Starting phenix.real_space_refine on Tue Feb 13 14:04:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zon_11325/02_2024/6zon_11325.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zon_11325/02_2024/6zon_11325.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zon_11325/02_2024/6zon_11325.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zon_11325/02_2024/6zon_11325.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zon_11325/02_2024/6zon_11325.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zon_11325/02_2024/6zon_11325.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 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 1711 5.49 5 S 356 5.16 5 C 62162 2.51 5 N 19856 2.21 5 O 25113 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a GLU 12": "OE1" <-> "OE2" Residue "a GLU 13": "OE1" <-> "OE2" Residue "a PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 118": "OE1" <-> "OE2" Residue "a GLU 136": "OE1" <-> "OE2" Residue "a GLU 196": "OE1" <-> "OE2" Residue "a GLU 211": "OE1" <-> "OE2" Residue "a GLU 213": "OE1" <-> "OE2" Residue "p PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 68": "NH1" <-> "NH2" Residue "d GLU 92": "OE1" <-> "OE2" Residue "d GLU 268": "OE1" <-> "OE2" Residue "Q GLU 46": "OE1" <-> "OE2" Residue "Q GLU 90": "OE1" <-> "OE2" Residue "q GLU 97": "OE1" <-> "OE2" Residue "q ARG 198": "NH1" <-> "NH2" Residue "q ARG 200": "NH1" <-> "NH2" Residue "q ARG 252": "NH1" <-> "NH2" Residue "W ARG 2": "NH1" <-> "NH2" Residue "W ARG 23": "NH1" <-> "NH2" Residue "r GLU 44": "OE1" <-> "OE2" Residue "r ARG 170": "NH1" <-> "NH2" Residue "r GLU 208": "OE1" <-> "OE2" Residue "r GLU 219": "OE1" <-> "OE2" Residue "s GLU 29": "OE1" <-> "OE2" Residue "s GLU 42": "OE1" <-> "OE2" Residue "s GLU 50": "OE1" <-> "OE2" Residue "s GLU 52": "OE1" <-> "OE2" Residue "s GLU 188": "OE1" <-> "OE2" Residue "t GLU 70": "OE1" <-> "OE2" Residue "t GLU 194": "OE1" <-> "OE2" Residue "c PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 162": "NH1" <-> "NH2" Residue "n GLU 49": "OE1" <-> "OE2" Residue "i GLU 51": "OE1" <-> "OE2" Residue "i ARG 104": "NH1" <-> "NH2" Residue "i ARG 121": "NH1" <-> "NH2" Residue "i GLU 130": "OE1" <-> "OE2" Residue "i ARG 146": "NH1" <-> "NH2" Residue "i ARG 150": "NH1" <-> "NH2" Residue "y GLU 38": "OE1" <-> "OE2" Residue "y GLU 64": "OE1" <-> "OE2" Residue "f GLU 49": "OE1" <-> "OE2" Residue "j ARG 11": "NH1" <-> "NH2" Residue "z PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 16": "NH1" <-> "NH2" Residue "R ARG 80": "NH1" <-> "NH2" Residue "w GLU 87": "OE1" <-> "OE2" Residue "w GLU 94": "OE1" <-> "OE2" Residue "g GLU 40": "OE1" <-> "OE2" Residue "g ARG 71": "NH1" <-> "NH2" Residue "g ARG 125": "NH1" <-> "NH2" Residue "g GLU 128": "OE1" <-> "OE2" Residue "b ARG 54": "NH1" <-> "NH2" Residue "b GLU 81": "OE1" <-> "OE2" Residue "b ARG 117": "NH1" <-> "NH2" Residue "b ARG 178": "NH1" <-> "NH2" Residue "b GLU 212": "OE1" <-> "OE2" Residue "e ARG 55": "NH1" <-> "NH2" Residue "e GLU 106": "OE1" <-> "OE2" Residue "e GLU 160": "OE1" <-> "OE2" Residue "e GLU 171": "OE1" <-> "OE2" Residue "e GLU 195": "OE1" <-> "OE2" Residue "u TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 20": "OE1" <-> "OE2" Residue "v ARG 36": "NH1" <-> "NH2" Residue "v GLU 58": "OE1" <-> "OE2" Residue "o GLU 31": "OE1" <-> "OE2" Residue "o GLU 71": "OE1" <-> "OE2" Residue "o GLU 74": "OE1" <-> "OE2" Residue "k ARG 14": "NH1" <-> "NH2" Residue "k GLU 58": "OE1" <-> "OE2" Residue "k GLU 65": "OE1" <-> "OE2" Residue "k GLU 109": "OE1" <-> "OE2" Residue "k GLU 112": "OE1" <-> "OE2" Residue "x GLU 50": "OE1" <-> "OE2" Residue "h ARG 19": "NH1" <-> "NH2" Residue "h PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 96": "OE1" <-> "OE2" Residue "P GLU 90": "OE1" <-> "OE2" Residue "S GLU 64": "OE1" <-> "OE2" Residue "S ARG 66": "NH1" <-> "NH2" Residue "S ARG 67": "NH1" <-> "NH2" Residue "l ARG 12": "NH1" <-> "NH2" Residue "U ARG 116": "NH1" <-> "NH2" Residue "V ARG 88": "NH1" <-> "NH2" Residue "V ARG 100": "NH1" <-> "NH2" Residue "B ARG 492": "NH1" <-> "NH2" Residue "B ARG 501": "NH1" <-> "NH2" Residue "B ARG 505": "NH1" <-> "NH2" Residue "B ARG 507": "NH1" <-> "NH2" Residue "B ARG 550": "NH1" <-> "NH2" Residue "B GLU 560": "OE1" <-> "OE2" Residue "B GLU 563": "OE1" <-> "OE2" Residue "A ARG 7": "NH1" <-> "NH2" Residue "A GLU 9": "OE1" <-> "OE2" Residue "A ARG 14": "NH1" <-> "NH2" Residue "A ARG 41": "NH1" <-> "NH2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A GLU 248": "OE1" <-> "OE2" Residue "A ARG 298": "NH1" <-> "NH2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A ARG 321": "NH1" <-> "NH2" Residue "A ARG 353": "NH1" <-> "NH2" Residue "A ARG 376": "NH1" <-> "NH2" Residue "A ARG 406": "NH1" <-> "NH2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A ARG 469": "NH1" <-> "NH2" Residue "A ARG 476": "NH1" <-> "NH2" Residue "A ARG 483": "NH1" <-> "NH2" Residue "A ARG 489": "NH1" <-> "NH2" Residue "A ARG 502": "NH1" <-> "NH2" Residue "A GLU 548": "OE1" <-> "OE2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ARG 571": "NH1" <-> "NH2" Residue "A ARG 572": "NH1" <-> "NH2" Residue "A ARG 578": "NH1" <-> "NH2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C GLU 100": "OE1" <-> "OE2" Residue "C GLU 114": "OE1" <-> "OE2" Residue "C GLU 122": "OE1" <-> "OE2" Residue "C ARG 142": "NH1" <-> "NH2" Residue "C GLU 352": "OE1" <-> "OE2" Residue "C ARG 439": "NH1" <-> "NH2" Residue "C ARG 450": "NH1" <-> "NH2" Residue "C GLU 498": "OE1" <-> "OE2" Residue "C ARG 563": "NH1" <-> "NH2" Residue "C ARG 708": "NH1" <-> "NH2" Residue "C ARG 719": "NH1" <-> "NH2" Residue "C GLU 759": "OE1" <-> "OE2" Residue "C GLU 812": "OE1" <-> "OE2" Residue "C GLU 829": "OE1" <-> "OE2" Residue "E GLU 99": "OE1" <-> "OE2" Residue "E GLU 126": "OE1" <-> "OE2" Residue "E GLU 176": "OE1" <-> "OE2" Residue "E GLU 187": "OE1" <-> "OE2" Residue "E GLU 294": "OE1" <-> "OE2" Residue "E GLU 330": "OE1" <-> "OE2" Residue "E GLU 365": "OE1" <-> "OE2" Residue "E ARG 369": "NH1" <-> "NH2" Residue "F GLU 111": "OE1" <-> "OE2" Residue "F GLU 130": "OE1" <-> "OE2" Residue "F GLU 141": "OE1" <-> "OE2" Residue "F GLU 151": "OE1" <-> "OE2" Residue "F GLU 181": "OE1" <-> "OE2" Residue "F GLU 188": "OE1" <-> "OE2" Residue "F ARG 210": "NH1" <-> "NH2" Residue "H GLU 56": "OE1" <-> "OE2" Residue "H GLU 102": "OE1" <-> "OE2" Residue "H GLU 145": "OE1" <-> "OE2" Residue "H GLU 185": "OE1" <-> "OE2" Residue "H GLU 195": "OE1" <-> "OE2" Residue "H GLU 219": "OE1" <-> "OE2" Residue "H ARG 249": "NH1" <-> "NH2" Residue "H GLU 284": "OE1" <-> "OE2" Residue "H GLU 332": "OE1" <-> "OE2" Residue "K GLU 5": "OE1" <-> "OE2" Residue "K GLU 30": "OE1" <-> "OE2" Residue "K GLU 39": "OE1" <-> "OE2" Residue "K GLU 96": "OE1" <-> "OE2" Residue "K GLU 123": "OE1" <-> "OE2" Residue "K GLU 160": "OE1" <-> "OE2" Residue "K GLU 193": "OE1" <-> "OE2" Residue "L GLU 210": "OE1" <-> "OE2" Residue "L ARG 262": "NH1" <-> "NH2" Residue "L GLU 298": "OE1" <-> "OE2" Residue "L GLU 310": "OE1" <-> "OE2" Residue "L GLU 438": "OE1" <-> "OE2" Residue "L GLU 483": "OE1" <-> "OE2" Residue "L PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 12": "OE1" <-> "OE2" Residue "M GLU 84": "OE1" <-> "OE2" Residue "M GLU 88": "OE1" <-> "OE2" Residue "M GLU 97": "OE1" <-> "OE2" Residue "M GLU 143": "OE1" <-> "OE2" Residue "M GLU 159": "OE1" <-> "OE2" Residue "M ARG 166": "NH1" <-> "NH2" Residue "M GLU 194": "OE1" <-> "OE2" Residue "M ARG 206": "NH1" <-> "NH2" Residue "M ARG 278": "NH1" <-> "NH2" Residue "M GLU 291": "OE1" <-> "OE2" Residue "M GLU 309": "OE1" <-> "OE2" Residue "M ARG 330": "NH1" <-> "NH2" Residue "M ARG 340": "NH1" <-> "NH2" Residue "D GLU 23": "OE1" <-> "OE2" Residue "D ARG 26": "NH1" <-> "NH2" Residue "D TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 183": "NH1" <-> "NH2" Residue "D GLU 194": "OE1" <-> "OE2" Residue "D GLU 200": "OE1" <-> "OE2" Residue "D ARG 218": "NH1" <-> "NH2" Residue "D ARG 271": "NH1" <-> "NH2" Residue "D ARG 329": "NH1" <-> "NH2" Residue "D GLU 333": "OE1" <-> "OE2" Residue "D GLU 345": "OE1" <-> "OE2" Residue "D ARG 362": "NH1" <-> "NH2" Residue "D ARG 402": "NH1" <-> "NH2" Residue "D ARG 434": "NH1" <-> "NH2" Residue "D ARG 462": "NH1" <-> "NH2" Residue "D GLU 485": "OE1" <-> "OE2" Residue "D GLU 503": "OE1" <-> "OE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 109201 Number of models: 1 Model: "" Number of chains: 51 Chain: "a" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1705 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain: "p" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1715 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 5, 'TRANS': 205} Chain: "d" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1674 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain: "Q" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 814 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "q" Number of atoms: 2031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2031 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 14, 'TRANS': 240} Chain: "W" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 230 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "r" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1794 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain: "s" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1399 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain breaks: 3 Chain: "t" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1638 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 7, 'TRANS': 191} Chain breaks: 1 Chain: "c" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1499 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "n" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1119 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain breaks: 1 Chain: "m" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "i" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 939 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "y" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 625 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "f" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "j" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1080 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 4, 'TRANS': 134} Chain: "z" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 999 Classifications: {'peptide': 122} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 116} Chain: "R" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 640 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "T" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 354 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain breaks: 1 Chain: "2" Number of atoms: 36718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1721, 36718 Inner-chain residues flagged as termini: ['pdbres=" U 2 140 "', 'pdbres=" U 2 287 "', 'pdbres=" G 2 330 "', 'pdbres=" C 2 746 "', 'pdbres=" C 2 791 "', 'pdbres=" G 2 841 "', 'pdbres=" G 21424 "', 'pdbres=" A 21438 "', 'pdbres=" G 21771 "'] Classifications: {'RNA': 1721} Modifications used: {'5*END': 10, 'rna2p_pur': 141, 'rna2p_pyr': 119, 'rna3p_pur': 770, 'rna3p_pyr': 691} Link IDs: {'rna2p': 259, 'rna3p': 1461} Chain breaks: 4 Chain: "w" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1011 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "g" Number of atoms: 1100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1100 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "b" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1745 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 11, 'TRANS': 212} Chain: "e" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1495 Classifications: {'peptide': 189} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 183} Chain: "u" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 799 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 7, 'TRANS': 87} Chain: "v" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 861 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 2, 'TRANS': 108} Chain breaks: 1 Chain: "o" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 980 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain: "k" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1162 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "x" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1094 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 4, 'TRANS': 136} Chain: "h" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 780 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "P" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 557 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "S" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 479 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "l" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 450 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 1, 'TRANS': 52} Chain: "U" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 465 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain breaks: 1 Chain: "V" Number of atoms: 2314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2314 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 10, 'TRANS': 285} Chain breaks: 2 Chain: "I" Number of atoms: 1497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 1497 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 261} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 292} Chain breaks: 1 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 