19 % Favored : 95.75 % Rotamer: Outliers : 3.31 % Allowed : 12.66 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.06 % Twisted Proline : 0.74 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.09), residues: 6729 helix: -0.22 (0.09), residues: 2726 sheet: -0.81 (0.16), residues: 947 loop : -1.45 (0.10), residues: 3056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP W 427 HIS 0.012 0.002 HIS Y 110 PHE 0.023 0.002 PHE z 98 TYR 0.026 0.002 TYR y 35 ARG 0.011 0.001 ARG o 165 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13458 Ramachandran restraints generated. 6729 Oldfield, 0 Emsley, 6729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13458 Ramachandran restraints generated. 6729 Oldfield, 0 Emsley, 6729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1296 residues out of total 5975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 1098 time to evaluate : 6.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 MET cc_start: 0.8444 (tmt) cc_final: 0.7894 (tmm) REVERT: B 53 MET cc_start: 0.5924 (mtt) cc_final: 0.5506 (ptp) REVERT: B 106 TRP cc_start: 0.7376 (m100) cc_final: 0.7134 (m100) REVERT: B 214 MET cc_start: 0.8524 (tpp) cc_final: 0.8259 (mmm) REVERT: B 308 MET cc_start: 0.4709 (mtp) cc_final: 0.3798 (mtt) REVERT: B 346 THR cc_start: 0.7806 (OUTLIER) cc_final: 0.7446 (p) REVERT: C 34 ILE cc_start: 0.9322 (mt) cc_final: 0.8985 (tt) REVERT: C 45 ASN cc_start: 0.8168 (m-40) cc_final: 0.7637 (m110) REVERT: D 146 GLN cc_start: 0.8647 (mt0) cc_final: 0.8335 (tt0) REVERT: D 164 LYS cc_start: 0.8210 (tppt) cc_final: 0.7542 (tppt) REVERT: G 130 TYR cc_start: 0.8029 (m-10) cc_final: 0.7681 (m-80) REVERT: G 202 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7667 (mm-30) REVERT: I 294 TYR cc_start: 0.7559 (m-80) cc_final: 0.7130 (m-80) REVERT: L 23 LYS cc_start: 0.8474 (tptt) cc_final: 0.8059 (tptt) REVERT: L 27 ASP cc_start: 0.8655 (p0) cc_final: 0.8308 (p0) REVERT: L 37 ASN cc_start: 0.8265 (m-40) cc_final: 0.7994 (m110) REVERT: L 46 ILE cc_start: 0.8903 (mm) cc_final: 0.8652 (mm) REVERT: L 53 LEU cc_start: 0.9259 (mp) cc_final: 0.8877 (mp) REVERT: L 124 ILE cc_start: 0.8599 (pp) cc_final: 0.8276 (pt) REVERT: M 114 ASP cc_start: 0.7247 (p0) cc_final: 0.7034 (p0) REVERT: N 123 GLN cc_start: 0.8129 (pp30) cc_final: 0.7732 (pp30) REVERT: P 31 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7549 (mm-30) REVERT: P 46 LYS cc_start: 0.8836 (tmmt) cc_final: 0.8420 (tmmt) REVERT: P 111 LYS cc_start: 0.8410 (mttm) cc_final: 0.7049 (mtpt) REVERT: P 118 GLN cc_start: 0.8280 (tt0) cc_final: 0.8016 (tt0) REVERT: P 121 GLN cc_start: 0.8268 (mt0) cc_final: 0.7968 (mt0) REVERT: P 145 HIS cc_start: 0.8154 (m-70) cc_final: 0.7917 (m170) REVERT: P 151 THR cc_start: 0.8963 (m) cc_final: 0.8646 (p) REVERT: V 24 ASN cc_start: 0.6958 (m-40) cc_final: 0.6343 (m-40) REVERT: V 32 ARG cc_start: 0.7480 (mmt90) cc_final: 0.7241 (mmt90) REVERT: V 74 MET cc_start: 0.6786 (tpt) cc_final: 0.6201 (pmm) REVERT: Y 7 ASP cc_start: 0.7447 (m-30) cc_final: 0.6989 (m-30) REVERT: 8 311 MET cc_start: 0.6612 (mmm) cc_final: 0.6111 (mmm) REVERT: 8 329 GLN cc_start: 0.8590 (mt0) cc_final: 0.8089 (mm-40) REVERT: 8 334 GLN cc_start: 0.8919 (mt0) cc_final: 0.8320 (mm-40) REVERT: 8 340 ILE cc_start: 0.8575 (mt) cc_final: 0.8172 (mt) REVERT: 8 353 ARG cc_start: 0.8858 (mtm110) cc_final: 0.8384 (mtm-85) REVERT: 8 382 ARG cc_start: 0.7796 (mtt180) cc_final: 0.6580 (ttt180) REVERT: b 66 ASP cc_start: 0.8273 (p0) cc_final: 0.7981 (p0) REVERT: b 109 THR cc_start: 0.6009 (OUTLIER) cc_final: 0.5605 (p) REVERT: b 221 MET cc_start: 0.8646 (tmm) cc_final: 0.6996 (tmm) REVERT: e 78 ASN cc_start: 0.8800 (p0) cc_final: 0.8554 (p0) REVERT: f 63 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8577 (mtpp) REVERT: h 27 GLU cc_start: 0.7457 (tp30) cc_final: 0.7200 (tp30) REVERT: h 58 ILE cc_start: 0.8769 (mt) cc_final: 0.8364 (tp) REVERT: h 59 ASN cc_start: 0.8365 (m110) cc_final: 0.7943 (m110) REVERT: h 96 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7708 (mp0) REVERT: i 54 GLU cc_start: 0.8348 (mt-10) cc_final: 0.8131 (mt-10) REVERT: i 88 GLU cc_start: 0.8224 (pp20) cc_final: 0.7839 (pp20) REVERT: i 90 MET cc_start: 0.8133 (mmm) cc_final: 0.6255 (mmm) REVERT: j 49 TRP cc_start: 0.7116 (p-90) cc_final: 0.5013 (t-100) REVERT: j 55 ARG cc_start: 0.8533 (ttm110) cc_final: 0.7794 (mtm-85) REVERT: n 36 CYS cc_start: 0.8309 (m) cc_final: 0.7593 (m) REVERT: n 69 GLN cc_start: 0.8987 (mt0) cc_final: 0.8781 (tp40) REVERT: n 165 GLN cc_start: 0.8190 (mt0) cc_final: 0.7987 (mt0) REVERT: p 138 MET cc_start: 0.8620 (mmm) cc_final: 0.7846 (mmm) REVERT: p 162 MET cc_start: 0.8630 (mmt) cc_final: 0.8383 (mmm) REVERT: p 217 LEU cc_start: 0.8953 (mt) cc_final: 0.8738 (mt) REVERT: s 295 LYS cc_start: 0.8939 (mtmm) cc_final: 0.8436 (ptpp) REVERT: s 392 LEU cc_start: 0.8947 (mm) cc_final: 0.8692 (mt) REVERT: s 395 TYR cc_start: 0.5509 (t80) cc_final: 0.5281 (t80) REVERT: t 155 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8523 (mt) REVERT: u 40 PHE cc_start: 0.8168 (t80) cc_final: 0.7960 (t80) REVERT: u 81 TYR cc_start: 0.6321 (t80) cc_final: 0.6114 (t80) REVERT: u 93 MET cc_start: 0.6769 (mtm) cc_final: 0.5658 (mtp) REVERT: v 113 ASP cc_start: 0.6634 (t0) cc_final: 0.6375 (t0) REVERT: v 136 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6656 (pp) REVERT: v 203 MET cc_start: 0.7338 (ptp) cc_final: 0.6208 (ptp) REVERT: w 234 LYS cc_start: 0.7574 (tttt) cc_final: 0.7365 (tmtt) REVERT: y 99 GLU cc_start: 0.5766 (OUTLIER) cc_final: 0.5454 (pm20) REVERT: y 138 PHE cc_start: 0.6335 (m-80) cc_final: 0.6055 (m-10) outliers start: 198 outliers final: 90 residues processed: 1232 average time/residue: 0.8613 time to fit residues: 1797.3808 Evaluate side-chains 922 residues out of total 5975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 826 time to evaluate : 5.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain C residue 160 GLN Chi-restraints excluded: chain D residue 28 CYS Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 182 ASP Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 191 ASN Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 141 LYS Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain I residue 239 ILE Chi-restraints excluded: chain K residue 152 ASP Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 81 LYS Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain M residue 56 GLN Chi-restraints excluded: chain N residue 16 SER Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 125 SER Chi-restraints excluded: chain N residue 182 ASN Chi-restraints excluded: chain N residue 190 THR Chi-restraints excluded: chain O residue 21 SER Chi-restraints excluded: chain O residue 57 PHE Chi-restraints excluded: chain O residue 89 SER Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 141 SER Chi-restraints excluded: chain P residue 142 SER Chi-restraints excluded: chain P residue 144 SER Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain Y residue 80 VAL Chi-restraints excluded: chain 7 residue 10 ASN Chi-restraints excluded: chain 7 residue 12 SER Chi-restraints excluded: chain 7 residue 45 THR Chi-restraints excluded: chain 7 residue 167 SER Chi-restraints excluded: chain 8 residue 347 LEU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 159 ASN Chi-restraints excluded: chain e residue 69 SER Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain f residue 29 LEU Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 63 LYS Chi-restraints excluded: chain h residue 79 ASP Chi-restraints excluded: chain h residue 93 THR Chi-restraints excluded: chain i residue 50 LEU Chi-restraints excluded: chain i residue 53 TYR Chi-restraints excluded: chain j residue 33 THR Chi-restraints excluded: chain j residue 67 LEU Chi-restraints excluded: chain n residue 38 PHE Chi-restraints excluded: chain n residue 73 HIS Chi-restraints excluded: chain n residue 114 LEU Chi-restraints excluded: chain n residue 166 TRP Chi-restraints excluded: chain n residue 251 LYS Chi-restraints excluded: chain o residue 89 TYR Chi-restraints excluded: chain o residue 120 VAL Chi-restraints excluded: chain o residue 147 ILE Chi-restraints excluded: chain p residue 175 LEU Chi-restraints excluded: chain p residue 314 LEU Chi-restraints excluded: chain t residue 155 ILE Chi-restraints excluded: chain t residue 169 VAL Chi-restraints excluded: chain t residue 247 VAL Chi-restraints excluded: chain u residue 22 VAL Chi-restraints excluded: chain u residue 96 ILE Chi-restraints excluded: chain u residue 117 GLU Chi-restraints excluded: chain v residue 80 THR Chi-restraints excluded: chain v residue 136 LEU Chi-restraints excluded: chain v residue 166 VAL Chi-restraints excluded: chain v residue 209 ASP Chi-restraints excluded: chain v residue 353 HIS Chi-restraints excluded: chain w residue 184 THR Chi-restraints excluded: chain w residue 197 LEU Chi-restraints excluded: chain w residue 198 PHE Chi-restraints excluded: chain w residue 238 LEU Chi-restraints excluded: chain y residue 53 ILE Chi-restraints excluded: chain y residue 99 GLU Chi-restraints excluded: chain z residue 137 GLN Chi-restraints excluded: chain z residue 228 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 857 random chunks: chunk 432 optimal weight: 2.9990 chunk 241 optimal weight: 0.9990 chunk 647 optimal weight: 0.9980 chunk 529 optimal weight: 0.9980 chunk 214 optimal weight: 1.9990 chunk 779 optimal weight: 8.9990 chunk 842 optimal weight: 6.9990 chunk 694 optimal weight: 0.0000 chunk 773 optimal weight: 9.9990 chunk 265 optimal weight: 2.9990 chunk 625 optimal weight: 20.0000 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 HIS D 110 GLN ** F 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 203 GLN ** K 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 45 GLN P 92 GLN Q 78 ASN S 3 HIS ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 429 ASN Y 120 GLN ** 7 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 31 GLN ** 7 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 254 GLN b 277 ASN e 20 HIS e 52 GLN f 42 GLN f 106 ASN h 34 GLN ** h 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 20 ASN n 73 HIS ** n 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 141 HIS ** p 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 181 ASN ** p 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 426 GLN ** t 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 13 ASN ** z 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 96776 Z= 0.174 Angle : 0.619 12.464 138381 Z= 0.314 Chirality : 0.037 0.266 16877 Planarity : 0.004 0.078 11636 Dihedral : 22.841 178.896 32810 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.55 % Favored : 95.39 % Rotamer: Outliers : 2.93 % Allowed : 14.60 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.06 % Twisted Proline : 0.74 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.10), residues: 6729 helix: 0.39 (0.09), residues: 2718 sheet: -0.71 (0.16), residues: 980 loop : -1.24 (0.11), residues: 3031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 7 HIS 0.011 0.001 HIS I 164 PHE 0.021 0.002 PHE G 91 TYR 0.029 0.002 TYR F 176 ARG 0.011 0.000 ARG G 185 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13458 Ramachandran restraints generated. 6729 Oldfield, 0 Emsley, 6729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13458 Ramachandran restraints generated. 6729 Oldfield, 0 Emsley, 6729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1097 residues out of total 5975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 922 time to evaluate : 6.