965 Unresolved non-hydrogen angles: 1241 Unresolved non-hydrogen dihedrals: 823 Unresolved non-hydrogen chiralities: 73 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 21, 'TYR:plan': 10, 'ASN:plan1': 16, 'TRP:plan': 5, 'HIS:plan': 11, 'PHE:plan': 18, 'GLU:plan': 18, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 570 Chain: "B" Number of atoms: 2966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 2966 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 388} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 509} Chain breaks: 3 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 1526 Unresolved non-hydrogen angles: 1965 Unresolved non-hydrogen dihedrals: 1337 Unresolved non-hydrogen chiralities: 109 Planarities with less than four sites: {'GLN:plan1': 22, 'ASP:plan': 30, 'TYR:plan': 14, 'ASN:plan1': 16, 'TRP:plan': 16, 'HIS:plan': 13, 'PHE:plan': 26, 'GLU:plan': 23, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 886 Chain: "A" Number of atoms: 5394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 694, 5394 Classifications: {'peptide': 694} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 23, 'TRANS': 670} Chain breaks: 4 Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 306 Unresolved non-hydrogen dihedrals: 102 Planarities with less than four sites: {'UNK:plan-1': 102} Unresolved non-hydrogen planarities: 102 Chain: "C" Number of atoms: 5070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 5070 Classifications: {'peptide': 625} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 17, 'TRANS': 607} Chain breaks: 4 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 3} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3437 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 404} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 2090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2090 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 10, 'TRANS': 258} Chain: "H" Number of atoms: 2413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2413 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 10, 'TRANS': 284} Chain breaks: 2 Chain: "K" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1750 Classifications: {'peptide': 217} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 3, 'TRANS': 210} Chain: "L" Number of atoms: 3111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 3111 Classifications: {'peptide': 372} Link IDs: {'CIS': 5, 'PTRANS': 11, 'TRANS': 355} Chain: "M" Number of atoms: 2718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2718 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 3617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3617 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 19, 'TRANS': 427} Chain breaks: 2 Chain: "Y" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 390 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'TRANS': 77} Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 234 Unresolved non-hydrogen dihedrals: 78 Planarities with less than four sites: {'UNK:plan-1': 78} Unresolved non-hydrogen planarities: 78 Chain: "J" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 244 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 28} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "l" 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 5272 SG CYS Q 23 81.866 175.793 106.187 1.00 15.35 S ATOM 5293 SG CYS Q 26 81.369 174.588 102.559 1.00 14.25 S ATOM 5676 SG CYS Q 74 83.909 172.617 104.867 1.00 22.22 S ATOM 5695 SG CYS Q 77 84.581 175.715 103.613 1.00 18.86 S ATOM 72129 SG CYS U 141 164.651 161.675 21.741 1.00100.81 S ATOM 72148 SG CYS U 144 165.782 164.184 24.087 1.00 86.04 S Time building chain proxies: 41.04, per 1000 atoms: 0.38 Number of scatterers: 109201 At special positions: 0 Unit cell: (224.508, 272.163, 303.933, 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 356 16.00 P 1711 15.00 O 25113 8.00 N 19856 7.00 C 62162 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: 38.09 Conformation dependent library (CDL) restraints added in 9.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Q 201 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 77 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 74 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 26 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 23 " pdb=" ZN U 500 " pdb="ZN ZN U 500 " - pdb=" SG CYS U 141 " pdb="ZN ZN U 500 " - pdb=" SG CYS U 144 " Number of angles added : 6 18022 Ramachandran restraints generated. 9011 Oldfield, 0 Emsley, 9011 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17644 Finding SS restraints... Secondary structure from input PDB file: 351 helices and 91 sheets defined 43.8% alpha, 12.5% beta 441 base pairs and 911 stacking pairs defined. Time for finding SS restraints: 30.63 Creating SS restraints... Processing helix chain 'a' and resid 11 through 22 Processing helix chain 'a' and resid 50 through 67 removed outlier: 3.562A pdb=" N ALA a 67 " --> pdb=" O ARG a 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 70 through 72 No H-bonds generated for 'chain 'a' and resid 70 through 72' Processing helix chain 'a' and resid 80 through 82 No H-bonds generated for 'chain 'a' and resid 80 through 82' Processing helix chain 'a' and resid 83 through 95 Processing helix chain 'a' and resid 130 through 138 removed outlier: 3.581A pdb=" N SER a 138 " --> pdb=" O LEU a 134 " (cutoff:3.500A) Processing helix chain 'a' and resid 167 through 186 Processing helix chain 'a' and resid 198 through 202 Processing helix chain 'a' and resid 206 through 215 Processing helix chain 'p' and resid 23 through 26 Processing helix chain 'p' and resid 58 through 63 removed outlier: 3.960A pdb=" N LYS p 63 " --> pdb=" O ASP p 60 " (cutoff:3.500A) Processing helix chain 'p' and resid 71 through 75 Processing helix chain 'p' and resid 106 through 112 Processing helix chain 'p' and resid 157 through 178 removed outlier: 3.606A pdb=" N VAL p 176 " --> pdb=" O MET p 172 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N THR p 178 " --> pdb=" O ARG p 174 " (cutoff:3.500A) Processing helix chain 'p' and resid 180 through 189 Processing helix chain 'p' and resid 191 through 201 removed outlier: 3.659A pdb=" N LYS p 195 " --> pdb=" O ASP p 191 " (cutoff:3.500A) Processing helix chain 'p' and resid 202 through 204 No H-bonds generated for 'chain 'p' and resid 202 through 204' Processing helix chain 'p' and resid 224 through 232 removed outlier: 3.728A pdb=" N LEU p 228 " --> pdb=" O GLU p 224 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 71 Processing helix chain 'd' and resid 78 through 83 Processing helix chain 'd' and resid 91 through 98 removed outlier: 3.527A pdb=" N ASP d 95 " --> pdb=" O SER d 91 " (cutoff:3.500A) Processing helix chain 'd' and resid 146 through 160 Processing helix chain 'd' and resid 207 through 218 removed outlier: 3.768A pdb=" N LEU d 213 " --> pdb=" O VAL d 209 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY d 218 " --> pdb=" O LEU d 214 " (cutoff:3.500A) Processing helix chain 'd' and resid 232 through 246 Processing helix chain 'd' and resid 247 through 249 No H-bonds generated for 'chain 'd' and resid 247 through 249' Processing helix chain 'd' and resid 264 through 269 Processing helix chain 'Q' and resid 49 through 55 removed outlier: 3.530A pdb=" N SER Q 54 " --> pdb=" O VAL Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 81 Processing helix chain 'Q' and resid 88 through 93 removed outlier: 3.961A pdb=" N LYS Q 93 " --> pdb=" O ARG Q 89 " (cutoff:3.500A) Processing helix chain 'q' and resid 15 through 19 Processing helix chain 'q' and resid 43 through 50 Processing helix chain 'q' and resid 57 through 66 removed outlier: 3.612A pdb=" N VAL q 61 " --> pdb=" O THR q 57 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS q 62 " --> pdb=" O GLY q 58 " (cutoff:3.500A) Processing helix chain 'q' and resid 117 through 119 No H-bonds generated for 'chain 'q' and resid 117 through 119' Processing helix chain 'q' and resid 247 through 255 Processing helix chain 'W' and resid 2 through 22 removed outlier: 3.580A pdb=" N GLN W 22 " --> pdb=" O ARG W 18 " (cutoff:3.500A) Processing helix chain 'r' and resid 20 through 24 Processing helix chain 'r' and resid 137 through 146 Processing helix chain 'r' and resid 152 through 156 removed outlier: 3.825A pdb=" N GLN r 155 " --> pdb=" O ASP r 152 " (cutoff:3.500A) Processing helix chain 'r' and resid 181 through 221 Processing helix chain 's' and resid 19 through 30 removed outlier: 4.023A pdb=" N LEU s 30 " --> pdb=" O ALA s 26 " (cutoff:3.500A) Processing helix chain 's' and resid 31 through 32 No H-bonds generated for 'chain 's' and resid 31 through 32' Processing helix chain 's' and resid 37 through 42 removed outlier: 3.650A pdb=" N LEU s 40 " --> pdb=" O LYS s 37 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU s 42 " --> pdb=" O GLN s 39 " (cutoff:3.500A) Processing helix chain 's' and resid 65 through 87 removed outlier: 4.193A pdb=" N LYS s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE s 75 " --> pdb=" O SER s 71 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N VAL s 77 " --> pdb=" O GLN s 73 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ARG s 78 " --> pdb=" O LYS s 74 " (cutoff:3.500A) Processing helix chain 's' and resid 117 through 120 Processing helix chain 's' and resid 121 through 134 removed outlier: 3.980A pdb=" N VAL s 134 " --> pdb=" O LEU s 130 " (cutoff:3.500A) Processing helix chain 's' and resid 162 through 167 removed outlier: 3.957A pdb=" N VAL s 166 " --> pdb=" O GLN s 162 " (cutoff:3.500A) Processing helix chain 's' and resid 169 through 181 Processing helix chain 't' and resid 25 through 29 Processing helix chain 't' and resid 88 through 93 removed outlier: 3.827A pdb=" N ARG t 92 " --> pdb=" O ASN t 88 " (cutoff:3.500A) Processing helix chain 't' and resid 106 through 117 Processing helix chain 't' and resid 131 through 138 removed outlier: 4.110A pdb=" N ILE t 136 " --> pdb=" O GLU t 132 " (cutoff:3.500A) Processing helix chain 't' and resid 142 through 152 removed outlier: 3.573A pdb=" N LYS t 148 " --> pdb=" O LYS t 144 " (cutoff:3.500A) Processing helix chain 't' and resid 159 through 167 removed outlier: 3.621A pdb=" N GLN t 165 " --> pdb=" O LEU t 161 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN t 167 " --> pdb=" O GLU t 163 " (cutoff:3.500A) Processing helix chain 't' and resid 192 through 206 Processing helix chain 'c' and resid 21 through 36 Processing helix chain 'c' and resid 40 through 61 removed outlier: 3.726A pdb=" N VAL c 46 " --> pdb=" O GLU c 42 " (cutoff:3.500A) Processing helix chain 'c' and resid 67 through 84 removed outlier: 3.750A pdb=" N ASN c 75 " --> pdb=" O LEU c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 93 through 100 removed outlier: 3.966A pdb=" N LEU c 98 " --> pdb=" O ASP c 95 " (cutoff:3.500A) Processing helix chain 'c' and resid 101 through 107 removed outlier: 4.081A pdb=" N PHE c 105 " --> pdb=" O LYS c 101 " (cutoff:3.500A) Processing helix chain 'c' and resid 109 through 117 Processing helix chain 'c' and resid 122 through 132 Processing helix chain 'c' and resid 153 through 155 No H-bonds generated for 'chain 'c' and resid 153 through 155' Processing helix chain 'c' and resid 171 through 179 removed outlier: 3.759A pdb=" N LYS c 179 " --> pdb=" O ARG c 175 " (cutoff:3.500A) Processing helix chain 'n' and resid 47 through 52 Processing helix chain 'm' and resid 29 through 42 Processing helix chain 'm' and resid 46 through 59 removed outlier: 3.637A pdb=" N HIS m 58 " --> pdb=" O LEU m 54 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY m 59 " --> pdb=" O ARG m 55 " (cutoff:3.500A) Processing helix chain 'm' and resid 62 through 67 removed outlier: 3.510A pdb=" N VAL m 66 " --> pdb=" O GLN m 62 " (cutoff:3.500A) Processing helix chain 'm' and resid 70 through 78 removed outlier: 3.646A pdb=" N LYS m 78 " --> pdb=" O ILE m 74 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 105 removed outlier: 3.967A pdb=" N ARG m 104 " --> pdb=" O LYS m 100 " (cutoff:3.500A) Processing helix chain 'm' and resid 108 through 132 removed outlier: 3.699A pdb=" N THR m 131 " --> pdb=" O ARG m 127 " (cutoff:3.500A) Processing helix chain 'm' and resid 145 through 150 removed outlier: 3.956A pdb=" N LEU m 149 " --> pdb=" O THR m 145 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL m 150 " --> pdb=" O ALA m 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 145 through 150' Processing helix chain 'i' and resid 59 through 61 No H-bonds generated for 'chain 'i' and resid 59 through 61' Processing helix chain 'i' and resid 64 through 68 removed outlier: 3.517A pdb=" N GLU i 68 " --> pdb=" O ASP i 65 " (cutoff:3.500A) Processing helix chain 'i' and resid 70 through 88 removed outlier: 3.611A pdb=" N GLU i 87 " --> pdb=" O GLN i 83 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU i 88 " --> pdb=" O ARG i 84 " (cutoff:3.500A) Processing helix chain 'i' and resid 110 through 122 removed outlier: 4.674A pdb=" N SER i 114 " --> pdb=" O PRO i 110 " (cutoff:3.500A) Processing helix chain 'y' and resid 56 through 62 Processing helix chain 'y' and resid 64 through 76 Processing helix chain 'f' and resid 5 through 21 Processing helix chain 'f' and resid 31 through 44 removed outlier: 3.693A pdb=" N VAL f 35 " --> pdb=" O SER f 31 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG f 36 " --> pdb=" O LYS f 32 