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: B 53 MET cc_start: 0.5777 (mtt) cc_final: 0.5436 (ptp) REVERT: B 308 MET cc_start: 0.4720 (mtp) cc_final: 0.4301 (mtp) REVERT: C 34 ILE cc_start: 0.9313 (mt) cc_final: 0.9069 (tt) REVERT: D 164 LYS cc_start: 0.8126 (tppt) cc_final: 0.7890 (tppt) REVERT: D 168 ASP cc_start: 0.8187 (m-30) cc_final: 0.7108 (m-30) REVERT: G 57 ARG cc_start: 0.8655 (ptt90) cc_final: 0.8410 (ptm-80) REVERT: G 61 GLN cc_start: 0.8391 (mt0) cc_final: 0.8155 (tt0) REVERT: I 33 MET cc_start: 0.7983 (tmm) cc_final: 0.7749 (tmm) REVERT: I 250 ASP cc_start: 0.7616 (p0) cc_final: 0.7391 (p0) REVERT: L 23 LYS cc_start: 0.8504 (tptt) cc_final: 0.8043 (tptt) REVERT: L 27 ASP cc_start: 0.8636 (p0) cc_final: 0.8291 (p0) REVERT: L 37 ASN cc_start: 0.7931 (m-40) cc_final: 0.7699 (m-40) REVERT: L 46 ILE cc_start: 0.8913 (mm) cc_final: 0.8601 (mm) REVERT: M 11 ASN cc_start: 0.6434 (t0) cc_final: 0.5703 (p0) REVERT: M 47 ASP cc_start: 0.7234 (t0) cc_final: 0.6622 (t0) REVERT: N 46 ASP cc_start: 0.8133 (p0) cc_final: 0.7576 (p0) REVERT: O 39 GLU cc_start: 0.8480 (pm20) cc_final: 0.7061 (pm20) REVERT: O 55 HIS cc_start: 0.8173 (m-70) cc_final: 0.7673 (m-70) REVERT: O 149 TYR cc_start: 0.8091 (m-80) cc_final: 0.7781 (m-80) REVERT: P 31 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7620 (mm-30) REVERT: P 53 ASP cc_start: 0.6658 (t70) cc_final: 0.6114 (t0) REVERT: P 118 GLN cc_start: 0.8294 (tt0) cc_final: 0.8072 (tt0) REVERT: P 125 GLN cc_start: 0.7887 (pm20) cc_final: 0.7459 (tt0) REVERT: P 145 HIS cc_start: 0.8082 (m-70) cc_final: 0.7658 (m170) REVERT: P 148 LEU cc_start: 0.9444 (pt) cc_final: 0.9227 (pp) REVERT: P 152 GLU cc_start: 0.8352 (mp0) cc_final: 0.8078 (mp0) REVERT: S 118 PHE cc_start: 0.7458 (t80) cc_final: 0.7158 (t80) REVERT: V 24 ASN cc_start: 0.6917 (m-40) cc_final: 0.6581 (m-40) REVERT: V 32 ARG cc_start: 0.7556 (mmt90) cc_final: 0.7254 (mmt90) REVERT: V 85 TRP cc_start: 0.6996 (p90) cc_final: 0.6727 (p90) REVERT: V 96 GLU cc_start: 0.6772 (tm-30) cc_final: 0.6310 (tm-30) REVERT: W 416 LEU cc_start: 0.7318 (mp) cc_final: 0.7109 (mp) REVERT: W 449 ILE cc_start: 0.7065 (OUTLIER) cc_final: 0.6750 (mm) REVERT: W 453 LEU cc_start: 0.8546 (mt) cc_final: 0.8213 (mt) REVERT: Y 7 ASP cc_start: 0.7293 (m-30) cc_final: 0.6996 (m-30) REVERT: 8 317 LEU cc_start: 0.8652 (mt) cc_final: 0.8429 (tp) REVERT: 8 382 ARG cc_start: 0.7620 (mtt180) cc_final: 0.6699 (ttt180) REVERT: b 98 TYR cc_start: 0.7295 (m-10) cc_final: 0.7083 (m-10) REVERT: h 27 GLU cc_start: 0.7700 (tp30) cc_final: 0.7254 (tp30) REVERT: h 31 LEU cc_start: 0.8782 (mp) cc_final: 0.8375 (mt) REVERT: h 59 ASN cc_start: 0.8457 (m110) cc_final: 0.8124 (m110) REVERT: h 96 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7734 (mp0) REVERT: i 54 GLU cc_start: 0.8262 (mt-10) cc_final: 0.8056 (mt-10) REVERT: i 88 GLU cc_start: 0.8234 (pp20) cc_final: 0.7825 (pp20) REVERT: i 89 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7530 (tm-30) REVERT: i 90 MET cc_start: 0.7844 (mmm) cc_final: 0.7434 (mmm) REVERT: j 43 LYS cc_start: 0.9040 (mmmt) cc_final: 0.8812 (mmtt) REVERT: j 49 TRP cc_start: 0.7092 (p-90) cc_final: 0.4973 (t-100) REVERT: j 52 LYS cc_start: 0.7663 (tmtt) cc_final: 0.6728 (tptm) REVERT: n 36 CYS cc_start: 0.8226 (m) cc_final: 0.7933 (m) REVERT: o 146 MET cc_start: 0.8340 (tpt) cc_final: 0.7758 (tpp) REVERT: o 158 MET cc_start: 0.7639 (tpp) cc_final: 0.7064 (mmp) REVERT: p 149 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8483 (mm) REVERT: p 162 MET cc_start: 0.8638 (mmt) cc_final: 0.8361 (mmp) REVERT: s 264 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7934 (ptt90) REVERT: s 294 LEU cc_start: 0.9124 (mt) cc_final: 0.8545 (mm) REVERT: u 40 PHE cc_start: 0.8274 (t80) cc_final: 0.8072 (t80) REVERT: v 32 GLN cc_start: 0.8108 (pm20) cc_final: 0.7765 (pm20) REVERT: v 82 LEU cc_start: 0.8871 (tt) cc_final: 0.8443 (tt) REVERT: v 136 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6704 (pp) REVERT: v 206 TYR cc_start: 0.6651 (m-80) cc_final: 0.5885 (m-80) outliers start: 175 outliers final: 104 residues processed: 1034 average time/residue: 0.8366 time to fit residues: 1483.8141 Evaluate side-chains 889 residues out of total 5975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 781 time to evaluate : 6.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 160 GLN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain D residue 28 CYS Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 185 ARG Chi-restraints excluded: chain G residue 191 ASN Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 139 CYS Chi-restraints excluded: chain I residue 141 LYS Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain I residue 246 TYR Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 152 ASP Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain K residue 301 LEU Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain M residue 38 ILE Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 135 LEU Chi-restraints excluded: chain N residue 16 SER Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain O residue 57 PHE Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 144 SER Chi-restraints excluded: chain P residue 149 VAL Chi-restraints excluded: chain S residue 16 THR Chi-restraints excluded: chain S residue 122 HIS Chi-restraints excluded: chain S residue 147 ASP Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain W residue 429 ASN Chi-restraints excluded: chain W residue 449 ILE Chi-restraints excluded: chain Y residue 80 VAL Chi-restraints excluded: chain 7 residue 10 ASN Chi-restraints excluded: chain 7 residue 12 SER Chi-restraints excluded: chain 7 residue 45 THR Chi-restraints excluded: chain 7 residue 199 MET Chi-restraints excluded: chain 7 residue 214 ASP Chi-restraints excluded: chain 8 residue 304 LEU Chi-restraints excluded: chain 8 residue 372 VAL Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain e residue 69 SER Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain h residue 19 SER Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 79 ASP Chi-restraints excluded: chain i residue 50 LEU Chi-restraints excluded: chain i residue 53 TYR Chi-restraints excluded: chain j residue 25 ARG Chi-restraints excluded: chain j residue 67 LEU Chi-restraints excluded: chain n residue 38 PHE Chi-restraints excluded: chain n residue 73 HIS Chi-restraints excluded: chain n residue 166 TRP Chi-restraints excluded: chain n residue 251 LYS Chi-restraints excluded: chain o residue 89 TYR Chi-restraints excluded: chain o residue 97 ARG Chi-restraints excluded: chain o residue 116 ASP Chi-restraints excluded: chain o residue 147 ILE Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain p residue 149 ILE Chi-restraints excluded: chain p residue 303 LYS Chi-restraints excluded: chain p residue 314 LEU Chi-restraints excluded: chain p residue 435 SER Chi-restraints excluded: chain s residue 264 ARG Chi-restraints excluded: chain t residue 168 LEU Chi-restraints excluded: chain t residue 169 VAL Chi-restraints excluded: chain t residue 175 VAL Chi-restraints excluded: chain t residue 247 VAL Chi-restraints excluded: chain u residue 17 HIS Chi-restraints excluded: chain u residue 22 VAL Chi-restraints excluded: chain u residue 29 PHE Chi-restraints excluded: chain u residue 96 ILE Chi-restraints excluded: chain u residue 117 GLU Chi-restraints excluded: chain v residue 80 THR Chi-restraints excluded: chain v residue 136 LEU Chi-restraints excluded: chain v residue 166 VAL Chi-restraints excluded: chain v residue 209 ASP Chi-restraints excluded: chain v residue 353 HIS Chi-restraints excluded: chain w residue 197 LEU Chi-restraints excluded: chain w residue 198 PHE Chi-restraints excluded: chain w residue 238 LEU Chi-restraints excluded: chain y residue 53 ILE Chi-restraints excluded: chain z residue 56 SER Chi-restraints excluded: chain z residue 137 GLN Chi-restraints excluded: chain z residue 228 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 857 random chunks: chunk 770 optimal weight: 10.0000 chunk 586 optimal weight: 3.9990 chunk 404 optimal weight: 0.9990 chunk 86 optimal weight: 8.9990 chunk 372 optimal weight: 0.9990 chunk 523 optimal weight: 1.9990 chunk 782 optimal weight: 20.0000 chunk 828 optimal weight: 9.9990 chunk 408 optimal weight: 10.0000 chunk 741 optimal weight: 50.0000 chunk 223 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 GLN ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 GLN E 120 ASN ** F 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 ASN ** K 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 GLN K 143 GLN K 176 GLN ** M 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 45 GLN P 92 GLN ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 63 GLN V 81 GLN W 454 GLN 7 48 GLN ** 7 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 254 GLN e 20 HIS e 52 GLN f 42 GLN h 108 GLN ** i 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 79 GLN n 73 HIS ** n 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 137 ASN ** v 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 39 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 96776 Z= 0.229 Angle : 0.618 15.163 138381 Z= 0.316 Chirality : 0.037 0.233 16877 Planarity : 0.004 0.083 11636 Dihedral : 22.659 179.605 32808 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.81 % Favored : 95.16 % Rotamer: Outliers : 3.35 % Allowed : 15.08 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.06 % Twisted Proline : 0.74 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.10), residues: 6729 helix: 0.75 (0.10), residues: 2725 sheet: -0.51 (0.16), residues: 976 loop : -1.15 (0.11), residues: 3028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP s 246 HIS 0.008 0.001 HIS p 141 PHE 0.024 0.002 PHE b 160 TYR 0.020 0.002 TYR h 75 ARG 0.006 0.001 ARG P 56 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13458 Ramachandran restraints generated. 6729 Oldfield, 0 Emsley, 6729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13458 Ramachandran restraints generated. 6729 Oldfield, 0 Emsley, 6729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1034 residues out of total 5975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 834 time to evaluate : 6.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 294 ILE cc_start: 0.8976 (mt) cc_final: 0.8659 (mt) REVERT: B 53 MET cc_start: 0.5776 (mtt) cc_final: 0.5358 (ptp) REVERT: B 308 MET cc_start: 0.4718 (mtp) cc_final: 0.4279 (mtp) REVERT: B 346 THR cc_start: 0.7748 (OUTLIER) cc_final: 0.7485 (m) REVERT: D 43 CYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8209 (t) REVERT: I 33 MET cc_start: 0.8187 (tmm) cc_final: 0.7875 (tmm) REVERT: K 79 GLN cc_start: 0.7653 (tp-100) cc_final: 0.7141 (tp40) REVERT: L 23 LYS cc_start: 0.8608 (tptt) cc_final: 0.8218 (tptt) REVERT: L 27 ASP cc_start: 0.8689 (p0) cc_final: 0.8350 (p0) REVERT: L 93 ILE cc_start: 0.9479 (mm) cc_final: 0.9152 (tp) REVERT: M 47 ASP cc_start: 0.7276 (t0) cc_final: 0.6722 (t0) REVERT: O 39 GLU cc_start: 0.8137 (pm20) cc_final: 0.7550 (pm20) REVERT: O 87 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.7915 (mmm) REVERT: O 149 TYR cc_start: 0.8205 (m-80) cc_final: 0.7941 (m-80) REVERT: P 31 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7583 (mm-30) REVERT: P 47 TYR cc_start: 0.8524 (t80) cc_final: 0.8292 (t80) REVERT: S 118 PHE cc_start: 0.7461 (t80) cc_final: 0.7147 (t80) REVERT: V 24 ASN cc_start: 0.7359 (m-40) cc_final: 0.6987 (m-40) REVERT: V 86 ARG cc_start: 0.8340 (ttm170) cc_final: 0.7858 (ttm-80) REVERT: W 416 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7241 (mp) REVERT: W 429 ASN cc_start: 0.8681 (OUTLIER) cc_final: 0.8193 (p0) REVERT: W 444 PHE cc_start: 0.8435 (t80) cc_final: 0.8019 (t80) REVERT: 8 332 MET cc_start: 0.8928 (mmm) cc_final: 0.8635 (mmm) REVERT: 8 340 ILE cc_start: 0.8774 (mm) cc_final: 0.8495 (mm) REVERT: 8 382 ARG cc_start: 0.7616 (mtt180) cc_final: 0.6797 (ttt180) REVERT: f 45 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8727 (mm) REVERT: h 31 LEU cc_start: 0.8814 (mp) cc_final: 0.8435 (mt) REVERT: h 59 ASN cc_start: 0.8548 (m110) cc_final: 0.8184 (m110) REVERT: h 96 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7678 (mp0) REVERT: i 89 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7303 (tm-30) REVERT: i 90 MET cc_start: 0.7686 (mmm) cc_final: 0.6945 (mmm) REVERT: j 49 TRP cc_start: 0.6979 (p-90) cc_final: 0.4914 (t-100) REVERT: n 36 CYS cc_start: 0.8104 (m) cc_final: 0.7045 (m) REVERT: n 404 MET cc_start: 0.6215 (mmm) cc_final: 0.5880 (mpp) REVERT: o 121 ARG cc_start: 0.7883 (mtm-85) cc_final: 0.7400 (mtm180) REVERT: o 146 MET cc_start: 0.8436 (tpt) cc_final: 0.8202 (tpp) REVERT: p 102 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7191 (pt0) REVERT: p 149 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8470 (mm) REVERT: p 162 MET cc_start: 0.8624 (mmt) cc_final: 0.8412 (mmp) REVERT: s 264 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.8124 (ptt90) REVERT: s 294 LEU cc_start: 0.9239 (mt) cc_final: 0.9028 (mm) REVERT: s 295 LYS cc_start: 0.8871 (mtmm) cc_final: 0.8528 (ptpp) REVERT: s 389 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8047 (mm-30) REVERT: u 40 PHE cc_start: 0.7988 (t80) cc_final: 0.7739 (t80) REVERT: v 32 GLN cc_start: 0.8119 (pm20) cc_final: 0.7831 (pm20) REVERT: v 119 ASP cc_start: 0.8028 (m-30) cc_final: 0.7747 (p0) REVERT: v 136 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.6823 (pp) REVERT: w 209 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8455 (mm-30) REVERT: y 138 PHE cc_start: 0.6786 (m-80) cc_final: 0.6359 (m-10) outliers start: 200 outliers final: 130 residues processed: 956 average time/residue: 0.8547 time to fit residues: 1401.1768 Evaluate side-chains 871 residues out of total 5975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 732 time to evaluate : 5.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 160 GLN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain D residue 28 CYS Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 43 CYS Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 182 ASP Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 122 LYS Chi-restraints excluded: chain G residue 191 ASN Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 139 CYS Chi-restraints excluded: chain I residue 141 LYS Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain I residue 246 TYR Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 127 LEU Chi-restraints excluded: chain K residue 152 ASP Chi-restraints excluded: chain K residue 154 ILE Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain K residue 301 LEU Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 135 LEU Chi-restraints excluded: chain N residue 16 SER Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 133 ILE Chi-restraints excluded: chain N residue 182 ASN Chi-restraints excluded: chain N residue 190 THR Chi-restraints excluded: chain N residue 196 THR Chi-restraints excluded: chain O residue 57 PHE Chi-restraints excluded: chain O residue 87 MET Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 151 ASP Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 141 SER Chi-restraints excluded: chain P residue 144 SER Chi-restraints excluded: chain P residue 149 VAL Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain S residue 16 THR Chi-restraints excluded: chain S residue 122 HIS Chi-restraints excluded: chain S residue 147 ASP Chi-restraints excluded: chain V residue 22 ILE Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain W residue 416 LEU Chi-restraints excluded: chain W residue 429 ASN Chi-restraints excluded: chain Y residue 80 VAL Chi-restraints excluded: chain 7 residue 10 ASN Chi-restraints excluded: chain 7 residue 12 SER Chi-restraints excluded: chain 7 residue 45 THR Chi-restraints excluded: chain 7 residue 199 MET Chi-restraints excluded: chain 7 residue 214 ASP Chi-restraints excluded: chain 8 residue 304 LEU Chi-restraints excluded: chain 8 residue 389 ILE Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 231 PHE Chi-restraints excluded: chain e residue 69 SER Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 85 LEU Chi-restraints excluded: chain e residue 109 LEU Chi-restraints excluded: chain e residue 115 LEU Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 45 LEU Chi-restraints excluded: chain f residue 72 THR Chi-restraints excluded: chain h residue 79 ASP Chi-restraints excluded: chain i residue 50 LEU Chi-restraints excluded: chain i residue 53 TYR Chi-restraints excluded: chain j residue 25 ARG Chi-restraints excluded: chain j residue 54 LYS Chi-restraints excluded: chain n residue 38 PHE Chi-restraints excluded: chain n residue 73 HIS Chi-restraints excluded: chain n residue 114 LEU Chi-restraints excluded: chain n residue 251 LYS Chi-restraints excluded: chain o residue 89 TYR Chi-restraints excluded: chain o residue 97 ARG Chi-restraints excluded: chain o residue 116 ASP Chi-restraints excluded: chain o residue 120 VAL Chi-restraints excluded: chain o residue 147 ILE Chi-restraints excluded: chain o residue 157 LEU Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain o residue 185 VAL Chi-restraints excluded: chain o residue 198 ASP Chi-restraints excluded: chain p residue 104 LEU Chi-restraints excluded: chain p residue 149 ILE Chi-restraints excluded: chain p residue 177 ASP Chi-restraints excluded: chain p residue 314 LEU Chi-restraints excluded: chain p residue 412 LEU Chi-restraints excluded: chain p residue 435 SER Chi-restraints excluded: chain s residue 264 ARG Chi-restraints excluded: chain s residue 271 ASN Chi-restraints excluded: chain t residue 145 VAL Chi-restraints excluded: chain t residue 168 LEU Chi-restraints excluded: chain t residue 169 VAL Chi-restraints excluded: chain t residue 247 VAL Chi-restraints excluded: chain u residue 22 VAL Chi-restraints excluded: chain u residue 29 PHE Chi-restraints excluded: chain u residue 117 GLU Chi-restraints excluded: chain v residue 136 LEU Chi-restraints excluded: chain v residue 166 VAL Chi-restraints excluded: chain v residue 209 ASP Chi-restraints excluded: chain v residue 339 LEU Chi-restraints excluded: chain v residue 353 HIS Chi-restraints excluded: chain w residue 184 THR Chi-restraints excluded: chain w residue 197 LEU Chi-restraints excluded: chain w residue 198 PHE Chi-restraints excluded: chain w residue 238 LEU Chi-restraints excluded: chain y residue 53 ILE Chi-restraints excluded: chain z residue 56 SER Chi-restraints excluded: chain z residue 137 GLN Chi-restraints excluded: chain z residue 228 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 857 random chunks: chunk 689 optimal weight: 6.9990 chunk 470 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 616 optimal weight: 7.9990 chunk 341 optimal weight: 3.9990 chunk 706 optimal weight: 0.5980 chunk 572 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 422 optimal weight: 6.9990 chunk 743 optimal weight: 50.0000 chunk 209 optimal weight: 9.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 ASN E 120 ASN ** F 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 145 ASN ** G 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 HIS ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 57 GLN ** O 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 92 GLN ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 413 ASN W 429 ASN 7 10 ASN 7 25 GLN 7 31 GLN 7 39 ASN ** 7 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 20 HIS e 52 GLN e 104 ASN ** i 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 48 ASN n 73 HIS ** n 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 181 ASN ** t 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 101 GLN ** v 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 20 ASN z 132 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 96776 Z= 0.382 Angle : 0.702 17.281 138381 Z= 0.360 Chirality : 0.041 0.375 16877 Planarity : 0.005 0.063 11636 Dihedral : 22.615 179.540 32806 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 22.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.66 % Favored : 94.29 % Rotamer: Outliers : 4.03 % Allowed : 15.87 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.06 % Twisted Proline : 0.74 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.10), residues: 6729 helix: 0.79 (0.10), residues: 2726 sheet: -0.41 (0.16), residues: 981 loop : -1.17 (0.11), residues: 3022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 99 HIS 0.013 0.002 HIS n 73 PHE 0.028 0.002 PHE P 63 TYR 0.023 0.002 TYR I 66 ARG 0.014 0.001 ARG u 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13458 Ramachandran restraints generated. 6729 Oldfield, 0 Emsley, 6729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13458 Ramachandran restraints generated. 6729 Oldfield, 0 Emsley, 6729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 990 residues out of total 5975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 749 time to evaluate : 6.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 ILE cc_start: 0.9016 (mt) cc_final: 0.8655 (mt) REVERT: B 53 MET cc_start: 0.6141 (mtt) cc_final: 0.5497 (ptp) REVERT: B 99 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8618 (tp) REVERT: B 308 MET cc_start: 0.5145 (mtp) cc_final: 0.4691 (mtp) REVERT: G 123 GLN cc_start: 0.7742 (pm20) cc_final: 0.7540 (pm20) REVERT: I 33 MET cc_start: 0.8470 (tmm) cc_final: 0.8251 (tmm) REVERT: L 27 ASP cc_start: 0.8777 (p0) cc_final: 0.8485 (p0) REVERT: L 37 ASN cc_start: 0.8205 (m-40) cc_final: 0.7678 (m-40) REVERT: L 93 ILE cc_start: 0.9495 (OUTLIER) cc_final: 0.9240 (tp) REVERT: M 47 ASP cc_start: 0.7647 (t0) cc_final: 0.7033 (t0) REVERT: O 149 TYR cc_start: 0.8374 (m-80) cc_final: 0.7949 (m-80) REVERT: P 31 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7579 (mm-30) REVERT: S 118 PHE cc_start: 0.7570 (t80) cc_final: 0.7256 (t80) REVERT: V 24 ASN cc_start: 0.7261 (m-40) cc_final: 0.6862 (m-40) REVERT: V 96 GLU cc_start: 0.6530 (tm-30) cc_final: 0.6270 (tm-30) REVERT: W 383 LYS cc_start: 0.7964 (ptpt) cc_final: 0.7721 (ptpp) REVERT: 7 49 ASN cc_start: 0.8614 (OUTLIER) cc_final: 0.8114 (t0) REVERT: 8 368 ARG cc_start: 0.8909 (mmm-85) cc_final: 0.8294 (mmm-85) REVERT: 8 382 ARG cc_start: 0.7542 (mtt180) cc_final: 0.6649 (ttt180) REVERT: f 45 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8988 (mm) REVERT: h 27 GLU cc_start: 0.7563 (tp30) cc_final: 0.6500 (tp30) REVERT: h 31 LEU cc_start: 0.8906 (mp) cc_final: 0.7232 (mp) REVERT: h 59 ASN cc_start: 0.8569 (m-40) cc_final: 0.8235 (m110) REVERT: h 96 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7770 (mp0) REVERT: i 20 MET cc_start: 0.7686 (tpp) cc_final: 0.7321 (tpp) REVERT: i 54 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8143 (mp0) REVERT: i 88 GLU cc_start: 0.8084 (pp20) cc_final: 0.7722 (pp20) REVERT: i 89 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7653 (tm-30) REVERT: i 90 MET cc_start: 0.7834 (mmm) cc_final: 0.7411 (mmm) REVERT: j 52 LYS cc_start: 0.7446 (tmtt) cc_final: 0.6686 (tptm) REVERT: n 36 CYS cc_start: 0.8732 (m) cc_final: 0.8228 (m) REVERT: o 146 MET cc_start: 0.8521 (tpt) cc_final: 0.8282 (tpp) REVERT: p 65 MET cc_start: 0.6688 (OUTLIER) cc_final: 0.6386 (ptm) REVERT: p 102 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7482 (pt0) REVERT: s 264 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.8339 (ptt90) REVERT: s 272 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8442 (mt-10) REVERT: s 295 LYS cc_start: 0.9004 (mtmm) cc_final: 0.8589 (ptpp) REVERT: t 245 ILE cc_start: 0.7814 (OUTLIER) cc_final: 0.7398 (mt) REVERT: u 20 MET cc_start: 0.5903 (tpp) cc_final: 0.5326 (tpp) REVERT: u 40 PHE cc_start: 0.8196 (t80) cc_final: 0.7947 (t80) REVERT: v 119 ASP cc_start: 0.8063 (m-30) cc_final: 0.7739 (p0) REVERT: v 136 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.6866 (pp) outliers start: 241 outliers final: 168 residues processed: 909 average time/residue: 0.8529 time to fit residues: 1329.5923 Evaluate side-chains 872 residues out of total 5975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 695 time to evaluate : 5.