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS f 44 " --> pdb=" O VAL f 40 " (cutoff:3.500A) Processing helix chain 'f' and resid 85 through 94 removed outlier: 3.570A pdb=" N LEU f 94 " --> pdb=" O GLN f 90 " (cutoff:3.500A) Processing helix chain 'f' and resid 113 through 120 Processing helix chain 'j' and resid 9 through 21 removed outlier: 3.505A pdb=" N ASP j 19 " --> pdb=" O SER j 15 " (cutoff:3.500A) Processing helix chain 'j' and resid 24 through 32 Processing helix chain 'j' and resid 33 through 39 Processing helix chain 'j' and resid 130 through 135 Processing helix chain 'z' and resid 36 through 49 Processing helix chain 'z' and resid 78 through 86 Processing helix chain 'z' and resid 87 through 93 Processing helix chain 'z' and resid 103 through 115 Processing helix chain 'z' and resid 119 through 123 Processing helix chain 'R' and resid 11 through 17 Processing helix chain 'T' and resid 11 through 16 removed outlier: 3.600A pdb=" N GLN T 15 " --> pdb=" O LYS T 11 " (cutoff:3.500A) Processing helix chain 'T' and resid 30 through 43 removed outlier: 3.614A pdb=" N VAL T 43 " --> pdb=" O ASN T 39 " (cutoff:3.500A) Processing helix chain 'w' and resid 11 through 19 Processing helix chain 'w' and resid 27 through 38 Processing helix chain 'w' and resid 43 through 61 Processing helix chain 'w' and resid 62 through 64 No H-bonds generated for 'chain 'w' and resid 62 through 64' Processing helix chain 'w' and resid 70 through 80 removed outlier: 4.057A pdb=" N GLN w 74 " --> pdb=" O SER w 70 " (cutoff:3.500A) Processing helix chain 'w' and resid 99 through 108 Processing helix chain 'g' and resid 44 through 48 Processing helix chain 'g' and resid 77 through 99 Processing helix chain 'g' and resid 101 through 113 removed outlier: 3.572A pdb=" N LYS g 105 " --> pdb=" O ASP g 101 " (cutoff:3.500A) Processing helix chain 'b' and resid 6 through 29 Processing helix chain 'b' and resid 63 through 76 Processing helix chain 'b' and resid 93 through 96 removed outlier: 3.574A pdb=" N LEU b 96 " --> pdb=" O THR b 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 93 through 96' Processing helix chain 'b' and resid 97 through 111 removed outlier: 3.642A pdb=" N GLN b 101 " --> pdb=" O CYS b 97 " (cutoff:3.500A) Processing helix chain 'b' and resid 114 through 130 removed outlier: 4.807A pdb=" N ALA b 118 " --> pdb=" O ALA b 114 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY b 130 " --> pdb=" O ILE b 126 " (cutoff:3.500A) Processing helix chain 'b' and resid 162 through 167 removed outlier: 3.659A pdb=" N TYR b 166 " --> pdb=" O PRO b 163 " (cutoff:3.500A) Processing helix chain 'e' and resid 18 through 22 Processing helix chain 'e' and resid 67 through 76 Processing helix chain 'e' and resid 86 through 102 Processing helix chain 'e' and resid 107 through 119 removed outlier: 3.684A pdb=" N VAL e 111 " --> pdb=" O ASN e 107 " (cutoff:3.500A) Processing helix chain 'e' and resid 142 through 156 Processing helix chain 'e' and resid 168 through 182 removed outlier: 3.983A pdb=" N CYS e 172 " --> pdb=" O THR e 168 " (cutoff:3.500A) Processing helix chain 'e' and resid 187 through 203 removed outlier: 4.205A pdb=" N ALA e 200 " --> pdb=" O LEU e 196 " (cutoff:3.500A) Processing helix chain 'u' and resid 4 through 18 removed outlier: 4.253A pdb=" N ARG u 8 " --> pdb=" O PRO u 4 " (cutoff:3.500A) Processing helix chain 'u' and resid 41 through 54 Processing helix chain 'u' and resid 72 through 83 Processing helix chain 'v' and resid 15 through 26 removed outlier: 5.407A pdb=" N VAL v 21 " --> pdb=" O ALA v 17 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU v 22 " --> pdb=" O LEU v 18 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LYS v 23 " --> pdb=" O GLN v 19 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N THR v 24 " --> pdb=" O GLU v 20 " (cutoff:3.500A) Processing helix chain 'v' and resid 34 through 44 Processing helix chain 'v' and resid 63 through 73 removed outlier: 3.556A pdb=" N GLN v 73 " --> pdb=" O CYS v 69 " (cutoff:3.500A) Processing helix chain 'v' and resid 84 through 89 Processing helix chain 'v' and resid 120 through 125 Processing helix chain 'o' and resid 22 through 26 Processing helix chain 'o' and resid 32 through 37 removed outlier: 3.877A pdb=" N LEU o 36 " --> pdb=" O GLN o 32 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR o 37 " --> pdb=" O LEU o 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 32 through 37' Processing helix chain 'o' and resid 38 through 47 Processing helix chain 'o' and resid 50 through 65 Processing helix chain 'o' and resid 108 through 112 removed outlier: 4.100A pdb=" N ILE o 112 " --> pdb=" O PRO o 109 " (cutoff:3.500A) Processing helix chain 'o' and resid 115 through 120 removed outlier: 4.572A pdb=" N PHE o 119 " --> pdb=" O TYR o 115 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER o 120 " --> pdb=" O LEU o 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 115 through 120' Processing helix chain 'k' and resid 14 through 18 removed outlier: 3.748A pdb=" N ASN k 17 " --> pdb=" O ARG k 14 " (cutoff:3.500A) Processing helix chain 'k' and resid 25 through 30 Processing helix chain 'k' and resid 31 through 33 No H-bonds generated for 'chain 'k' and resid 31 through 33' Processing helix chain 'k' and resid 38 through 48 Processing helix chain 'k' and resid 60 through 73 removed outlier: 3.939A pdb=" N ASN k 73 " --> pdb=" O THR k 69 " (cutoff:3.500A) Processing helix chain 'k' and resid 99 through 117 removed outlier: 3.791A pdb=" N ASP k 104 " --> pdb=" O ALA k 100 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ASN k 105 " --> pdb=" O ASN k 101 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE k 117 " --> pdb=" O ARG k 113 " (cutoff:3.500A) Processing helix chain 'k' and resid 119 through 127 Processing helix chain 'x' and resid 5 through 9 Processing helix chain 'x' and resid 12 through 26 removed outlier: 3.645A pdb=" N ARG x 16 " --> pdb=" O GLN x 12 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY x 26 " --> pdb=" O LEU x 22 " (cutoff:3.500A) Processing helix chain 'x' and resid 32 through 36 removed outlier: 4.534A pdb=" N ASP x 35 " --> pdb=" O GLU x 32 " (cutoff:3.500A) Processing helix chain 'x' and resid 51 through 67 removed outlier: 3.580A pdb=" N THR x 55 " --> pdb=" O ASN x 51 " (cutoff:3.500A) Processing helix chain 'x' and resid 71 through 79 removed outlier: 3.870A pdb=" N LYS x 77 " --> pdb=" O GLY x 73 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR x 79 " --> pdb=" O MET x 75 " (cutoff:3.500A) Processing helix chain 'x' and resid 96 through 110 removed outlier: 3.649A pdb=" N ALA x 100 " --> pdb=" O SER x 96 " (cutoff:3.500A) Processing helix chain 'x' and resid 124 through 142 removed outlier: 3.565A pdb=" N ILE x 134 " --> pdb=" O ASP x 130 " (cutoff:3.500A) Processing helix chain 'h' and resid 28 through 44 removed outlier: 3.910A pdb=" N LEU h 32 " --> pdb=" O ASN h 28 " (cutoff:3.500A) Processing helix chain 'h' and resid 94 through 103 removed outlier: 4.229A pdb=" N VAL h 98 " --> pdb=" O PRO h 94 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS h 99 " --> pdb=" O SER h 95 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLN h 100 " --> pdb=" O GLU h 96 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ILE h 101 " --> pdb=" O ILE h 97 " (cutoff:3.500A) Processing helix chain 'P' and resid 54 through 59 Processing helix chain 'P' and resid 61 through 65 Processing helix chain 'P' and resid 72 through 77 removed outlier: 4.087A pdb=" N ARG P 76 " --> pdb=" O VAL P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 80 through 91 Processing helix chain 'P' and resid 92 through 95 removed outlier: 3.550A pdb=" N GLY P 95 " --> pdb=" O LEU P 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 92 through 95' Processing helix chain 'l' and resid 39 through 46 Processing helix chain 'I' and resid 156 through 158 No H-bonds generated for 'chain 'I' and resid 156 through 158' Processing helix chain 'B' and resid 199 through 211 Processing helix chain 'B' and resid 239 through 249 removed outlier: 3.600A pdb=" N ALA B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL B 244 " --> pdb=" O PRO B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 294 removed outlier: 3.729A pdb=" N ARG B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 290 through 294' Processing helix chain 'B' and resid 714 through 721 Processing helix chain 'B' and resid 733 through 743 removed outlier: 4.057A pdb=" N LEU B 737 " --> pdb=" O GLN B 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 22 removed outlier: 4.135A pdb=" N LEU A 12 " --> pdb=" O PRO A 8 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS A 13 " --> pdb=" O GLU A 9 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG A 14 " --> pdb=" O ASN A 10 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 21 " --> pdb=" O GLU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 37 removed outlier: 3.530A pdb=" N ALA A 27 " --> pdb=" O LYS A 23 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 34 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 47 Processing helix chain 'A' and resid 48 through 62 removed outlier: 3.556A pdb=" N TYR A 54 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 78 Processing helix chain 'A' and resid 83 through 115 removed outlier: 3.738A pdb=" N ARG A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU A 99 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS A 100 " --> pdb=" O MET A 96 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LEU A 113 " --> pdb=" O GLN A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 133 removed outlier: 3.600A pdb=" N VAL A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 145 Processing helix chain 'A' and resid 146 through 164 removed outlier: 3.549A pdb=" N PHE A 152 " --> pdb=" O PRO A 148 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 161 " --> pdb=" O TYR A 157 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 169 No H-bonds generated for 'chain 'A' and resid 167 through 169' Processing helix chain 'A' and resid 170 through 189 removed outlier: 3.589A pdb=" N ALA A 178 " --> pdb=" O TYR A 174 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A 182 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LYS A 183 " --> pdb=" O GLN A 179 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N CYS A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 211 removed outlier: 3.517A pdb=" N ARG A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP A 199 " --> pdb=" O ARG A 195 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASN A 200 " --> pdb=" O LYS A 196 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 243 removed outlier: 3.545A pdb=" N ARG A 233 " --> pdb=" O HIS A 229 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASP A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER A 239 " --> pdb=" O VAL A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 263 removed outlier: 3.802A pdb=" N VAL A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 286 removed outlier: 3.645A pdb=" N MET A 272 " --> pdb=" O LYS A 268 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 279 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 306 removed outlier: 3.582A pdb=" N THR A 295 " --> pdb=" O PHE A 291 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 296 " --> pdb=" O HIS A 292 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 302 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU A 305 " --> pdb=" O HIS A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 327 removed outlier: 3.558A pdb=" N SER A 319 " --> pdb=" O MET A 315 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A 321 " --> pdb=" O ARG A 317 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 325 " --> pdb=" O ARG A 321 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 326 " --> pdb=" O VAL A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 352 through 358 removed outlier: 3.585A pdb=" N LEU A 358 " --> pdb=" O ARG A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 377 removed outlier: 3.578A pdb=" N ILE A 371 " --> pdb=" O ARG A 367 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG A 376 " --> pdb=" O ASN A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 382 Processing helix chain 'A' and resid 389 through 395 Processing helix chain 'A' and resid 399 through 407 removed outlier: 4.124A pdb=" N CYS A 404 " --> pdb=" O PRO A 400 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N GLU A 405 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 416 removed outlier: 3.814A pdb=" N ASN A 412 " --> pdb=" O THR A 408 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TRP A 413 " --> pdb=" O LYS A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 425 removed outlier: 3.533A pdb=" N GLN A 425 " --> pdb=" O PRO A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 446 removed outlier: 3.871A pdb=" N ILE A 436 " --> pdb=" O GLN A 432 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A 437 " --> pdb=" O ASN A 433 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG A 438 " --> pdb=" O ASN A 434 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN A 442 " --> pdb=" O ARG A 438 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLN A 445 " --> pdb=" O GLN A 441 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 446 " --> pdb=" O GLN A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 459 Processing helix chain 'A' and resid 463 