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 160 GLN Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 182 ASP Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 122 LYS Chi-restraints excluded: chain G residue 191 ASN Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 139 CYS Chi-restraints excluded: chain I residue 141 LYS Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain I residue 246 TYR Chi-restraints excluded: chain I residue 251 ASN Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 152 ASP Chi-restraints excluded: chain K residue 154 ILE Chi-restraints excluded: chain K residue 159 ASP Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain K residue 301 LEU Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 135 LEU Chi-restraints excluded: chain N residue 16 SER Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 123 GLN Chi-restraints excluded: chain N residue 125 SER Chi-restraints excluded: chain N residue 133 ILE Chi-restraints excluded: chain N residue 182 ASN Chi-restraints excluded: chain N residue 190 THR Chi-restraints excluded: chain N residue 196 THR Chi-restraints excluded: chain O residue 57 PHE Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 151 ASP Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 118 GLN Chi-restraints excluded: chain P residue 141 SER Chi-restraints excluded: chain P residue 142 SER Chi-restraints excluded: chain P residue 149 VAL Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain S residue 16 THR Chi-restraints excluded: chain S residue 122 HIS Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain S residue 147 ASP Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain S residue 170 THR Chi-restraints excluded: chain V residue 22 ILE Chi-restraints excluded: chain V residue 69 LEU Chi-restraints excluded: chain V residue 92 PHE Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain Y residue 80 VAL Chi-restraints excluded: chain 7 residue 10 ASN Chi-restraints excluded: chain 7 residue 12 SER Chi-restraints excluded: chain 7 residue 45 THR Chi-restraints excluded: chain 7 residue 49 ASN Chi-restraints excluded: chain 7 residue 167 SER Chi-restraints excluded: chain 7 residue 199 MET Chi-restraints excluded: chain 7 residue 214 ASP Chi-restraints excluded: chain 8 residue 304 LEU Chi-restraints excluded: chain 8 residue 334 GLN Chi-restraints excluded: chain b residue 86 VAL Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 142 ARG Chi-restraints excluded: chain b residue 175 HIS Chi-restraints excluded: chain b residue 231 PHE Chi-restraints excluded: chain b residue 287 ASP Chi-restraints excluded: chain e residue 18 LYS Chi-restraints excluded: chain e residue 69 SER Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 85 LEU Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 45 LEU Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain h residue 36 LEU Chi-restraints excluded: chain h residue 79 ASP Chi-restraints excluded: chain i residue 50 LEU Chi-restraints excluded: chain i residue 53 TYR Chi-restraints excluded: chain i residue 54 GLU Chi-restraints excluded: chain i residue 63 ASN Chi-restraints excluded: chain j residue 33 THR Chi-restraints excluded: chain j residue 46 SER Chi-restraints excluded: chain j residue 58 THR Chi-restraints excluded: chain n residue 38 PHE Chi-restraints excluded: chain n residue 73 HIS Chi-restraints excluded: chain n residue 114 LEU Chi-restraints excluded: chain n residue 166 TRP Chi-restraints excluded: chain n residue 251 LYS Chi-restraints excluded: chain o residue 92 ILE Chi-restraints excluded: chain o residue 97 ARG Chi-restraints excluded: chain o residue 116 ASP Chi-restraints excluded: chain o residue 120 VAL Chi-restraints excluded: chain o residue 147 ILE Chi-restraints excluded: chain o residue 161 LEU Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain o residue 185 VAL Chi-restraints excluded: chain o residue 193 VAL Chi-restraints excluded: chain o residue 198 ASP Chi-restraints excluded: chain p residue 65 MET Chi-restraints excluded: chain p residue 104 LEU Chi-restraints excluded: chain p residue 177 ASP Chi-restraints excluded: chain p residue 279 LEU Chi-restraints excluded: chain p residue 303 LYS Chi-restraints excluded: chain p residue 314 LEU Chi-restraints excluded: chain p residue 372 ASP Chi-restraints excluded: chain p residue 412 LEU Chi-restraints excluded: chain p residue 435 SER Chi-restraints excluded: chain s residue 264 ARG Chi-restraints excluded: chain s residue 271 ASN Chi-restraints excluded: chain s residue 283 ILE Chi-restraints excluded: chain t residue 145 VAL Chi-restraints excluded: chain t residue 168 LEU Chi-restraints excluded: chain t residue 169 VAL Chi-restraints excluded: chain t residue 175 VAL Chi-restraints excluded: chain t residue 245 ILE Chi-restraints excluded: chain t residue 247 VAL Chi-restraints excluded: chain u residue 8 PHE Chi-restraints excluded: chain u residue 17 HIS Chi-restraints excluded: chain u residue 22 VAL Chi-restraints excluded: chain u residue 52 THR Chi-restraints excluded: chain u residue 117 GLU Chi-restraints excluded: chain u residue 119 ASP Chi-restraints excluded: chain v residue 80 THR Chi-restraints excluded: chain v residue 136 LEU Chi-restraints excluded: chain v residue 166 VAL Chi-restraints excluded: chain v residue 195 ASP Chi-restraints excluded: chain v residue 209 ASP Chi-restraints excluded: chain v residue 339 LEU Chi-restraints excluded: chain v residue 353 HIS Chi-restraints excluded: chain w residue 184 THR Chi-restraints excluded: chain w residue 197 LEU Chi-restraints excluded: chain w residue 198 PHE Chi-restraints excluded: chain y residue 53 ILE Chi-restraints excluded: chain z residue 56 SER Chi-restraints excluded: chain z residue 137 GLN Chi-restraints excluded: chain z residue 228 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 857 random chunks: chunk 278 optimal weight: 2.9990 chunk 745 optimal weight: 50.0000 chunk 163 optimal weight: 0.6980 chunk 486 optimal weight: 2.9990 chunk 204 optimal weight: 7.9990 chunk 829 optimal weight: 9.9990 chunk 688 optimal weight: 6.9990 chunk 383 optimal weight: 0.0470 chunk 68 optimal weight: 10.0000 chunk 274 optimal weight: 0.7980 chunk 435 optimal weight: 7.9990 overall best weight: 1.5082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 ASN ** F 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 57 GLN O 31 GLN ** O 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 34 GLN P 92 GLN ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 454 GLN ** Y 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 10 ASN ** 7 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 31 GLN ** 7 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 175 HIS b 239 ASN e 20 HIS e 31 ASN e 52 GLN f 42 GLN ** i 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 26 GLN n 73 HIS ** n 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 175 ASN ** y 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 132 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 96776 Z= 0.184 Angle : 0.609 14.443 138381 Z= 0.310 Chirality : 0.037 0.290 16877 Planarity : 0.004 0.060 11636 Dihedral : 22.563 179.923 32806 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.11 % Favored : 94.86 % Rotamer: Outliers : 3.13 % Allowed : 17.31 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.06 % Twisted Proline : 0.74 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.10), residues: 6729 helix: 1.00 (0.10), residues: 2721 sheet: -0.30 (0.16), residues: 965 loop : -1.05 (0.11), residues: 3043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP j 49 HIS 0.013 0.001 HIS n 73 PHE 0.035 0.001 PHE P 63 TYR 0.023 0.002 TYR I 66 ARG 0.021 0.000 ARG I 51 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13458 Ramachandran restraints generated. 6729 Oldfield, 0 Emsley, 6729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13458 Ramachandran restraints generated. 6729 Oldfield, 0 Emsley, 6729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 997 residues out of total 5975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 810 time to evaluate : 5.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 ILE cc_start: 0.8972 (mt) cc_final: 0.8641 (mt) REVERT: B 53 MET cc_start: 0.5995 (mtt) cc_final: 0.5326 (ptp) REVERT: B 99 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8485 (tp) REVERT: B 308 MET cc_start: 0.5051 (mtp) cc_final: 0.4563 (mtp) REVERT: G 202 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8071 (mm-30) REVERT: I 33 MET cc_start: 0.8399 (tmm) cc_final: 0.8111 (tmm) REVERT: K 129 ASP cc_start: 0.7570 (p0) cc_final: 0.7162 (p0) REVERT: L 27 ASP cc_start: 0.8650 (p0) cc_final: 0.8388 (p0) REVERT: M 47 ASP cc_start: 0.7485 (t0) cc_final: 0.6909 (t0) REVERT: M 121 MET cc_start: 0.8532 (tpt) cc_final: 0.8304 (tpt) REVERT: N 8 GLU cc_start: 0.8066 (tp30) cc_final: 0.7853 (tp30) REVERT: N 138 GLN cc_start: 0.8679 (mm-40) cc_final: 0.8436 (mm-40) REVERT: N 152 CYS cc_start: 0.8855 (m) cc_final: 0.8470 (m) REVERT: O 149 TYR cc_start: 0.8298 (m-80) cc_final: 0.7887 (m-80) REVERT: P 31 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7448 (mm-30) REVERT: P 121 GLN cc_start: 0.8307 (mt0) cc_final: 0.8003 (mt0) REVERT: P 125 GLN cc_start: 0.7909 (pm20) cc_final: 0.7126 (mm110) REVERT: S 118 PHE cc_start: 0.7495 (t80) cc_final: 0.7199 (t80) REVERT: V 86 ARG cc_start: 0.7712 (ttm170) cc_final: 0.7200 (mmt90) REVERT: V 96 GLU cc_start: 0.6693 (tm-30) cc_final: 0.6251 (tm-30) REVERT: W 444 PHE cc_start: 0.8370 (t80) cc_final: 0.8129 (t80) REVERT: 8 317 LEU cc_start: 0.8556 (mt) cc_final: 0.8131 (tp) REVERT: 8 334 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8255 (mm-40) REVERT: 8 368 ARG cc_start: 0.8898 (mmm-85) cc_final: 0.8350 (mmm-85) REVERT: 8 379 ARG cc_start: 0.8358 (mmm160) cc_final: 0.8075 (mmm160) REVERT: 8 382 ARG cc_start: 0.7565 (mtt180) cc_final: 0.6660 (ttt180) REVERT: b 221 MET cc_start: 0.8702 (tmm) cc_final: 0.8112 (tmm) REVERT: e 92 TYR cc_start: 0.8360 (m-80) cc_final: 0.8008 (m-80) REVERT: f 45 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8768 (mm) REVERT: h 27 GLU cc_start: 0.7670 (tp30) cc_final: 0.6803 (tp30) REVERT: h 30 GLU cc_start: 0.6962 (pp20) cc_final: 0.6378 (pp20) REVERT: h 59 ASN cc_start: 0.8509 (m-40) cc_final: 0.8094 (m110) REVERT: h 96 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7680 (mp0) REVERT: i 60 LEU cc_start: 0.9095 (mt) cc_final: 0.8882 (mp) REVERT: i 75 LYS cc_start: 0.8813 (mmmm) cc_final: 0.8537 (mmmm) REVERT: i 88 GLU cc_start: 0.7963 (pp20) cc_final: 0.7641 (pp20) REVERT: i 89 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7453 (tm-30) REVERT: i 90 MET cc_start: 0.7776 (mmm) cc_final: 0.7282 (mmm) REVERT: j 47 TYR cc_start: 0.5535 (m-80) cc_final: 0.5105 (m-80) REVERT: j 49 TRP cc_start: 0.6859 (p-90) cc_final: 0.6293 (p-90) REVERT: n 36 CYS cc_start: 0.8204 (m) cc_final: 0.7864 (m) REVERT: n 82 GLU cc_start: 0.7785 (pp20) cc_final: 0.7305 (tm-30) REVERT: o 121 ARG cc_start: 0.7950 (mtm-85) cc_final: 0.7692 (mtm180) REVERT: o 146 MET cc_start: 0.8434 (tpt) cc_final: 0.8183 (tpp) REVERT: p 65 MET cc_start: 0.6664 (OUTLIER) cc_final: 0.6268 (ptm) REVERT: p 102 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7569 (pt0) REVERT: p 131 PHE cc_start: 0.8424 (t80) cc_final: 0.8109 (t80) REVERT: p 314 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7237 (pp) REVERT: s 295 LYS cc_start: 0.8875 (mtmm) cc_final: 0.8432 (ptpp) REVERT: t 209 GLN cc_start: 0.7805 (pt0) cc_final: 0.7593 (pt0) REVERT: t 245 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7427 (mt) REVERT: u 40 PHE cc_start: 0.8207 (t80) cc_final: 0.7977 (t80) REVERT: v 32 GLN cc_start: 0.8081 (pm20) cc_final: 0.7676 (pm20) REVERT: v 111 VAL cc_start: 0.9111 (OUTLIER) cc_final: 0.8889 (p) REVERT: v 136 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.6841 (pp) outliers start: 187 outliers final: 133 residues processed: 930 average time/residue: 0.8311 time to fit residues: 1338.2530 Evaluate side-chains 864 residues out of total 5975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 723 time to evaluate : 5.