through 477 removed outlier: 4.078A pdb=" N ASP A 473 " --> pdb=" O ARG A 469 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 520 Processing helix chain 'A' and resid 521 through 538 removed outlier: 3.662A pdb=" N VAL A 529 " --> pdb=" O ALA A 525 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA A 531 " --> pdb=" O SER A 527 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU A 535 " --> pdb=" O ALA A 531 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL A 536 " --> pdb=" O LYS A 532 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 537 " --> pdb=" O ALA A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 555 removed outlier: 3.713A pdb=" N GLN A 544 " --> pdb=" O ALA A 540 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU A 545 " --> pdb=" O HIS A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 561 Processing helix chain 'A' and resid 563 through 576 removed outlier: 3.893A pdb=" N ARG A 567 " --> pdb=" O LYS A 563 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE A 568 " --> pdb=" O GLU A 564 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU A 569 " --> pdb=" O HIS A 565 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 575 " --> pdb=" O ARG A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 598 removed outlier: 3.518A pdb=" N GLN A 588 " --> pdb=" O SER A 584 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU A 592 " --> pdb=" O GLN A 588 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU A 598 " --> pdb=" O LEU A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 635 removed outlier: 3.584A pdb=" N UNK A 609 " --> pdb=" O UNK A 605 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N UNK A 617 " --> pdb=" O UNK A 613 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N UNK A 622 " --> pdb=" O UNK A 618 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N UNK A 623 " --> pdb=" O UNK A 619 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N UNK A 624 " --> pdb=" O UNK A 620 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N UNK A 627 " --> pdb=" O UNK A 623 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N UNK A 629 " --> pdb=" O UNK A 625 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N UNK A 630 " --> pdb=" O UNK A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 640 removed outlier: 3.857A pdb=" N UNK A 640 " --> pdb=" O UNK A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 683 Processing helix chain 'A' and resid 708 through 725 removed outlier: 3.528A pdb=" N UNK A 717 " --> pdb=" O UNK A 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 56 removed outlier: 3.526A pdb=" N ARG C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 62 Processing helix chain 'C' and resid 63 through 73 removed outlier: 3.897A pdb=" N LYS C 72 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE C 73 " --> pdb=" O ASN C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 82 Processing helix chain 'C' and resid 82 through 92 removed outlier: 3.593A pdb=" N GLY C 87 " --> pdb=" O PHE C 83 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LYS C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 95 No H-bonds generated for 'chain 'C' and resid 93 through 95' Processing helix chain 'C' and resid 96 through 100 Processing helix chain 'C' and resid 103 through 121 removed outlier: 3.836A pdb=" N ILE C 109 " --> pdb=" O PHE C 105 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU C 120 " --> pdb=" O TYR C 116 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRP C 121 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 149 removed outlier: 4.019A pdb=" N SER C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 334 removed outlier: 3.511A pdb=" N VAL C 329 " --> pdb=" O THR C 325 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS C 331 " --> pdb=" O ALA C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 360 removed outlier: 3.588A pdb=" N ILE C 351 " --> pdb=" O ARG C 347 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU C 352 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU C 354 " --> pdb=" O GLN C 350 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN C 359 " --> pdb=" O GLN C 355 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE C 360 " --> pdb=" O LEU C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 384 removed outlier: 3.672A pdb=" N ILE C 371 " --> pdb=" O GLY C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 415 removed outlier: 3.894A pdb=" N LYS C 400 " --> pdb=" O GLU C 396 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP C 403 " --> pdb=" O GLY C 399 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE C 405 " --> pdb=" O CYS C 401 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ASN C 406 " --> pdb=" O LEU C 402 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE C 411 " --> pdb=" O GLU C 407 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN C 415 " --> pdb=" O ILE C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 460 removed outlier: 3.613A pdb=" N LEU C 447 " --> pdb=" O CYS C 443 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE C 458 " --> pdb=" O GLU C 454 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET C 459 " --> pdb=" O PHE C 455 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN C 460 " --> pdb=" O THR C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 473 removed outlier: 3.505A pdb=" N HIS C 472 " --> pdb=" O GLU C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 490 Processing helix chain 'C' and resid 495 through 509 removed outlier: 4.928A pdb=" N ARG C 501 " --> pdb=" O GLU C 497 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU C 504 " --> pdb=" O CYS C 500 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU C 505 " --> pdb=" O ARG C 501 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG C 506 " --> pdb=" O ILE C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 558 removed outlier: 3.640A pdb=" N LYS C 553 " --> pdb=" O GLU C 549 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N TYR C 554 " --> pdb=" O ARG C 550 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE C 555 " --> pdb=" O LEU C 551 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA C 557 " --> pdb=" O LYS C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 579 removed outlier: 3.848A pdb=" N THR C 566 " --> pdb=" O ASP C 562 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N HIS C 579 " --> pdb=" O HIS C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 593 removed outlier: 3.757A pdb=" N ASP C 587 " --> pdb=" O TYR C 583 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU C 588 " --> pdb=" O GLN C 584 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET C 589 " --> pdb=" O ALA C 585 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU C 590 " --> pdb=" O ARG C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 598 removed outlier: 3.973A pdb=" N ASN C 597 " --> pdb=" O HIS C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 622 removed outlier: 4.357A pdb=" N LEU C 608 " --> pdb=" O PRO C 604 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN C 615 " --> pdb=" O ARG C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 633 removed outlier: 3.801A pdb=" N LEU C 633 " --> pdb=" O ALA C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 639 Processing helix chain 'C' and resid 641 through 646 Processing helix chain 'C' and resid 662 through 667 Processing helix chain 'C' and resid 672 through 676 Processing helix chain 'C' and resid 678 through 689 Processing helix chain 'C' and resid 694 through 702 Processing helix chain 'C' and resid 711 through 721 Processing helix chain 'C' and resid 732 through 737 Processing helix chain 'C' and resid 737 through 746 removed outlier: 3.578A pdb=" N LYS C 742 " --> pdb=" O VAL C 738 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET C 746 " --> pdb=" O LYS C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 754 Processing helix chain 'C' and resid 759 through 765 Processing helix chain 'C' and resid 766 through 769 removed outlier: 3.543A pdb=" N PHE C 769 " --> pdb=" O TRP C 766 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 766 through 769' Processing helix chain 'C' and resid 771 through 796 removed outlier: 3.688A pdb=" N VAL C 775 " --> pdb=" O GLU C 771 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER C 787 " --> pdb=" O ILE C 783 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR C 790 " --> pdb=" O GLU C 786 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU C 792 " --> pdb=" O LEU C 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 797 through 799 No H-bonds generated for 'chain 'C' and resid 797 through 799' Processing helix chain 'C' and resid 804 through 811 Processing helix chain 'C' and resid 814 through 828 removed outlier: 3.582A pdb=" N SER C 823 " --> pdb=" O HIS C 819 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS C 824 " --> pdb=" O SER C 820 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET C 825 " --> pdb=" O ILE C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 878 removed outlier: 3.908A pdb=" N LEU C 855 " --> pdb=" O ALA C 851 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU C 861 " --> pdb=" O LEU C 857 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS C 862 " --> pdb=" O GLN C 858 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU C 868 " --> pdb=" O GLY C 864 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN C 869 " --> pdb=" O SER C 865 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE C 874 " --> pdb=" O ASN C 870 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP C 875 " --> pdb=" O GLU C 871 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 11 Processing helix chain 'E' and resid 12 through 14 No H-bonds generated for 'chain 'E' and resid 12 through 14' Processing helix chain 'E' and resid 19 through 27 removed outlier: 3.606A pdb=" N LEU E 26 " --> pdb=" O LEU E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 48 removed outlier: 3.611A pdb=" N LEU E 37 " --> pdb=" O ASN E 33 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP E 43 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU E 44 " --> pdb=" O GLY E 40 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU E 45 " --> pdb=" O LYS E 41 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP E 47 " --> pdb=" O ASP E 43 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR E 48 " --> pdb=" O LEU E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 59 removed outlier: 3.713A pdb=" N LYS E 59 " --> pdb=" O MET E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 94 removed outlier: 3.726A pdb=" N LYS E 73 " --> pdb=" O ALA E 69 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR E 75 " --> pdb=" O ARG E 71 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN E 83 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU E 84 " --> pdb=" O GLN E 80 " (cutoff:3.500A) Proline residue: E 90 - end of helix Processing helix chain 'E' and resid 111 through 119 Processing helix chain 'E' and resid 124 through 127 Processing helix chain 'E' and resid 128 through 142 Processing helix chain 'E' and resid 145 through 158 removed outlier: 3.519A pdb=" N LEU E 157 " --> pdb=" O PHE E 153 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL E 158 " --> pdb=" O PHE E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 179 removed outlier: 3.540A pdb=" N LEU E 169 " --> pdb=" O ALA E 165 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA E 174 " --> pdb=" O TRP E 170 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET E 179 " --> pdb=" O SER E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 198 removed outlier: 4.235A pdb=" N GLU E 187 " --> pdb=" O ASP E 183 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU E 192 " --> pdb=" O ASP E 188 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE E 196 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP E 197 " --> pdb=" O LYS E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 225 removed outlier: 3.749A pdb=" N TRP E 217 " --> pdb=" O TRP E 213 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU E 219 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N PHE E 220 " --> pdb=" O HIS E 216 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL E 221 " --> pdb=" O TRP E 217 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE E 223 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASN E 224 " --> pdb=" O PHE E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 236 removed outlier: 4.033A pdb=" N ILE E 232 " --> pdb=" O GLY E 228 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP E 234 " --> pdb=" O ASP E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 249 removed outlier: 3.923A pdb=" N ALA E 245 " --> pdb=" O GLN E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 263 removed outlier: 3.593A pdb=" N THR E 259 " --> pdb=" O ARG E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 282 removed outlier: 4.021A pdb=" N GLN E 272 " --> pdb=" O ARG E 268 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL E 273 " --> pdb=" O LYS E 269 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS E 275 " --> pdb=" O ARG E 271 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ASP E 276 " --> pdb=" O GLN E 272 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LYS E 279 " --> pdb=" O LYS E 275 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL E 280 " --> pdb=" O ASP E 276 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN E 282 " --> pdb=" O VAL E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 301 removed outlier: 3.772A pdb=" N VAL E 296 " --> pdb=" O ILE E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 320 removed outlier: 4.513A pdb=" N GLU E 316 " --> pdb=" O LEU E 312 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N SER E 317 " --> pdb=" O ARG E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 348 removed outlier: 3.615A pdb=" N ILE E 333 " --> pdb=" O LEU E 329 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR E 343 " --> pdb=" O PHE E 339 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE E 344 " --> pdb=" O ILE E 340 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG E 346 " --> pdb=" O GLU E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 358 removed outlier: 3.765A pdb=" N ASP E 358 " --> pdb=" O ASN E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 377 removed outlier: 3.535A pdb=" N ARG E 376 " --> pdb=" O VAL E 372 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASN E 377 " --> pdb=" O ASN E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 406 removed outlier: 3.512A pdb=" N GLN E 403 " --> pdb=" O SER E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 410 through 421 removed outlier: 3.900A pdb=" N GLN E 416 " --> pdb=" O SER E 412 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN E 421 " --> pdb=" O MET E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 426 removed outlier: 3.674A pdb=" N LEU E 426 " --> pdb=" O ILE E 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 107 removed outlier: 3.652A pdb=" N LEU F 99 " --> pdb=" O HIS F 95 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP F 104 " --> pdb=" O ALA F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 162 removed outlier: 4.470A pdb=" N ALA F 153 " --> pdb=" O ASP F 149 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS F 154 " --> pdb=" O MET F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 193 removed outlier: 3.792A pdb=" N LEU F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE F 186 " --> pdb=" O HIS F 182 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS F 187 " --> pdb=" O SER F 183 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU F 193 " --> pdb=" O TYR F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 247 Processing helix chain 'F' and resid 248 through 254 removed outlier: 4.115A pdb=" N ILE F 252 " --> pdb=" O GLY F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 296 removed outlier: 4.198A pdb=" N LEU F 287 " --> pdb=" O LEU F 283 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR F 289 " --> pdb=" O THR F 285 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU F 294 " --> pdb=" O ALA F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 305 removed outlier: 3.655A pdb=" N VAL F 304 " --> pdb=" O ALA F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 314 Processing helix chain 'F' and resid 320 through 356 removed outlier: 4.447A pdb=" N SER F 329 " --> pdb=" O THR F 325 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU F 334 " --> pdb=" O ASN F 330 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN F 342 " --> pdb=" O THR F 338 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN F 347 " --> pdb=" O LEU F 343 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 56 removed outlier: 4.072A pdb=" N VAL H 46 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU H 47 " --> pdb=" O GLY H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 110 removed outlier: 3.590A pdb=" N MET H 103 " --> pdb=" O TYR H 99 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU H 107 " --> pdb=" O MET H 103 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG H 108 " --> pdb=" O MET H 104 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS H 109 " --> pdb=" O ARG H 105 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL H 110 " --> pdb=" O SER H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 144 removed outlier: 3.939A pdb=" N ASP H 135 " --> pdb=" O ARG H 131 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER H 136 " --> pdb=" O ALA H 132 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN H 137 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE H 144 " --> pdb=" O TYR H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 159 removed outlier: 3.549A pdb=" N THR H 157 " --> pdb=" O ASP H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 180 removed outlier: 3.873A pdb=" N GLU H 179 " --> pdb=" O GLU H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 190 Processing helix chain 'H' and resid 208 through 221 removed outlier: 3.762A pdb=" N LEU H 214 " --> pdb=" O LEU H 210 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS H 220 " --> pdb=" O TRP H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 236 through 286 removed outlier: 3.630A pdb=" N ASN H 242 " --> pdb=" O HIS H 238 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU H 243 " --> pdb=" O LEU H 239 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASP H 248 " --> pdb=" O GLN H 244 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ARG H 249 " --> pdb=" O LEU H 245 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP H 256 " --> pdb=" O GLU H 252 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE H 257 " --> pdb=" O MET H 253 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN H 272 " --> pdb=" O SER H 268 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU H 284 " --> pdb=" O ARG H 280 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN H 285 " --> pdb=" O ARG H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 314 through 323 removed outlier: 3.514A pdb=" N LEU H 318 " --> pdb=" O MET H 314 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA H 320 " --> pdb=" O SER H 316 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 342 removed outlier: 4.096A pdb=" N ASN H 329 " --> pdb=" O THR H 325 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE H 342 " --> pdb=" O LEU H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 342 through 351 removed outlier: 4.282A pdb=" N TYR H 350 " --> pdb=" O ALA H 346 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ASN H 351 " --> pdb=" O LEU H 347 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 15 removed outlier: 3.915A pdb=" N LYS K 13 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU K 14 " --> pdb=" O ASN K 10 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU K 15 " --> pdb=" O VAL K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 17 through 21 removed outlier: 4.051A pdb=" N ARG K 20 " --> pdb=" O GLY K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 25 removed outlier: 3.737A pdb=" N ASN K 25 " --> pdb=" O ASN K 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 22 through 25' Processing helix chain 'K' and resid 26 through 31 removed outlier: 3.902A pdb=" N ARG K 31 " --> pdb=" O ALA K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 31 through 39 removed outlier: 3.820A pdb=" N GLU K 39 " --> pdb=" O THR K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 57 removed outlier: 3.866A pdb=" N VAL K 50 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LEU K 51 " --> pdb=" O ASN K 47 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU K 53 " --> pdb=" O ALA K 49 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TYR K 54 " --> pdb=" O VAL K 50 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLN K 55 " --> pdb=" O LEU K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 61 removed outlier: 3.822A pdb=" N PHE K 61 " --> pdb=" O PRO K 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 58 through 61' Processing helix chain 'K' and resid 62 through 75 removed outlier: 3.667A pdb=" N THR K 66 " --> pdb=" O GLN K 62 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN K 68 " --> pdb=" O THR K 64 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE K 69 " --> pdb=" O VAL K 65 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU K 70 " --> pdb=" O THR K 66 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU K 71 " --> pdb=" O ALA K 67 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 85 removed outlier: 3.648A pdb=" N LEU K 84 " --> pdb=" O THR K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 89 removed outlier: 4.080A pdb=" N ILE K 89 " --> pdb=" O LYS K 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 86 through 89' Processing helix chain 'K' and resid 98 through 111 removed outlier: 3.576A pdb=" N TYR K 104 " --> pdb=" O ARG K 100 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP K 107 " --> pdb=" O LEU K 103 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU K 108 " --> pdb=" O TYR K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 114 through 119 Processing helix chain 'K' and resid 126 through 131 Processing helix chain 'K' and resid 133 through 149 removed outlier: 3.796A pdb=" N LYS K 140 " --> pdb=" O ASP K 136 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N PHE K 141 " --> pdb=" O SER K 137 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL K 145 " --> pdb=" O PHE K 141 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL K 146 " --> pdb=" O ILE K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 154 through 162 Processing helix chain 'K' and resid 166 through 171 Processing helix chain 'K' and resid 171 through 176 Processing helix chain 'K' and resid 192 through 196 Processing helix chain 'K' and resid 206 through 218 removed outlier: 3.832A pdb=" N VAL K 210 " --> pdb=" O ASP K 206 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER K 212 " --> pdb=" O ASP K 208 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ILE K 213 " --> pdb=" O SER K 209 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER K 216 " --> pdb=" O SER K 212 " (cutoff:3.500A) Processing helix chain 'L' and resid 186 through 202 removed outlier: 4.764A pdb=" N TYR L 192 " --> pdb=" O ASP L 188 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG L 201 " --> pdb=" O PHE L 197 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N CYS L 202 " --> pdb=" O SER L 198 " (cutoff:3.500A) Processing helix chain 'L' and resid 209 through 218 removed outlier: 3.754A pdb=" N LEU L 215 " --> pdb=" O GLU L 211 " (cutoff:3.500A) Processing helix chain 'L' and resid 223 through 245 removed outlier: 4.782A pdb=" N ASN L 229 " --> pdb=" O HIS L 225 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL L 230 " --> pdb=" O SER L 226 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N HIS L 232 " --> pdb=" O LEU L 228 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU L 234 " --> pdb=" O VAL L 230 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL L 235 " --> pdb=" O LEU L 231 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS L 237 " --> pdb=" O SER L 233 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER L 238 " --> pdb=" O LEU L 234 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ASN L 241 " --> pdb=" O LYS L 237 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG L 242 " --> pdb=" O SER L 238 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU L 245 " --> pdb=" O ASN L 241 " (cutoff:3.500A) Processing helix chain 'L' and resid 251 through 258 removed outlier: 3.818A pdb=" N VAL L 256 " --> pdb=" O ASP L 252 " (cutoff:3.500A) Processing helix chain 'L' and resid 274 through 290 removed outlier: 3.813A pdb=" N LEU L 278 " --> pdb=" O LEU L 274 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU L 280 " --> pdb=" O GLY L 276 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLN L 289 " --> pdb=" O GLY L 285 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA L 290 " --> pdb=" O ASP L 286 " (cutoff:3.500A) Processing helix chain 'L' and resid 297 through 301 removed outlier: 3.618A pdb=" N ASN L 300 " --> pdb=" O ILE L 297 " (cutoff:3.500A) Processing helix chain 'L' and resid 311 through 326 removed outlier: 3.738A pdb=" N TYR L 317 " --> pdb=" O VAL L 313 " (cutoff:3.500A) Processing helix chain 'L' and resid 328 through 336 removed outlier: 4.436A pdb=" N ARG L 334 " --> pdb=" O GLN L 330 " (cutoff:3.500A) Processing helix chain 'L' and resid 356 through 373 removed outlier: 3.715A pdb=" N ILE L 360 " --> pdb=" O LYS L 356 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS L 362 " --> pdb=" O GLU L 358 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU L 365 " --> pdb=" O ASN L 361 " (cutoff:3.500A) Processing helix chain 'L' and resid 388 through 393 removed outlier: 4.203A pdb=" N LYS L 393 " --> pdb=" O GLN L 389 " (cutoff:3.500A) Processing helix chain 'L' and resid 394 through 403 removed outlier: 3.879A pdb=" N LEU L 399 " --> pdb=" O GLY L 395 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET L 401 " --> pdb=" O LYS L 397 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLN L 402 " --> pdb=" O MET L 398 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N LYS L 403 " --> pdb=" O LEU L 399 " (cutoff:3.500A) Processing helix chain 'L' and resid 407 through 415 removed outlier: 3.679A pdb=" N PHE L 413 " --> pdb=" O TYR L 409 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR L 415 " --> pdb=" O GLU L 411 " (cutoff:3.500A) Processing helix chain 'L' and resid 449 through 461 removed outlier: 3.585A pdb=" N LEU L 457 " --> pdb=" O GLN L 453 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER L 458 " --> pdb=" O GLN L 454 " (cutoff:3.500A) Processing helix chain 'L' and resid 471 through 483 removed outlier: 4.070A pdb=" N ASP L 