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 160 GLN Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 28 CYS Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 182 ASP Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 122 LYS Chi-restraints excluded: chain G residue 191 ASN Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 139 CYS Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain I residue 246 TYR Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 154 ILE Chi-restraints excluded: chain K residue 159 ASP Chi-restraints excluded: chain K residue 301 LEU Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 135 LEU Chi-restraints excluded: chain N residue 16 SER Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 196 THR Chi-restraints excluded: chain O residue 57 PHE Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 151 ASP Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 118 GLN Chi-restraints excluded: chain P residue 141 SER Chi-restraints excluded: chain P residue 142 SER Chi-restraints excluded: chain P residue 149 VAL Chi-restraints excluded: chain Q residue 67 ILE Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain S residue 16 THR Chi-restraints excluded: chain S residue 122 HIS Chi-restraints excluded: chain S residue 147 ASP Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain S residue 170 THR Chi-restraints excluded: chain V residue 92 PHE Chi-restraints excluded: chain W residue 429 ASN Chi-restraints excluded: chain Y residue 80 VAL Chi-restraints excluded: chain 7 residue 12 SER Chi-restraints excluded: chain 7 residue 45 THR Chi-restraints excluded: chain 7 residue 77 ILE Chi-restraints excluded: chain 7 residue 199 MET Chi-restraints excluded: chain 7 residue 214 ASP Chi-restraints excluded: chain 8 residue 304 LEU Chi-restraints excluded: chain 8 residue 334 GLN Chi-restraints excluded: chain 8 residue 347 LEU Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 231 PHE Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 109 LEU Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 45 LEU Chi-restraints excluded: chain h residue 79 ASP Chi-restraints excluded: chain i residue 50 LEU Chi-restraints excluded: chain i residue 53 TYR Chi-restraints excluded: chain j residue 54 LYS Chi-restraints excluded: chain n residue 27 VAL Chi-restraints excluded: chain n residue 38 PHE Chi-restraints excluded: chain n residue 114 LEU Chi-restraints excluded: chain n residue 166 TRP Chi-restraints excluded: chain n residue 251 LYS Chi-restraints excluded: chain o residue 92 ILE Chi-restraints excluded: chain o residue 97 ARG Chi-restraints excluded: chain o residue 116 ASP Chi-restraints excluded: chain o residue 120 VAL Chi-restraints excluded: chain o residue 147 ILE Chi-restraints excluded: chain o residue 164 VAL Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain o residue 185 VAL Chi-restraints excluded: chain p residue 65 MET Chi-restraints excluded: chain p residue 104 LEU Chi-restraints excluded: chain p residue 177 ASP Chi-restraints excluded: chain p residue 279 LEU Chi-restraints excluded: chain p residue 314 LEU Chi-restraints excluded: chain p residue 412 LEU Chi-restraints excluded: chain p residue 435 SER Chi-restraints excluded: chain s residue 271 ASN Chi-restraints excluded: chain t residue 145 VAL Chi-restraints excluded: chain t residue 168 LEU Chi-restraints excluded: chain t residue 175 VAL Chi-restraints excluded: chain t residue 245 ILE Chi-restraints excluded: chain t residue 247 VAL Chi-restraints excluded: chain t residue 321 LEU Chi-restraints excluded: chain u residue 17 HIS Chi-restraints excluded: chain u residue 22 VAL Chi-restraints excluded: chain u residue 52 THR Chi-restraints excluded: chain u residue 117 GLU Chi-restraints excluded: chain u residue 119 ASP Chi-restraints excluded: chain v residue 59 LEU Chi-restraints excluded: chain v residue 111 VAL Chi-restraints excluded: chain v residue 136 LEU Chi-restraints excluded: chain v residue 166 VAL Chi-restraints excluded: chain v residue 195 ASP Chi-restraints excluded: chain v residue 209 ASP Chi-restraints excluded: chain v residue 339 LEU Chi-restraints excluded: chain v residue 353 HIS Chi-restraints excluded: chain w residue 184 THR Chi-restraints excluded: chain w residue 197 LEU Chi-restraints excluded: chain w residue 198 PHE Chi-restraints excluded: chain y residue 53 ILE Chi-restraints excluded: chain z residue 25 LEU Chi-restraints excluded: chain z residue 29 LEU Chi-restraints excluded: chain z residue 56 SER Chi-restraints excluded: chain z residue 228 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 857 random chunks: chunk 799 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 472 optimal weight: 2.9990 chunk 605 optimal weight: 10.0000 chunk 469 optimal weight: 3.9990 chunk 697 optimal weight: 0.6980 chunk 463 optimal weight: 0.8980 chunk 826 optimal weight: 0.0570 chunk 516 optimal weight: 6.9990 chunk 503 optimal weight: 10.0000 chunk 381 optimal weight: 9.9990 overall best weight: 1.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 ASN ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 ASN F 244 ASN ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 GLN ** O 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 34 GLN P 45 GLN P 92 GLN Q 73 GLN ** Q 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 10 ASN ** 7 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 20 HIS e 104 ASN ** f 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 181 ASN ** t 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 81 HIS ** v 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 96776 Z= 0.194 Angle : 0.609 14.514 138381 Z= 0.309 Chirality : 0.037 0.271 16877 Planarity : 0.004 0.064 11636 Dihedral : 22.453 179.752 32806 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.10 % Favored : 94.86 % Rotamer: Outliers : 3.11 % Allowed : 18.20 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.06 % Twisted Proline : 0.37 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.10), residues: 6729 helix: 1.02 (0.10), residues: 2729 sheet: -0.22 (0.16), residues: 971 loop : -1.01 (0.11), residues: 3029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP b 100 HIS 0.012 0.001 HIS D 99 PHE 0.020 0.001 PHE b 112 TYR 0.023 0.001 TYR b 98 ARG 0.007 0.000 ARG I 253 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13458 Ramachandran restraints generated. 6729 Oldfield, 0 Emsley, 6729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13458 Ramachandran restraints generated. 6729 Oldfield, 0 Emsley, 6729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 956 residues out of total 5975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 770 time to evaluate : 6.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 ILE cc_start: 0.8942 (mt) cc_final: 0.8580 (mt) REVERT: A 348 ASN cc_start: 0.8424 (m-40) cc_final: 0.8192 (p0) REVERT: B 53 MET cc_start: 0.5859 (mtt) cc_final: 0.5242 (ptp) REVERT: B 99 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8495 (tp) REVERT: B 308 MET cc_start: 0.5089 (mtp) cc_final: 0.4561 (mtp) REVERT: G 202 GLU cc_start: 0.8390 (mm-30) cc_final: 0.7998 (mm-30) REVERT: L 27 ASP cc_start: 0.8664 (p0) cc_final: 0.8401 (p0) REVERT: M 47 ASP cc_start: 0.7425 (t0) cc_final: 0.6886 (t0) REVERT: N 138 GLN cc_start: 0.8707 (mm-40) cc_final: 0.8460 (mm-40) REVERT: O 43 ILE cc_start: 0.9425 (mm) cc_final: 0.9073 (mm) REVERT: O 149 TYR cc_start: 0.8302 (m-80) cc_final: 0.7903 (m-80) REVERT: P 31 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7485 (mm-30) REVERT: P 53 ASP cc_start: 0.6956 (t0) cc_final: 0.6732 (t0) REVERT: P 121 GLN cc_start: 0.8322 (mt0) cc_final: 0.8006 (mt0) REVERT: P 125 GLN cc_start: 0.7902 (pm20) cc_final: 0.7192 (mm110) REVERT: S 118 PHE cc_start: 0.7508 (t80) cc_final: 0.7249 (t80) REVERT: V 86 ARG cc_start: 0.7884 (ttm170) cc_final: 0.7417 (mmt90) REVERT: V 96 GLU cc_start: 0.6716 (tm-30) cc_final: 0.6223 (tm-30) REVERT: W 444 PHE cc_start: 0.8354 (t80) cc_final: 0.8092 (t80) REVERT: 7 49 ASN cc_start: 0.8167 (OUTLIER) cc_final: 0.7952 (t160) REVERT: 8 317 LEU cc_start: 0.8556 (mt) cc_final: 0.8163 (tp) REVERT: 8 334 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8371 (mm-40) REVERT: 8 368 ARG cc_start: 0.8862 (mmm-85) cc_final: 0.8333 (mmm-85) REVERT: 8 379 ARG cc_start: 0.8303 (mmm160) cc_final: 0.7973 (mmm160) REVERT: 8 382 ARG cc_start: 0.7507 (mtt180) cc_final: 0.6679 (ttt180) REVERT: b 160 PHE cc_start: 0.6999 (m-80) cc_final: 0.6792 (m-10) REVERT: e 19 ARG cc_start: 0.8129 (mtp180) cc_final: 0.7647 (mtp180) REVERT: e 92 TYR cc_start: 0.8439 (m-80) cc_final: 0.8121 (m-80) REVERT: f 45 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8762 (mm) REVERT: f 57 LYS cc_start: 0.8225 (mtmt) cc_final: 0.7947 (ptpp) REVERT: h 27 GLU cc_start: 0.7759 (tp30) cc_final: 0.7489 (tm-30) REVERT: h 59 ASN cc_start: 0.8544 (m-40) cc_final: 0.8203 (m110) REVERT: i 88 GLU cc_start: 0.7974 (pp20) cc_final: 0.7619 (pp20) REVERT: i 89 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7902 (tm-30) REVERT: i 90 MET cc_start: 0.7735 (mmm) cc_final: 0.7415 (mmm) REVERT: j 47 TYR cc_start: 0.5536 (m-80) cc_final: 0.4755 (m-80) REVERT: j 49 TRP cc_start: 0.6823 (p-90) cc_final: 0.5996 (p-90) REVERT: n 23 ARG cc_start: 0.8267 (ptp90) cc_final: 0.8001 (mtm110) REVERT: n 36 CYS cc_start: 0.8301 (m) cc_final: 0.7924 (m) REVERT: n 82 GLU cc_start: 0.7782 (pp20) cc_final: 0.7299 (tm-30) REVERT: o 121 ARG cc_start: 0.7920 (mtm-85) cc_final: 0.7698 (mtm180) REVERT: o 146 MET cc_start: 0.8463 (tpt) cc_final: 0.8179 (tpp) REVERT: p 65 MET cc_start: 0.6713 (OUTLIER) cc_final: 0.5997 (ptm) REVERT: p 102 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7459 (pt0) REVERT: p 131 PHE cc_start: 0.8412 (t80) cc_final: 0.8110 (t80) REVERT: p 314 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7227 (pp) REVERT: s 295 LYS cc_start: 0.8853 (mtmm) cc_final: 0.8423 (ptpp) REVERT: t 245 ILE cc_start: 0.7746 (OUTLIER) cc_final: 0.7442 (mt) REVERT: u 40 PHE cc_start: 0.8209 (t80) cc_final: 0.7979 (t80) REVERT: v 32 GLN cc_start: 0.8092 (pm20) cc_final: 0.7747 (pm20) REVERT: v 111 VAL cc_start: 0.9099 (OUTLIER) cc_final: 0.8877 (p) REVERT: v 136 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.6857 (pp) outliers start: 186 outliers final: 147 residues processed: 895 average time/residue: 0.8326 time to fit residues: 1290.9366 Evaluate side-chains 883 residues out of total 5975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 727 time to evaluate : 5.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 160 GLN Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 28 CYS Chi-restraints excluded: chain D residue 43 CYS Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 182 ASP Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 122 LYS Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 191 ASN Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 139 CYS Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain I residue 246 TYR Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain K residue 154 ILE Chi-restraints excluded: chain K residue 159 ASP Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain K residue 301 LEU Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 135 LEU Chi-restraints excluded: chain N residue 16 SER Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 23 GLN Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 190 THR Chi-restraints excluded: chain O residue 57 PHE Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 151 ASP Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 118 GLN Chi-restraints excluded: chain P residue 141 SER Chi-restraints excluded: chain P residue 149 VAL Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 67 ILE Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain S residue 16 THR Chi-restraints excluded: chain S residue 122 HIS Chi-restraints excluded: chain S residue 147 ASP Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain S residue 170 THR Chi-restraints excluded: chain V residue 69 LEU Chi-restraints excluded: chain V residue 92 PHE Chi-restraints excluded: chain W residue 429 ASN Chi-restraints excluded: chain Y residue 73 VAL Chi-restraints excluded: chain Y residue 80 VAL Chi-restraints excluded: chain 7 residue 12 SER Chi-restraints excluded: chain 7 residue 45 THR Chi-restraints excluded: chain 7 residue 49 ASN Chi-restraints excluded: chain 7 residue 199 MET Chi-restraints excluded: chain 7 residue 214 ASP Chi-restraints excluded: chain 8 residue 304 LEU Chi-restraints excluded: chain 8 residue 334 GLN Chi-restraints excluded: chain b residue 109 THR Chi-restraints excluded: chain b residue 175 HIS Chi-restraints excluded: chain b residue 225 LEU Chi-restraints excluded: chain b residue 231 PHE Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 109 LEU Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 45 LEU Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain h residue 79 ASP Chi-restraints excluded: chain i residue 50 LEU Chi-restraints excluded: chain i residue 53 TYR Chi-restraints excluded: chain j residue 54 LYS Chi-restraints excluded: chain n residue 27 VAL Chi-restraints excluded: chain n residue 38 PHE Chi-restraints excluded: chain n residue 114 LEU Chi-restraints excluded: chain n residue 166 TRP Chi-restraints excluded: chain n residue 251 LYS Chi-restraints excluded: chain o residue 92 ILE Chi-restraints excluded: chain o residue 97 ARG Chi-restraints excluded: chain o residue 116 ASP Chi-restraints excluded: chain o residue 120 VAL Chi-restraints excluded: chain o residue 147 ILE Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain o residue 185 VAL Chi-restraints excluded: chain o residue 193 VAL Chi-restraints excluded: chain p residue 65 MET Chi-restraints excluded: chain p residue 104 LEU Chi-restraints excluded: chain p residue 177 ASP Chi-restraints excluded: chain p residue 279 LEU Chi-restraints excluded: chain p residue 314 LEU Chi-restraints excluded: chain p residue 346 THR Chi-restraints excluded: chain p residue 412 LEU Chi-restraints excluded: chain p residue 435 SER Chi-restraints excluded: chain s residue 271 ASN Chi-restraints excluded: chain s residue 374 LEU Chi-restraints excluded: chain t residue 145 VAL Chi-restraints excluded: chain t residue 168 LEU Chi-restraints excluded: chain t residue 175 VAL Chi-restraints excluded: chain t residue 245 ILE Chi-restraints excluded: chain t residue 247 VAL Chi-restraints excluded: chain t residue 283 LEU Chi-restraints excluded: chain t residue 321 LEU Chi-restraints excluded: chain u residue 8 PHE Chi-restraints excluded: chain u residue 22 VAL Chi-restraints excluded: chain u residue 117 GLU Chi-restraints excluded: chain u residue 119 ASP Chi-restraints excluded: chain v residue 111 VAL Chi-restraints excluded: chain v residue 136 LEU Chi-restraints excluded: chain v residue 166 VAL Chi-restraints excluded: chain v residue 195 ASP Chi-restraints excluded: chain v residue 209 ASP Chi-restraints excluded: chain v residue 353 HIS Chi-restraints excluded: chain w residue 184 THR Chi-restraints excluded: chain w residue 197 LEU Chi-restraints excluded: chain w residue 198 PHE Chi-restraints excluded: chain y residue 53 ILE Chi-restraints excluded: chain z residue 25 LEU Chi-restraints excluded: chain z residue 56 SER Chi-restraints excluded: chain z residue 228 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 857 random chunks: chunk 511 optimal weight: 5.9990 chunk 329 optimal weight: 0.9990 chunk 493 optimal weight: 10.0000 chunk 248 optimal weight: 3.9990 chunk 162 optimal weight: 9.9990 chunk 160 optimal weight: 0.8980 chunk 525 optimal weight: 2.9990 chunk 562 optimal weight: 20.0000 chunk 408 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 649 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 ASN ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 34 GLN ** P 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 92 GLN ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 75 ASN ** b 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 20 HIS ** f 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 181 ASN p 287 ASN ** t 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 11 ASN ** y 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 132 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 96776 Z= 0.262 Angle : 0.637 14.741 138381 Z= 0.325 Chirality : 0.038 0.311 16877 Planarity : 0.004 0.060 11636 Dihedral : 22.402 179.815 32806 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.56 % Favored : 94.40 % Rotamer: Outliers : 3.11 % Allowed : 18.58 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.06 % Twisted Proline : 0.37 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.10), residues: 6729 helix: 1.03 (0.10), residues: 2724 sheet: -0.21 (0.16), residues: 951 loop : -0.98 (0.11), residues: 3054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP b 100 HIS 0.012 0.001 HIS D 99 PHE 0.032 0.002 PHE O 174 TYR 0.030 0.002 TYR b 98 ARG 0.013 0.001 ARG s 264 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13458 Ramachandran restraints generated. 6729 Oldfield, 0 Emsley, 6729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13458 Ramachandran restraints generated. 6729 Oldfield, 0 Emsley, 6729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 921 residues out of total 5975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 735 time to evaluate : 6.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 ILE cc_start: 0.8940 (mt) cc_final: 0.8573 (mt) REVERT: B 53 MET cc_start: 0.5969 (mtt) cc_final: 0.5194 (ptt) REVERT: B 99 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8617 (tp) REVERT: B 308 MET cc_start: 0.5099 (mtp) cc_final: 0.4642 (mtp) REVERT: B 380 MET cc_start: 0.8134 (tpp) cc_final: 0.7507 (tpp) REVERT: F 82 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7192 (pttm) REVERT: G 202 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8013 (mm-30) REVERT: I 250 ASP cc_start: 0.8851 (p0) cc_final: 0.8559 (p0) REVERT: L 27 ASP cc_start: 0.8660 (p0) cc_final: 0.8391 (p0) REVERT: L 93 ILE cc_start: 0.9371 (mt) cc_final: 0.8787 (tt) REVERT: M 47 ASP cc_start: 0.7492 (t0) cc_final: 0.6944 (t0) REVERT: N 138 GLN cc_start: 0.8777 (mm-40) cc_final: 0.8515 (mm-40) REVERT: O 43 ILE cc_start: 0.9500 (mm) cc_final: 0.9171 (mm) REVERT: O 149 TYR cc_start: 0.8376 (m-80) cc_final: 0.7905 (m-80) REVERT: P 31 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7502 (mm-30) REVERT: P 121 GLN cc_start: 0.8325 (mt0) cc_final: 0.8009 (mt0) REVERT: P 125 GLN cc_start: 0.7903 (pm20) cc_final: 0.7379 (tp40) REVERT: S 118 PHE cc_start: 0.7525 (t80) cc_final: 0.7254 (t80) REVERT: V 86 ARG cc_start: 0.7855 (ttm170) cc_final: 0.7480 (mmt90) REVERT: W 444 PHE cc_start: 0.8350 (t80) cc_final: 0.8137 (t80) REVERT: 7 49 ASN cc_start: 0.8438 (OUTLIER) cc_final: 0.8164 (t160) REVERT: 8 334 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8407 (mm-40) REVERT: 8 368 ARG cc_start: 0.8889 (mmm-85) cc_final: 0.8310 (mmm-85) REVERT: 8 379 ARG cc_start: 0.8300 (mmm160) cc_final: 0.7969 (mmm160) REVERT: 8 382 ARG cc_start: 0.7504 (mtt180) cc_final: 0.6678 (ttt180) REVERT: e 19 ARG cc_start: 0.8193 (mtp180) cc_final: 0.7696 (mtp180) REVERT: e 92 TYR cc_start: 0.8474 (m-80) cc_final: 0.8185 (m-80) REVERT: f 45 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8840 (mm) REVERT: f 57 LYS cc_start: 0.8234 (mtmt) cc_final: 0.7465 (ptpt) REVERT: f 63 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8092 (mtpp) REVERT: h 59 ASN cc_start: 0.8513 (m-40) cc_final: 0.8148 (m110) REVERT: i 75 LYS cc_start: 0.8777 (mmmm) cc_final: 0.8532 (mmmm) REVERT: i 88 GLU cc_start: 0.8007 (pp20) cc_final: 0.7553 (pp20) REVERT: i 89 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7383 (tm-30) REVERT: i 90 MET cc_start: 0.7838 (mmm) cc_final: 0.7186 (mmm) REVERT: i 92 ASN cc_start: 0.8743 (m-40) cc_final: 0.7675 (m110) REVERT: j 49 TRP cc_start: 0.6926 (p-90) cc_final: 0.6014 (p-90) REVERT: j 66 TYR cc_start: 0.8694 (t80) cc_final: 0.8440 (t80) REVERT: n 36 CYS cc_start: 0.8349 (m) cc_final: 0.7998 (m) REVERT: n 82 GLU cc_start: 0.7856 (pp20) cc_final: 0.7376 (tm-30) REVERT: o 121 ARG cc_start: 0.7930 (mtm-85) cc_final: 0.7689 (mtm180) REVERT: o 146 MET cc_start: 0.8499 (tpt) cc_final: 0.8242 (tpp) REVERT: p 65 MET cc_start: 0.6742 (OUTLIER) cc_final: 0.6349 (ptm) REVERT: p 102 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7540 (pt0) REVERT: p 131 PHE cc_start: 0.8435 (t80) cc_final: 0.8116 (t80) REVERT: p 314 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7229 (pp) REVERT: t 245 ILE cc_start: 0.7761 (OUTLIER) cc_final: 0.7461 (mt) REVERT: u 40 PHE cc_start: 0.8302 (t80) cc_final: 0.8071 (t80) REVERT: v 32 GLN cc_start: 0.8099 (pm20) cc_final: 0.7757 (pm20) REVERT: v 136 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.6870 (pp) REVERT: z 229 ASN cc_start: 0.8315 (p0) cc_final: 0.8083 (p0) outliers start: 186 outliers final: 158 residues processed: 861 average time/residue: 0.8997 time to fit residues: 1349.4538 Evaluate side-chains 877 residues out of total 5975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 709 time to evaluate : 5.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 160 GLN Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 28 CYS Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 182 ASP Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 122 LYS Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 191 ASN Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 139 CYS Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain I residue 231 THR Chi-restraints excluded: chain I residue 246 TYR Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 154 ILE Chi-restraints excluded: chain K residue 159 ASP Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain K residue 301 LEU Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 135 LEU Chi-restraints excluded: chain N residue 16 SER Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 23 GLN Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 182 ASN Chi-restraints excluded: chain O residue 57 PHE Chi-restraints excluded: chain O residue 77 SER Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 151 ASP Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 118 GLN Chi-restraints excluded: chain P residue 141 SER Chi-restraints excluded: chain P residue 142 SER Chi-restraints excluded: chain P residue 149 VAL Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 67 ILE Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain S residue 16 THR Chi-restraints excluded: chain S residue 122 HIS Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain S residue 147 ASP Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain S residue 170 THR Chi-restraints excluded: chain V residue 92 PHE Chi-restraints excluded: chain W residue 429 ASN Chi-restraints excluded: chain Y residue 73 VAL Chi-restraints excluded: chain Y residue 80 VAL Chi-restraints excluded: chain 7 residue 10 ASN Chi-restraints excluded: chain 7 residue 12 SER Chi-restraints excluded: chain 7 residue 45 THR Chi-restraints excluded: chain 7 residue 49 ASN Chi-restraints excluded: chain 7 residue 199 MET Chi-restraints excluded: chain 7 residue 214 ASP Chi-restraints excluded: chain 8 residue 304 LEU Chi-restraints excluded: chain 8 residue 334 GLN Chi-restraints excluded: chain b residue 175 HIS Chi-restraints excluded: chain b residue 225 LEU Chi-restraints excluded: chain b residue 231 PHE Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 45 LEU Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 