480 " --> pdb=" O ALA L 476 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU L 481 " --> pdb=" O GLY L 477 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU L 483 " --> pdb=" O LEU L 479 " (cutoff:3.500A) Processing helix chain 'L' and resid 489 through 494 Processing helix chain 'L' and resid 495 through 497 No H-bonds generated for 'chain 'L' and resid 495 through 497' Processing helix chain 'L' and resid 525 through 543 removed outlier: 3.539A pdb=" N GLY L 540 " --> pdb=" O ALA L 536 " (cutoff:3.500A) Processing helix chain 'L' and resid 544 through 549 Processing helix chain 'M' and resid 12 through 26 removed outlier: 3.934A pdb=" N LYS M 23 " --> pdb=" O ARG M 19 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N SER M 24 " --> pdb=" O ALA M 20 " (cutoff:3.500A) Processing helix chain 'M' and resid 39 through 47 removed outlier: 3.880A pdb=" N ILE M 45 " --> pdb=" O ASP M 41 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 72 removed outlier: 3.700A pdb=" N VAL M 68 " --> pdb=" O MET M 64 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER M 69 " --> pdb=" O ASN M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 91 removed outlier: 3.505A pdb=" N ILE M 83 " --> pdb=" O GLN M 79 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU M 86 " --> pdb=" O LEU M 82 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU M 88 " --> pdb=" O GLU M 84 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS M 89 " --> pdb=" O SER M 85 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL M 91 " --> pdb=" O CYS M 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 111 removed outlier: 3.814A pdb=" N ARG M 102 " --> pdb=" O ARG M 98 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU M 103 " --> pdb=" O PRO M 99 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN M 104 " --> pdb=" O SER M 100 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU M 105 " --> pdb=" O LEU M 101 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU M 106 " --> pdb=" O ARG M 102 " (cutoff:3.500A) Processing helix chain 'M' and resid 119 through 133 removed outlier: 3.510A pdb=" N SER M 133 " --> pdb=" O LYS M 129 " (cutoff:3.500A) Processing helix chain 'M' and resid 143 through 155 removed outlier: 3.568A pdb=" N ARG M 148 " --> pdb=" O LEU M 144 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER M 152 " --> pdb=" O ARG M 148 " (cutoff:3.500A) Processing helix chain 'M' and resid 157 through 166 removed outlier: 3.632A pdb=" N ARG M 166 " --> pdb=" O HIS M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 166 through 173 removed outlier: 3.561A pdb=" N ALA M 171 " --> pdb=" O LEU M 167 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL M 173 " --> pdb=" O TYR M 169 " (cutoff:3.500A) Processing helix chain 'M' and resid 177 through 192 removed outlier: 3.516A pdb=" N LYS M 183 " --> pdb=" O ASP M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 198 removed outlier: 3.579A pdb=" N ALA M 197 " --> pdb=" O GLU M 194 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER M 198 " --> pdb=" O ASP M 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 194 through 198' Processing helix chain 'M' and resid 201 through 214 removed outlier: 4.411A pdb=" N ILE M 208 " --> pdb=" O ALA M 204 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG M 210 " --> pdb=" O ARG M 206 " (cutoff:3.500A) Processing helix chain 'M' and resid 221 through 225 Processing helix chain 'M' and resid 226 through 232 Processing helix chain 'M' and resid 237 through 246 removed outlier: 3.534A pdb=" N VAL M 245 " --> pdb=" O LEU M 241 " (cutoff:3.500A) Processing helix chain 'M' and resid 248 through 259 removed outlier: 4.313A pdb=" N LYS M 254 " --> pdb=" O ALA M 250 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN M 259 " --> pdb=" O PHE M 255 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 264 removed outlier: 4.027A pdb=" N ILE M 263 " --> pdb=" O ASN M 259 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASP M 264 " --> pdb=" O LYS M 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 259 through 264' Processing helix chain 'M' and resid 270 through 289 removed outlier: 3.791A pdb=" N ALA M 275 " --> pdb=" O GLU M 271 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LYS M 276 " --> pdb=" O GLN M 272 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL M 287 " --> pdb=" O MET M 283 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLU M 288 " --> pdb=" O GLY M 284 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASN M 289 " --> pdb=" O MET M 285 " (cutoff:3.500A) Processing helix chain 'M' and resid 295 through 301 removed outlier: 3.679A pdb=" N GLN M 299 " --> pdb=" O ASP M 295 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 316 removed outlier: 3.670A pdb=" N ALA M 310 " --> pdb=" O ASP M 306 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE M 313 " --> pdb=" O GLU M 309 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ASP M 314 " --> pdb=" O ALA M 310 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA M 315 " --> pdb=" O PHE M 311 " (cutoff:3.500A) Processing helix chain 'M' and resid 343 through 370 removed outlier: 3.644A pdb=" N GLN M 349 " --> pdb=" O GLN M 345 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N THR M 353 " --> pdb=" O GLN M 349 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU M 354 " --> pdb=" O LEU M 350 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ASN M 366 " --> pdb=" O ASN M 362 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N SER M 367 " --> pdb=" O LYS M 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 59 removed outlier: 3.648A pdb=" N LYS D 58 " --> pdb=" O ARG D 54 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N TYR D 59 " --> pdb=" O TYR D 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 54 through 59' Processing helix chain 'D' and resid 176 through 180 Processing helix chain 'D' and resid 204 through 209 removed outlier: 3.827A pdb=" N ARG D 208 " --> pdb=" O ALA D 205 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE D 209 " --> pdb=" O PHE D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 240 removed outlier: 3.555A pdb=" N LYS D 240 " --> pdb=" O ARG D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 256 Processing helix chain 'D' and resid 311 through 327 removed outlier: 3.669A pdb=" N GLU D 315 " --> pdb=" O ASN D 311 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA D 316 " --> pdb=" O LEU D 312 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR D 317 " --> pdb=" O ALA D 313 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N GLN D 325 " --> pdb=" O HIS D 321 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N CYS D 327 " --> pdb=" O PHE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 424 Processing helix chain 'D' and resid 432 through 443 removed outlier: 3.572A pdb=" N CYS D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS D 438 " --> pdb=" O ARG D 434 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA D 439 " --> pdb=" O TRP D 435 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU D 440 " --> pdb=" O THR D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 498 removed outlier: 4.619A pdb=" N VAL D 494 " --> pdb=" O ILE D 490 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) Processing helix chain 'Y' and resid 14 through 22 Processing helix chain 'Y' and resid 53 through 62 removed outlier: 4.195A pdb=" N UNK Y 57 " --> pdb=" O UNK Y 53 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N UNK Y 58 " --> pdb=" O UNK Y 54 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N UNK Y 59 " --> pdb=" O UNK Y 55 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N UNK Y 60 " --> pdb=" O UNK Y 56 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N UNK Y 61 " --> pdb=" O UNK Y 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 161 removed outlier: 3.518A pdb=" N PHE J 157 " --> pdb=" O PRO J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 165 through 178 removed outlier: 3.534A pdb=" N GLU J 176 " --> pdb=" O GLU J 172 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 38 through 41 removed outlier: 6.878A pdb=" N ILE a 48 " --> pdb=" O TYR a 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 97 through 100 removed outlier: 6.591A pdb=" N VAL a 74 " --> pdb=" O THR a 97 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ILE a 99 " --> pdb=" O VAL a 74 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL a 76 " --> pdb=" O ILE a 99 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU a 122 " --> pdb=" O ILE a 145 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N LEU a 147 " --> pdb=" O LEU a 122 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VAL a 124 " --> pdb=" O LEU a 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'p' and resid 43 through 50 removed outlier: 4.111A pdb=" N GLY p 45 " --> pdb=" O VAL p 33 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR p 47 " --> pdb=" O TYR p 31 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N CYS p 96 " --> pdb=" O VAL p 91 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL p 91 " --> pdb=" O CYS p 96 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N THR p 98 " --> pdb=" O GLU p 89 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N GLU p 89 " --> pdb=" O THR p 98 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N PHE p 100 " --> pdb=" O ILE p 87 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ILE p 87 " --> pdb=" O PHE p 100 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'p' and resid 43 through 50 removed outlier: 4.111A pdb=" N GLY p 45 " --> pdb=" O VAL p 33 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR p 47 " --> pdb=" O TYR p 31 " (cutoff:3.500A) removed outlier: 13.672A pdb=" N ASN p 99 " --> pdb=" O LYS p 219 " (cutoff:3.500A) removed outlier: 13.061A pdb=" N LYS p 219 " --> pdb=" O ASN p 99 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N HIS p 101 " --> pdb=" O MET p 217 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N MET p 217 " --> pdb=" O HIS p 101 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N ARG p 213 " --> pdb=" O LEU p 105 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N VAL p 212 " --> pdb=" O VAL p 140 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL p 140 " --> pdb=" O VAL p 212 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS p 214 " --> pdb=" O PHE p 138 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU p 134 " --> pdb=" O LEU p 218 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA p 123 " --> pdb=" O CYS p 139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'd' and resid 102 through 116 removed outlier: 6.767A pdb=" N PHE d 127 " --> pdb=" O LEU d 107 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE d 109 " --> pdb=" O LYS d 125 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LYS d 125 " --> pdb=" O ILE d 109 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ARG d 123 " --> pdb=" O PRO d 111 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLN d 113 " --> pdb=" O ARG d 121 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG d 121 " --> pdb=" O GLN d 113 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N GLN d 115 " --> pdb=" O GLY d 119 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLY d 119 " --> pdb=" O GLN d 115 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP d 132 " --> pdb=" O HIS d 136 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N HIS d 136 " --> pdb=" O ASP d 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'd' and resid 184 through 188 Processing sheet with id=AA7, first strand: chain 'Q' and resid 20 through 22 Processing sheet with id=AA8, first strand: chain 'Q' and resid 36 through 43 Processing sheet with id=AA9, first strand: chain 'q' and resid 75 through 76 removed outlier: 4.185A pdb=" N HIS q 112 " --> pdb=" O ARG q 100 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'q' and resid 146 through 148 removed outlier: 3.727A pdb=" N ILE q 136 " --> pdb=" O GLY q 132 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR q 159 " --> pdb=" O PHE q 172 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N PHE q 172 " --> pdb=" O THR q 159 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLN q 161 " --> pdb=" O THR q 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'q' and resid 217 through 221 removed outlier: 6.568A pdb=" N VAL q 207 " --> pdb=" O ARG q 198 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ARG q 198 " --> pdb=" O VAL q 207 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N HIS q 209 " --> pdb=" O THR q 196 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'q' and resid 229 through 230 Processing sheet with id=AB4, first strand: chain 'r' and resid 13 through 16 removed outlier: 5.923A pdb=" N LEU r 106 " --> pdb=" O ASP r 57 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASP r 57 " --> pdb=" O LEU r 106 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL r 108 " --> pdb=" O GLY r 55 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLY r 55 " --> pdb=" O VAL r 108 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ASN r 110 " --> pdb=" O SER r 53 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL r 49 " --> pdb=" O VAL r 114 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'r' and resid 72 through 77 Processing sheet with id=AB6, first strand: chain 'r' and resid 160 through 162 Processing sheet with id=AB7, first strand: chain 's' and