63 LYS Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 79 ASP Chi-restraints excluded: chain i residue 53 TYR Chi-restraints excluded: chain j residue 33 THR Chi-restraints excluded: chain j residue 54 LYS Chi-restraints excluded: chain n residue 27 VAL Chi-restraints excluded: chain n residue 38 PHE Chi-restraints excluded: chain n residue 114 LEU Chi-restraints excluded: chain n residue 133 ASP Chi-restraints excluded: chain n residue 166 TRP Chi-restraints excluded: chain n residue 251 LYS Chi-restraints excluded: chain o residue 92 ILE Chi-restraints excluded: chain o residue 97 ARG Chi-restraints excluded: chain o residue 116 ASP Chi-restraints excluded: chain o residue 120 VAL Chi-restraints excluded: chain o residue 147 ILE Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain o residue 185 VAL Chi-restraints excluded: chain o residue 193 VAL Chi-restraints excluded: chain o residue 198 ASP Chi-restraints excluded: chain p residue 65 MET Chi-restraints excluded: chain p residue 104 LEU Chi-restraints excluded: chain p residue 177 ASP Chi-restraints excluded: chain p residue 279 LEU Chi-restraints excluded: chain p residue 314 LEU Chi-restraints excluded: chain p residue 346 THR Chi-restraints excluded: chain p residue 412 LEU Chi-restraints excluded: chain p residue 435 SER Chi-restraints excluded: chain s residue 271 ASN Chi-restraints excluded: chain s residue 374 LEU Chi-restraints excluded: chain t residue 81 LEU Chi-restraints excluded: chain t residue 155 ILE Chi-restraints excluded: chain t residue 168 LEU Chi-restraints excluded: chain t residue 245 ILE Chi-restraints excluded: chain t residue 247 VAL Chi-restraints excluded: chain t residue 283 LEU Chi-restraints excluded: chain t residue 321 LEU Chi-restraints excluded: chain u residue 22 VAL Chi-restraints excluded: chain u residue 52 THR Chi-restraints excluded: chain u residue 117 GLU Chi-restraints excluded: chain u residue 119 ASP Chi-restraints excluded: chain v residue 59 LEU Chi-restraints excluded: chain v residue 80 THR Chi-restraints excluded: chain v residue 136 LEU Chi-restraints excluded: chain v residue 166 VAL Chi-restraints excluded: chain v residue 195 ASP Chi-restraints excluded: chain v residue 209 ASP Chi-restraints excluded: chain v residue 353 HIS Chi-restraints excluded: chain w residue 184 THR Chi-restraints excluded: chain w residue 197 LEU Chi-restraints excluded: chain w residue 198 PHE Chi-restraints excluded: chain y residue 53 ILE Chi-restraints excluded: chain z residue 25 LEU Chi-restraints excluded: chain z residue 56 SER Chi-restraints excluded: chain z residue 137 GLN Chi-restraints excluded: chain z residue 228 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 857 random chunks: chunk 751 optimal weight: 6.9990 chunk 791 optimal weight: 10.0000 chunk 721 optimal weight: 50.0000 chunk 769 optimal weight: 0.9990 chunk 463 optimal weight: 0.6980 chunk 335 optimal weight: 0.5980 chunk 604 optimal weight: 9.9990 chunk 236 optimal weight: 0.7980 chunk 695 optimal weight: 8.9990 chunk 728 optimal weight: 40.0000 chunk 767 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 ASN ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 92 GLN ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 72 GLN b 84 ASN ** b 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 20 HIS ** f 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 34 GLN ** i 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 79 GLN ** n 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 230 HIS ** n 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 181 ASN p 397 ASN ** t 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 73 HIS z 132 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.079 96776 Z= 0.153 Angle : 0.607 15.479 138381 Z= 0.306 Chirality : 0.036 0.298 16877 Planarity : 0.004 0.073 11636 Dihedral : 22.348 179.964 32805 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.16 % Favored : 94.81 % Rotamer: Outliers : 2.44 % Allowed : 19.24 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.06 % Twisted Proline : 0.37 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.10), residues: 6729 helix: 1.07 (0.10), residues: 2738 sheet: -0.23 (0.16), residues: 982 loop : -0.93 (0.11), residues: 3009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP b 100 HIS 0.010 0.001 HIS D 99 PHE 0.032 0.001 PHE P 63 TYR 0.038 0.001 TYR I 66 ARG 0.009 0.000 ARG j 25 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13458 Ramachandran restraints generated. 6729 Oldfield, 0 Emsley, 6729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13458 Ramachandran restraints generated. 6729 Oldfield, 0 Emsley, 6729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 937 residues out of total 5975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 791 time to evaluate : 6.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 ILE cc_start: 0.8882 (mt) cc_final: 0.8579 (mt) REVERT: B 53 MET cc_start: 0.5661 (mtt) cc_final: 0.5003 (ptt) REVERT: D 32 TYR cc_start: 0.8666 (m-80) cc_final: 0.8431 (m-80) REVERT: F 243 MET cc_start: 0.8456 (mmm) cc_final: 0.7940 (mmp) REVERT: G 173 MET cc_start: 0.8231 (mmm) cc_final: 0.7988 (mmm) REVERT: G 202 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7918 (mm-30) REVERT: L 27 ASP cc_start: 0.8604 (p0) cc_final: 0.8328 (p0) REVERT: L 93 ILE cc_start: 0.9325 (mt) cc_final: 0.9097 (mm) REVERT: M 47 ASP cc_start: 0.7392 (t0) cc_final: 0.6851 (t0) REVERT: N 138 GLN cc_start: 0.8450 (mm-40) cc_final: 0.8179 (mm-40) REVERT: O 43 ILE cc_start: 0.9459 (mm) cc_final: 0.9149 (mm) REVERT: O 149 TYR cc_start: 0.8235 (m-80) cc_final: 0.7777 (m-80) REVERT: P 31 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7416 (mm-30) REVERT: P 121 GLN cc_start: 0.8226 (mt0) cc_final: 0.7774 (mt0) REVERT: P 125 GLN cc_start: 0.7909 (pm20) cc_final: 0.7472 (mm110) REVERT: P 155 GLU cc_start: 0.7871 (mp0) cc_final: 0.7333 (mp0) REVERT: S 118 PHE cc_start: 0.7513 (t80) cc_final: 0.7253 (t80) REVERT: V 32 ARG cc_start: 0.7034 (mmt90) cc_final: 0.6560 (mpt180) REVERT: V 86 ARG cc_start: 0.7827 (ttm170) cc_final: 0.7449 (mmt90) REVERT: V 96 GLU cc_start: 0.6654 (tm-30) cc_final: 0.6356 (tm-30) REVERT: 8 317 LEU cc_start: 0.8507 (mt) cc_final: 0.8169 (tp) REVERT: 8 334 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8435 (mm-40) REVERT: 8 368 ARG cc_start: 0.8896 (mmm-85) cc_final: 0.8424 (mmm-85) REVERT: 8 379 ARG cc_start: 0.8324 (mmm160) cc_final: 0.8027 (mmm160) REVERT: 8 382 ARG cc_start: 0.7533 (mtt180) cc_final: 0.6713 (ttt180) REVERT: e 19 ARG cc_start: 0.8179 (mtp180) cc_final: 0.7755 (mtp180) REVERT: e 92 TYR cc_start: 0.8389 (m-80) cc_final: 0.8079 (m-80) REVERT: f 57 LYS cc_start: 0.8175 (mtmt) cc_final: 0.7474 (ptpt) REVERT: f 63 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.7998 (mtpp) REVERT: h 15 GLU cc_start: 0.7837 (pp20) cc_final: 0.7627 (pp20) REVERT: h 59 ASN cc_start: 0.8455 (m-40) cc_final: 0.8101 (m110) REVERT: i 75 LYS cc_start: 0.8739 (mmmm) cc_final: 0.8533 (mmmm) REVERT: i 89 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7823 (tm-30) REVERT: i 90 MET cc_start: 0.7711 (mmm) cc_final: 0.7331 (mmm) REVERT: j 25 ARG cc_start: 0.7485 (tpp80) cc_final: 0.7207 (tpt90) REVERT: j 49 TRP cc_start: 0.6814 (p-90) cc_final: 0.5936 (p-90) REVERT: j 66 TYR cc_start: 0.8496 (t80) cc_final: 0.8268 (t80) REVERT: n 23 ARG cc_start: 0.8236 (ptp90) cc_final: 0.7831 (mtm110) REVERT: n 36 CYS cc_start: 0.8282 (m) cc_final: 0.7916 (m) REVERT: n 82 GLU cc_start: 0.7740 (pp20) cc_final: 0.7184 (tm-30) REVERT: o 146 MET cc_start: 0.8423 (tpt) cc_final: 0.8144 (tpp) REVERT: p 65 MET cc_start: 0.6805 (OUTLIER) cc_final: 0.6342 (ptm) REVERT: p 102 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7432 (pt0) REVERT: p 131 PHE cc_start: 0.8360 (t80) cc_final: 0.8063 (t80) REVERT: u 40 PHE cc_start: 0.8211 (t80) cc_final: 0.7976 (t80) REVERT: v 32 GLN cc_start: 0.8209 (pm20) cc_final: 0.7871 (pm20) REVERT: v 136 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6856 (pp) REVERT: v 168 MET cc_start: 0.8882 (tpt) cc_final: 0.8613 (tpt) REVERT: y 62 MET cc_start: 0.6703 (tpp) cc_final: 0.6428 (tpp) REVERT: z 229 ASN cc_start: 0.8266 (p0) cc_final: 0.8004 (p0) outliers start: 146 outliers final: 116 residues processed: 886 average time/residue: 0.8296 time to fit residues: 1273.7552 Evaluate side-chains 864 residues out of total 5975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 744 time to evaluate : 5.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 160 GLN Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain D residue 28 CYS Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 182 ASP Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 122 LYS Chi-restraints excluded: chain G residue 191 ASN Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 139 CYS Chi-restraints excluded: chain I residue 246 TYR Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 154 ILE Chi-restraints excluded: chain K residue 301 LEU Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 118 GLU Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 135 LEU Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 23 GLN Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain O residue 57 PHE Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 151 ASP Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 141 SER Chi-restraints excluded: chain Q residue 67 ILE Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain S residue 16 THR Chi-restraints excluded: chain S residue 122 HIS Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain S residue 170 THR Chi-restraints excluded: chain V residue 92 PHE Chi-restraints excluded: chain W residue 429 ASN Chi-restraints excluded: chain Y residue 73 VAL Chi-restraints excluded: chain 7 residue 45 THR Chi-restraints excluded: chain 7 residue 46 MET Chi-restraints excluded: chain 7 residue 199 MET Chi-restraints excluded: chain 7 residue 214 ASP Chi-restraints excluded: chain 8 residue 304 LEU Chi-restraints excluded: chain 8 residue 334 GLN Chi-restraints excluded: chain b residue 231 PHE Chi-restraints excluded: chain b residue 284 LEU Chi-restraints excluded: chain e residue 69 SER Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 109 LEU Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 63 LYS Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 92 LEU Chi-restraints excluded: chain i residue 53 TYR Chi-restraints excluded: chain n residue 27 VAL Chi-restraints excluded: chain n residue 38 PHE Chi-restraints excluded: chain n residue 114 LEU Chi-restraints excluded: chain n residue 251 LYS Chi-restraints excluded: chain o residue 92 ILE Chi-restraints excluded: chain o residue 97 ARG Chi-restraints excluded: chain o residue 116 ASP Chi-restraints excluded: chain o residue 120 VAL Chi-restraints excluded: chain o residue 147 ILE Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain o residue 185 VAL Chi-restraints excluded: chain o residue 193 VAL Chi-restraints excluded: chain p residue 65 MET Chi-restraints excluded: chain p residue 104 LEU Chi-restraints excluded: chain p residue 346 THR Chi-restraints excluded: chain p residue 412 LEU Chi-restraints excluded: chain p residue 435 SER Chi-restraints excluded: chain s residue 271 ASN Chi-restraints excluded: chain s residue 374 LEU Chi-restraints excluded: chain t residue 155 ILE Chi-restraints excluded: chain t residue 168 LEU Chi-restraints excluded: chain t residue 247 VAL Chi-restraints excluded: chain t residue 283 LEU Chi-restraints excluded: chain t residue 321 LEU Chi-restraints excluded: chain u residue 52 THR Chi-restraints excluded: chain u residue 119 ASP Chi-restraints excluded: chain v residue 80 THR Chi-restraints excluded: chain v residue 136 LEU Chi-restraints excluded: chain v residue 166 VAL Chi-restraints excluded: chain v residue 209 ASP Chi-restraints excluded: chain v residue 353 HIS