resid 50 through 52 removed outlier: 3.734A pdb=" N HIS s 91 " --> pdb=" O LYS s 58 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 's' and resid 185 through 188 removed outlier: 3.580A pdb=" N GLY s 141 " --> pdb=" O HIS s 157 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYS s 142 " --> pdb=" O ASP f 54 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE f 50 " --> pdb=" O VAL s 146 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 't' and resid 42 through 47 removed outlier: 6.294A pdb=" N ARG t 42 " --> pdb=" O LEU t 58 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LYS t 37 " --> pdb=" O LEU t 60 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N THR t 36 " --> pdb=" O LEU t 96 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 't' and resid 62 through 67 removed outlier: 6.482A pdb=" N LEU t 103 " --> pdb=" O ILE t 79 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N VAL t 81 " --> pdb=" O ILE t 101 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ILE t 101 " --> pdb=" O VAL t 81 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N CYS t 100 " --> pdb=" O ILE t 175 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N GLY t 187 " --> pdb=" O VAL t 62 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASN t 64 " --> pdb=" O GLY t 187 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N VAL t 189 " --> pdb=" O ASN t 64 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER t 66 " --> pdb=" O VAL t 189 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'c' and resid 135 through 137 Processing sheet with id=AC3, first strand: chain 'n' and resid 72 through 79 removed outlier: 17.803A pdb=" N ILE n 72 " --> pdb=" O LEU n 93 " (cutoff:3.500A) removed outlier: 15.188A pdb=" N LEU n 93 " --> pdb=" O ILE n 72 " (cutoff:3.500A) removed outlier: 8.968A pdb=" N SER n 74 " --> pdb=" O ASP n 91 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASP n 91 " --> pdb=" O SER n 74 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL n 87 " --> pdb=" O THR n 78 " (cutoff:3.500A) removed outlier: 9.250A pdb=" N VAL n 138 " --> pdb=" O ASN n 108 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N SER n 110 " --> pdb=" O VAL n 138 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N PHE n 140 " --> pdb=" O SER n 110 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N THR n 127 " --> pdb=" O LEU n 143 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N VAL n 145 " --> pdb=" O ILE n 125 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE n 125 " --> pdb=" O VAL n 145 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'i' and resid 52 through 57 removed outlier: 7.222A pdb=" N LEU i 93 " --> pdb=" O GLY i 127 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE i 129 " --> pdb=" O LEU i 93 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE i 95 " --> pdb=" O ILE i 129 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ASP i 131 " --> pdb=" O ILE i 95 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU i 97 " --> pdb=" O ASP i 131 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'y' and resid 32 through 39 removed outlier: 4.898A pdb=" N GLN y 49 " --> pdb=" O GLU y 38 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'f' and resid 71 through 74 Processing sheet with id=AC7, first strand: chain 'f' and resid 71 through 74 removed outlier: 5.508A pdb=" N ILE f 125 " --> pdb=" O THR f 105 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N THR f 105 " --> pdb=" O ILE f 125 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'j' and resid 128 through 129 removed outlier: 6.320A pdb=" N LEU j 101 " --> pdb=" O VAL j 123 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N VAL j 125 " --> pdb=" O GLU j 99 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLU j 99 " --> pdb=" O VAL j 125 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG j 71 " --> pdb=" O LEU j 52 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N LYS j 54 " --> pdb=" O CYS j 69 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N CYS j 69 " --> pdb=" O LYS j 54 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLY j 56 " --> pdb=" O ARG j 67 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ARG j 67 " --> pdb=" O GLY j 56 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N PHE j 120 " --> pdb=" O THR j 82 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'z' and resid 7 through 9 Processing sheet with id=AD1, first strand: chain 'z' and resid 7 through 9 removed outlier: 6.333A pdb=" N THR z 70 " --> pdb=" O PHE z 60 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N PHE z 60 " --> pdb=" O THR z 70 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'R' and resid 32 through 36 Processing sheet with id=AD3, first strand: chain 'R' and resid 64 through 65 Processing sheet with id=AD4, first strand: chain 'R' and resid 78 through 79 Processing sheet with id=AD5, first strand: chain 'w' and resid 39 through 40 removed outlier: 4.168A pdb=" N SER b 209 " --> pdb=" O ILE w 40 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'w' and resid 96 through 98 Processing sheet with id=AD7, first strand: chain 'g' and resid 10 through 15 removed outlier: 3.888A pdb=" N VAL g 10 " --> pdb=" O CYS g 25 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA g 21 " --> pdb=" O GLY g 14 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ARG g 69 " --> pdb=" O HIS g 24 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS g 26 " --> pdb=" O ASP g 67 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP g 67 " --> pdb=" O LYS g 26 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU g 31 " --> pdb=" O ILE g 68 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N VAL g 70 " --> pdb=" O LEU g 31 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N LYS g 33 " --> pdb=" O VAL g 70 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'b' and resid 137 through 138 removed outlier: 3.713A pdb=" N VAL b 138 " --> pdb=" O MET b 150 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET b 150 " --> pdb=" O VAL b 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'b' and resid 171 through 172 removed outlier: 3.513A pdb=" N ALA b 171 " --> pdb=" O VAL b 186 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL b 186 " --> pdb=" O ALA b 171 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'b' and resid 223 through 226 Processing sheet with id=AE2, first strand: chain 'e' and resid 127 through 128 removed outlier: 3.529A pdb=" N ILE e 128 " --> pdb=" O ARG e 135 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG e 135 " --> pdb=" O ILE e 128 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'e' and resid 140 through 141 removed outlier: 6.189A pdb=" N ASP e 140 " --> pdb=" O LYS S 47 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'u' and resid 20 through 23 Processing sheet with id=AE5, first strand: chain 'v' and resid 49 through 51 Processing sheet with id=AE6, first strand: chain 'o' and resid 16 through 17 Processing sheet with id=AE7, first strand: chain 'o' and resid 76 through 77 removed outlier: 3.927A pdb=" N VAL o 76 " --> pdb=" O MET o 93 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY o 95 " --> pdb=" O VAL o 76 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL o 94 " --> pdb=" O VAL o 105 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL o 105 " --> pdb=" O VAL o 94 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'k' and resid 12 through 13 Processing sheet with id=AE9, first strand: chain 'x' and resid 113 through 115 Processing sheet with id=AF1, first strand: chain 'h' and resid 54 through 55 removed outlier: 3.771A pdb=" N THR h 25 " --> pdb=" O GLU h 111 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU h 111 " --> pdb=" O THR h 25 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'h' and resid 49 through 50 removed outlier: 4.030A pdb=" N LYS h 49 " --> pdb=" O HIS h 92 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'h' and resid 63 through 66 Processing sheet with id=AF4, first strand: chain 'P' and resid 97 through 101 removed outlier: 3.562A pdb=" N THR P 110 " --> pdb=" O LYS P 98 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE P 108 " --> pdb=" O VAL P 100 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'S' and resid 12 through 13 removed outlier: 4.073A pdb=" N ALA S 12 " --> pdb=" O LEU S 56 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'S' and resid 17 through 21 Processing sheet with id=AF7, first strand: chain 'S' and resid 32 through 33 Processing sheet with id=AF8, first strand: chain 'U' and resid 106 through 107 removed outlier: 4.188A pdb=" N SER U 115 " --> pdb=" O LYS U 107 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'U' and resid 133 through 134 removed outlier: 3.502A pdb=" N TYR U 140 " --> pdb=" O ALA U 133 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'V' and resid 6 through 9 removed outlier: 3.615A pdb=" N THR V 6 " --> pdb=" O GLN V 311 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN V 311 " --> pdb=" O THR V 6 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL V 309 " --> pdb=" O ARG V 8 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU V 306 " --> pdb=" O TYR V 302 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N THR V 297 " --> pdb=" O TRP V 291 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N TRP V 291 " --> pdb=" O THR V 297 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N PHE V 299 " --> pdb=" O LEU V 289 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LEU V 289 " --> pdb=" O PHE V 299 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLY V 301 " --> pdb=" O THR V 287 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'V' and resid 30 through 33 removed outlier: 3.533A pdb=" N ILE V 31 " --> pdb=" O TRP V 43 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TRP V 43 " --> pdb=" O ILE V 31 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N SER V 33 " --> pdb=" O ILE V 41 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE V 41 " --> pdb=" O SER V 33 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE V 40 " --> pdb=" O ALA V 58 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ALA V 58 " --> pdb=" O ILE V 40 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N MET V 42 " --> pdb=" O GLN V 56 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'V' and resid 70 through 71 removed outlier: 6.940A pdb=" N LEU V 89 " --> pdb=" O THR V 98 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'V' and resid 108 through 113 Processing sheet with id=AG5, first strand: chain 'V' and resid 195 through 198 Processing sheet with id=AG6, first strand: chain 'V' and resid 239 through 240 Processing sheet with id=AG7, first strand: chain 'V' and resid 257 through 259 removed outlier: 8.101A pdb=" N ILE V 258 " --> pdb=" O VAL V 267 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL V 267 " --> pdb=" O ILE V 258 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'I' and resid 2 through 6 removed outlier: 3.743A pdb=" N VAL I 309 " --> pdb=" O LEU I 6 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'I' and resid 13 through 18 removed outlier: 3.984A pdb=" N GLN I 15 " --> pdb=" O VAL I 28 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N TYR I 38 " --> pdb=" O ARG I 44 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ARG I 44 " --> pdb=" O TYR I 38 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'I' and resid 55 through 60 removed outlier: 3.775A pdb=" N ARG I 77 " --> pdb=" O THR I 69 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER I 71 " --> pdb=" O SER I 75 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N SER I 75 " --> pdb=" O SER I 71 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ASP I 80 " --> pdb=" O GLN I 86 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N GLN I 86 " --> pdb=" O ASP I 80 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'I' and resid 99 through 101 removed outlier: 3.622A pdb=" N MET I 140 " --> pdb=" O PHE I 124 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ASP I 126 " --> pdb=" O PRO I 138 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ARG I 128 " --> pdb=" O ASN I 136 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ASN I 136 " --> pdb=" O ARG I 128 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'I' and resid 149 through 154 removed outlier: 3.749A pdb=" N SER I 151 " --> pdb=" O GLY I 164 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA I 163 " --> pdb=" O ASN I 171 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN I 171 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLU I 169 " --> pdb=" O HIS I 165 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL I 182 " --> pdb=" O GLN I 172 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N SER I 174 " --> pdb=" O VAL I 180 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL I 180 " --> pdb=" O SER I 174 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'I' and resid 191 through 196 removed outlier: 3.995A pdb=" N LYS I 213 " --> pdb=" O THR I 205 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N SER I 207 " --> pdb=" O THR I 211 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N THR I 211 " --> pdb=" O SER I 207 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS I 224 " --> pdb=" O LEU I 214 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ASP I 216 " --> pdb=" O HIS I 222 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N