Chi-restraints excluded: chain w residue 184 THR Chi-restraints excluded: chain w residue 197 LEU Chi-restraints excluded: chain w residue 198 PHE Chi-restraints excluded: chain z residue 25 LEU Chi-restraints excluded: chain z residue 56 SER Chi-restraints excluded: chain z residue 228 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 857 random chunks: chunk 505 optimal weight: 0.0670 chunk 813 optimal weight: 40.0000 chunk 496 optimal weight: 30.0000 chunk 386 optimal weight: 9.9990 chunk 565 optimal weight: 2.9990 chunk 853 optimal weight: 20.0000 chunk 785 optimal weight: 10.0000 chunk 679 optimal weight: 5.9990 chunk 70 optimal weight: 20.0000 chunk 525 optimal weight: 0.6980 chunk 416 optimal weight: 0.4980 overall best weight: 2.0522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 GLN ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 194 GLN ** O 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 34 GLN P 50 GLN P 92 GLN ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 72 GLN ** b 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 20 HIS e 52 GLN ** f 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 165 GLN ** n 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 300 GLN v 81 HIS ** v 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 96776 Z= 0.213 Angle : 0.625 14.781 138381 Z= 0.316 Chirality : 0.037 0.317 16877 Planarity : 0.004 0.080 11636 Dihedral : 22.270 179.918 32804 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.13 % Favored : 94.83 % Rotamer: Outliers : 2.18 % Allowed : 19.67 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.06 % Twisted Proline : 0.37 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.10), residues: 6729 helix: 1.11 (0.10), residues: 2735 sheet: -0.19 (0.16), residues: 975 loop : -0.90 (0.11), residues: 3019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP b 100 HIS 0.014 0.001 HIS D 99 PHE 0.033 0.002 PHE W 444 TYR 0.030 0.002 TYR i 53 ARG 0.022 0.000 ARG o 121 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13458 Ramachandran restraints generated. 6729 Oldfield, 0 Emsley, 6729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13458 Ramachandran restraints generated. 6729 Oldfield, 0 Emsley, 6729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 5975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 743 time to evaluate : 6.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 ILE cc_start: 0.8882 (mt) cc_final: 0.8559 (mt) REVERT: B 53 MET cc_start: 0.5469 (mtt) cc_final: 0.4746 (ptt) REVERT: B 214 MET cc_start: 0.8616 (tpp) cc_final: 0.8388 (tpp) REVERT: B 380 MET cc_start: 0.8268 (tpp) cc_final: 0.7626 (tpp) REVERT: D 32 TYR cc_start: 0.8643 (m-80) cc_final: 0.8434 (m-80) REVERT: G 57 ARG cc_start: 0.8566 (ptt90) cc_final: 0.8275 (mmt180) REVERT: G 173 MET cc_start: 0.8302 (mmm) cc_final: 0.8063 (mmm) REVERT: L 37 ASN cc_start: 0.8213 (p0) cc_final: 0.7650 (p0) REVERT: L 93 ILE cc_start: 0.9376 (mt) cc_final: 0.9152 (mm) REVERT: M 47 ASP cc_start: 0.7339 (t0) cc_final: 0.6836 (t0) REVERT: N 138 GLN cc_start: 0.8686 (mm-40) cc_final: 0.8428 (mm-40) REVERT: O 43 ILE cc_start: 0.9518 (mm) cc_final: 0.9208 (mm) REVERT: O 149 TYR cc_start: 0.8243 (m-80) cc_final: 0.7807 (m-80) REVERT: P 31 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7466 (mm-30) REVERT: P 121 GLN cc_start: 0.8270 (mt0) cc_final: 0.7804 (mt0) REVERT: P 125 GLN cc_start: 0.7843 (pm20) cc_final: 0.7505 (tp40) REVERT: P 155 GLU cc_start: 0.7968 (mp0) cc_final: 0.7441 (mp0) REVERT: S 118 PHE cc_start: 0.7549 (t80) cc_final: 0.7272 (t80) REVERT: V 86 ARG cc_start: 0.7827 (ttm170) cc_final: 0.7429 (mmt90) REVERT: V 96 GLU cc_start: 0.6634 (tm-30) cc_final: 0.6328 (tm-30) REVERT: 8 334 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8465 (mm-40) REVERT: 8 341 ARG cc_start: 0.2812 (ptt180) cc_final: 0.2237 (ptt180) REVERT: 8 368 ARG cc_start: 0.8912 (mmm-85) cc_final: 0.8388 (mmm-85) REVERT: 8 379 ARG cc_start: 0.8276 (mmm160) cc_final: 0.7952 (mmm160) REVERT: 8 382 ARG cc_start: 0.7472 (mtt180) cc_final: 0.6652 (ttt180) REVERT: e 19 ARG cc_start: 0.8225 (mtp180) cc_final: 0.7787 (mtp180) REVERT: e 92 TYR cc_start: 0.8439 (m-80) cc_final: 0.8155 (m-80) REVERT: f 57 LYS cc_start: 0.8213 (mtmt) cc_final: 0.7987 (ptpt) REVERT: f 103 TYR cc_start: 0.8869 (p90) cc_final: 0.8653 (p90) REVERT: h 15 GLU cc_start: 0.7863 (pp20) cc_final: 0.7663 (pp20) REVERT: h 59 ASN cc_start: 0.8495 (m-40) cc_final: 0.8140 (m110) REVERT: i 88 GLU cc_start: 0.8173 (pp20) cc_final: 0.7586 (pp20) REVERT: i 89 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7283 (tm-30) REVERT: i 90 MET cc_start: 0.7751 (mmm) cc_final: 0.7103 (mmm) REVERT: i 92 ASN cc_start: 0.9180 (m110) cc_final: 0.8654 (m-40) REVERT: j 66 TYR cc_start: 0.8629 (t80) cc_final: 0.8370 (t80) REVERT: n 36 CYS cc_start: 0.8305 (m) cc_final: 0.7617 (m) REVERT: n 82 GLU cc_start: 0.7804 (pp20) cc_final: 0.7239 (tm-30) REVERT: o 146 MET cc_start: 0.8483 (tpt) cc_final: 0.8226 (tpp) REVERT: p 65 MET cc_start: 0.6643 (OUTLIER) cc_final: 0.6204 (ptm) REVERT: p 102 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7407 (pt0) REVERT: p 131 PHE cc_start: 0.8400 (t80) cc_final: 0.8078 (t80) REVERT: u 20 MET cc_start: 0.6532 (mmm) cc_final: 0.5845 (mmm) REVERT: v 32 GLN cc_start: 0.8226 (pm20) cc_final: 0.7887 (pm20) REVERT: v 136 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.6865 (pp) REVERT: v 168 MET cc_start: 0.8894 (tpt) cc_final: 0.8628 (tpt) REVERT: y 62 MET cc_start: 0.6976 (tpp) cc_final: 0.6735 (tpp) REVERT: z 229 ASN cc_start: 0.8374 (p0) cc_final: 0.8139 (p0) outliers start: 130 outliers final: 116 residues processed: 827 average time/residue: 0.8395 time to fit residues: 1199.9759 Evaluate side-chains 836 residues out of total 5975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 717 time to evaluate : 5.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 160 GLN Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 28 CYS Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 182 ASP Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 122 LYS Chi-restraints excluded: chain G residue 191 ASN Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 139 CYS Chi-restraints excluded: chain I residue 231 THR Chi-restraints excluded: chain I residue 246 TYR Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 154 ILE Chi-restraints excluded: chain K residue 301 LEU Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 135 LEU Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 23 GLN Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain O residue 57 PHE Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 151 ASP Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 141 SER Chi-restraints excluded: chain Q residue 67 ILE Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain S residue 16 THR Chi-restraints excluded: chain S residue 122 HIS Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain S residue 170 THR Chi-restraints excluded: chain V residue 92 PHE Chi-restraints excluded: chain W residue 429 ASN Chi-restraints excluded: chain 7 residue 10 ASN Chi-restraints excluded: chain 7 residue 45 THR Chi-restraints excluded: chain 7 residue 214 ASP Chi-restraints excluded: chain 8 residue 304 LEU Chi-restraints excluded: chain 8 residue 334 GLN Chi-restraints excluded: chain b residue 231 PHE Chi-restraints excluded: chain e residue 69 SER Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 109 LEU Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 79 ASP Chi-restraints excluded: chain h residue 92 LEU Chi-restraints excluded: chain i residue 53 TYR Chi-restraints excluded: chain n residue 27 VAL Chi-restraints excluded: chain n residue 38 PHE Chi-restraints excluded: chain n residue 114 LEU Chi-restraints excluded: chain n residue 251 LYS Chi-restraints excluded: chain o residue 92 ILE Chi-restraints excluded: chain o residue 97 ARG Chi-restraints excluded: chain o residue 116 ASP Chi-restraints excluded: chain o residue 120 VAL Chi-restraints excluded: chain o residue 147 ILE Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain o residue 185 VAL Chi-restraints excluded: chain o residue 193 VAL Chi-restraints excluded: chain p residue 65 MET Chi-restraints excluded: chain p residue 104 LEU Chi-restraints excluded: chain p residue 346 THR Chi-restraints excluded: chain p residue 412 LEU Chi-restraints excluded: chain p residue 435 SER Chi-restraints excluded: chain s residue 271 ASN Chi-restraints excluded: chain s residue 374 LEU Chi-restraints excluded: chain t residue 145 VAL Chi-restraints excluded: chain t residue 155 ILE Chi-restraints excluded: chain t residue 168 LEU Chi-restraints excluded: chain t residue 247 VAL Chi-restraints excluded: chain t residue 283 LEU Chi-restraints excluded: chain t residue 321 LEU Chi-restraints excluded: chain u residue 17 HIS Chi-restraints excluded: chain u residue 52 THR Chi-restraints excluded: chain u residue 119 ASP Chi-restraints excluded: chain v residue 59 LEU Chi-restraints excluded: chain v residue 136 LEU Chi-restraints excluded: chain v residue 166 VAL Chi-restraints excluded: chain v residue 195 ASP Chi-restraints excluded: chain v residue 209 ASP Chi-restraints excluded: chain v residue 353 HIS Chi-restraints excluded: chain w residue 184 THR Chi-restraints excluded: chain w residue 197 LEU Chi-restraints excluded: chain w residue 198 PHE Chi-restraints excluded: chain z residue 25 LEU Chi-restraints excluded: chain z residue 56 SER Chi-restraints excluded: chain z residue 228 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 857 random chunks: chunk 540 optimal weight: 10.0000 chunk 724 optimal weight: 40.0000 chunk 208 optimal weight: 8.9990 chunk 626 optimal weight: 20.0000 chunk 100 optimal weight: 20.0000 chunk 188 optimal weight: 3.9990 chunk 680 optimal weight: 6.9990 chunk 284 optimal weight: 7.9990 chunk 699 optimal weight: 8.9990 chunk 86 optimal weight: 8.9990 chunk 125 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 HIS A 324 GLN ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 HIS G 61 GLN ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 164 HIS ** K 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 200 ASN ** O 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 20 HIS e 52 GLN e 104 ASN ** n 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 181 ASN ** t 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 284 ASN u 7 HIS v 87 GLN ** v 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 73 HIS z 132 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.063200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.042053 restraints weight = 504224.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.043231 restraints weight = 206935.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.043927 restraints weight = 130674.339| |-----------------------------------------------------------------------------| r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.5121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.144 96776 Z= 0.608 Angle : 0.899 15.991 138381 Z= 0.456 Chirality : 0.048 0.377 16877 Planarity : 0.006 0.071 11636 Dihedral : 22.468 179.970 32804 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 28.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.75 % Favored : 93.18 % Rotamer: Outliers : 2.76 % Allowed : 19.50 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.06 % Twisted Proline : 0.74 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.10), residues: 6729 helix: 0.47 (0.10), residues: 2730 sheet: -0.58 (0.16), residues: 972 loop : -1.19 (0.11), residues: 3027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 247 HIS 0.022 0.002 HIS D 99 PHE 0.034 0.003 PHE P 63 TYR 0.045 0.003 TYR I 66 ARG 0.016 0.001 ARG C 246 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22503.97 seconds wall clock time: 398 minutes 49.28 seconds (23929.28 seconds total)