HIS I 222 " --> pdb=" O ASP I 216 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'I' and resid 232 through 237 removed outlier: 3.718A pdb=" N SER I 234 " --> pdb=" O GLY I 247 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N GLY I 248 " --> pdb=" O GLU I 266 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLU I 266 " --> pdb=" O GLY I 248 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N PHE I 265 " --> pdb=" O LYS I 282 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N LYS I 282 " --> pdb=" O PHE I 265 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ALA I 267 " --> pdb=" O ARG I 280 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ARG I 280 " --> pdb=" O ALA I 267 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N PHE I 269 " --> pdb=" O PHE I 278 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'B' and resid 219 through 221 removed outlier: 3.761A pdb=" N ASN B 219 " --> pdb=" O GLU B 236 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE B 221 " --> pdb=" O PHE B 234 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'B' and resid 224 through 225 Processing sheet with id=AH8, first strand: chain 'B' and resid 315 through 317 removed outlier: 3.537A pdb=" N SER B 317 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU B 703 " --> pdb=" O SER B 307 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'B' and resid 357 through 359 Processing sheet with id=AI1, first strand: chain 'B' and resid 378 through 381 Processing sheet with id=AI2, first strand: chain 'B' and resid 404 through 407 removed outlier: 4.209A pdb=" N ILE B 404 " --> pdb=" O PHE B 418 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N PHE B 418 " --> pdb=" O ILE B 404 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'B' and resid 437 through 439 Processing sheet with id=AI4, first strand: chain 'B' and resid 480 through 483 removed outlier: 6.560A pdb=" N ALA B 491 " --> pdb=" O ASN B 508 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ASN B 508 " --> pdb=" O ALA B 491 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL B 493 " --> pdb=" O VAL B 506 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL B 506 " --> pdb=" O VAL B 493 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N LEU B 495 " --> pdb=" O ILE B 504 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN B 502 " --> pdb=" O GLN B 497 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'B' and resid 515 through 516 removed outlier: 3.720A pdb=" N GLU B 545 " --> pdb=" O VAL B 528 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL B 530 " --> pdb=" O ASN B 543 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASN B 543 " --> pdb=" O VAL B 530 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'B' and resid 569 through 570 Processing sheet with id=AI7, first strand: chain 'B' and resid 613 through 614 Processing sheet with id=AI8, first strand: chain 'B' and resid 658 through 659 removed outlier: 3.530A pdb=" N GLU B 658 " --> pdb=" O VAL B 667 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'B' and resid 681 through 682 removed outlier: 4.053A pdb=" N ASN B 694 " --> pdb=" O TYR B 681 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'A' and resid 482 through 485 removed outlier: 5.495A pdb=" N GLN A 448 " --> pdb=" O PHE A 493 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N TYR M 322 " --> pdb=" O SER M 335 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'C' and resid 801 through 803 Processing sheet with id=AJ3, first strand: chain 'E' and resid 350 through 352 removed outlier: 3.796A pdb=" N VAL E 392 " --> pdb=" O LYS E 383 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS E 383 " --> pdb=" O VAL E 392 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'F' and resid 128 through 130 removed outlier: 7.067A pdb=" N VAL F 91 " --> pdb=" O VAL F 129 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N VAL F 92 " --> pdb=" O LYS F 238 " (cutoff:3.500A) removed outlier: 10.194A pdb=" N ILE F 198 " --> pdb=" O LEU F 168 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LEU F 170 " --> pdb=" O ILE F 198 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N LEU F 200 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N TRP F 172 " --> pdb=" O LEU F 200 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU F 170 " --> pdb=" O LEU F 120 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU F 120 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TRP F 172 " --> pdb=" O GLY F 118 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLY F 118 " --> pdb=" O TRP F 172 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'F' and resid 139 through 140 Processing sheet with id=AJ6, first strand: chain 'H' and resid 71 through 72 Processing sheet with id=AJ7, first strand: chain 'H' and resid 80 through 84 removed outlier: 3.779A pdb=" N ASN H 80 " --> pdb=" O LEU H 68 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE H 82 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL H 66 " --> pdb=" O PHE H 82 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN H 64 " --> pdb=" O PHE H 84 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY H 65 " --> pdb=" O TYR H 120 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N TYR H 120 " --> pdb=" O GLY H 65 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY H 118 " --> pdb=" O LEU H 67 " (cutoff:3.500A) removed outlier: 9.385A pdb=" N LEU H 150 " --> pdb=" O VAL H 117 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N TRP H 119 " --> pdb=" O LEU H 150 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N TYR H 152 " --> pdb=" O TRP H 119 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLN H 121 " --> pdb=" O TYR H 152 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'D' and resid 173 through 175 removed outlier: 4.150A pdb=" N MET D 174 " --> pdb=" O ILE D 517 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE D 517 " --> pdb=" O MET D 174 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU D 507 " --> pdb=" O TYR D 520 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLY D 504 " --> pdb=" O ARG D 271 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG D 271 " --> pdb=" O GLY D 504 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR D 506 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE D 267 " --> pdb=" O ILE D 508 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS D 510 " --> pdb=" O TRP D 265 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N TRP D 265 " --> pdb=" O LYS D 510 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N THR D 248 " --> pdb=" O PHE D 278 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL D 245 " --> pdb=" O ILE D 372 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ARG D 374 " --> pdb=" O VAL D 245 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ALA D 247 " --> pdb=" O ARG D 374 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU D 371 " --> pdb=" O TRP D 363 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL D 373 " --> pdb=" O ARG D 361 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG D 361 " --> pdb=" O VAL D 373 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU D 194 " --> pdb=" O TYR D 360 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ARG D 362 " --> pdb=" O ASP D 192 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ASP D 192 " --> pdb=" O ARG D 362 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'D' and resid 328 through 329 removed outlier: 3.935A pdb=" N TYR D 201 " --> pdb=" O ARG D 329 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N PHE D 390 " --> pdb=" O TYR D 446 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N LYS D 448 " --> pdb=" O PHE D 390 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASN D 392 " --> pdb=" O LYS D 448 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N GLY D 450 " --> pdb=" O ASN D 392 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LYS D 394 " --> pdb=" O GLY D 450 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL D 452 " --> pdb=" O LYS D 394 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU D 396 " --> pdb=" O VAL D 452 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ARG D 454 " --> pdb=" O LEU D 396 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLU D 398 " --> pdb=" O ARG D 454 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'Y' and resid 30 through 35 removed outlier: 5.380A pdb=" N UNK Y 45 " --> pdb=" O UNK Y 34 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N UNK Y 4 " --> pdb=" O UNK Y 48 " (cutoff:3.500A) 2766 hydrogen bonds defined for protein. 7911 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1103 hydrogen bonds 1750 hydrogen bond angles 0 basepair planarities 441 basepair parallelities 911 stacking parallelities Total time for adding SS restraints: 70.06 Time building geometry restraints manager: 41.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 14130 1.30 - 1.43: 39895 1.43 - 1.56: 56729 1.56 - 1.70: 3419 1.70 - 1.83: 567 Bond restraints: 114740 Sorted by residual: bond pdb=" C VAL m 134 " pdb=" N LEU m 135 " ideal model delta sigma weight residual 1.333 1.214 0.118 2.74e-02 1.33e+03 1.86e+01 bond pdb=" CB THR d 179 " pdb=" CG2 THR d 179 " ideal model delta sigma weight residual 1.521 1.393 0.128 3.30e-02 9.18e+02 1.50e+01 bond pdb=" C GLU L 438 " pdb=" N PRO L 439 " ideal model delta sigma weight residual 1.337 1.381 -0.044 1.24e-02 6.50e+03 1.27e+01 bond pdb=" CB VAL Q 84 " pdb=" CG1 VAL Q 84 " ideal model delta sigma weight residual 1.521 1.404 0.117 3.30e-02 9.18e+02 1.26e+01 bond pdb=" CB THR d 202 " pdb=" CG2 THR d 202 " ideal model delta sigma weight residual 1.521 1.405 0.116 3.30e-02 9.18e+02 1.24e+01 ... (remaining 114735 not shown) Histogram of bond angle deviations from ideal: 96.79 - 104.90: 8806 104.90 - 113.01: 65043 113.01 - 121.12: 57902 121.12 - 129.23: 29827 129.23 - 137.34: 1727 Bond angle restraints: 163305 Sorted by residual: angle pdb=" N VAL C 665 " pdb=" CA VAL C 665 " pdb=" C VAL C 665 " ideal model delta sigma weight residual 113.71 106.42 7.29 9.50e-01 1.11e+00 5.89e+01 angle pdb=" C PRO L 379 " pdb=" N MET L 380 " pdb=" CA MET L 380 " ideal model delta sigma weight residual 121.70 133.27 -11.57 1.80e+00 3.09e-01 4.13e+01 angle pdb=" C SER L 348 " pdb=" N MET L 349 " pdb=" CA MET L 349 " ideal model delta sigma weight residual 121.70 133.23 -11.53 1.80e+00 3.09e-01 4.10e+01 angle pdb=" C SER z 103 " pdb=" N ARG z 104 " pdb=" CA ARG z 104 " ideal model delta sigma weight residual 122.79 111.93 10.86 1.78e+00 3.16e-01 3.72e+01 angle pdb=" C THR L 353 " pdb=" N THR L 354 " pdb=" CA THR L 354 " ideal model delta sigma weight residual 121.70 132.36 -10.66 1.80e+00 3.09e-01 3.51e+01 ... (remaining 163300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 66492 36.00 - 72.00: 4974 72.00 - 107.99: 548 107.99 - 143.99: 13 143.99 - 179.99: 31 Dihedral angle restraints: 72058 sinusoidal: 44866 harmonic: 27192 Sorted by residual: dihedral pdb=" CA HIS L 432 " pdb=" C HIS L 432 " pdb=" N PRO L 433 " pdb=" CA PRO L 433 " ideal model delta harmonic sigma weight residual 180.00 123.93 56.07 0 5.00e+00 4.00e-02 1.26e+02 dihedral pdb=" CA VAL V 174 " pdb=" C VAL V 174 " pdb=" N LYS V 175 " pdb=" CA LYS V 175 " ideal model delta harmonic sigma weight residual 180.00 129.64 50.36 0 5.00e+00 4.00e-02 1.01e+02 dihedral pdb=" O4' U 2 148 " pdb=" C1' U 2 148 " pdb=" N1 U 2 148 " pdb=" C2 U 2 148 " ideal model delta sinusoidal sigma weight residual -160.00 19.93 -179.93 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 72055 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 18857 0.120 - 0.240: 894 0.240 - 0.359: 48 0.359 - 0.479: 1 0.479 - 0.599: 1 Chirality restraints: 19801 Sorted by residual: chirality pdb=" C1' A 21119 " pdb=" O4' A 21119 " pdb=" C2' A 21119 " pdb=" N9 A 21119 " both_signs ideal model delta sigma weight residual False 2.46 1.86 0.60 2.00e-01 2.50e+01 8.97e+00 chirality pdb=" CB ILE F 198 " pdb=" CA ILE F 198 " pdb=" CG1 ILE F 198 " pdb=" CG2 ILE F 198 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CA PHE q 86 " pdb=" N PHE q 86 " pdb=" C PHE q 86 " pdb=" CB PHE q 86 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.02e+00 ... (remaining 19798 not shown) Planarity restraints: 14483 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U 2 344 " 0.071 2.00e-02 2.50e+03 3.69e-02 3.06e+01 pdb=" N1 U 2 344 " -0.078 2.00e-02 2.50e+03 pdb=" C2 U 2 344 " -0.006 2.00e-02 2.50e+03 pdb=" O2 U 2 344 " -0.006 2.00e-02 2.50e+03 pdb=" N3 U 2 344 " -0.000 2.00e-02 2.50e+03 pdb=" C4 U 2 344 " 0.026 2.00e-02 2.50e+03 pdb=" O4 U 2 344 " 0.016 2.00e-02 2.50e+03 pdb=" C5 U 2 344 " -0.007 2.00e-02 2.50e+03 pdb=" C6 U 2 344 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 21055 " 0.073 2.00e-02 2.50e+03 3.21e-02 2.84e+01 pdb=" N9 A 21055 " -0.070 2.00e-02 2.50e+03 pdb=" C8 A 21055 " -0.005 2.00e-02 2.50e+03 pdb=" N7 A 21055 " 0.003 2.00e-02 2.50e+03 pdb=" C5 A 21055 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A 21055 " 0.011 2.00e-02 2.50e+03 pdb=" N6 A 21055 " 0.018 2.00e-02 2.50e+03 pdb=" N1 A 21055 " 0.007 2.00e-02 2.50e+03 pdb=" C2 A 21055 " -0.007 2.00e-02 2.50e+03 pdb=" N3 A 21055 " -0.009 2.00e-02 2.50e+03 pdb=" C4 A 21055 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 2 638 " -0.060 2.00e-02 2.50e+03 3.28e-02 2.42e+01 pdb=" N1 C 2 638 " 0.073 2.00e-02 2.50e+03 pdb=" C2 C 2 638 " 0.016 2.00e-02 2.50e+03 pdb=" O2 C 2 638 " -0.002 2.00e-02 2.50e+03 pdb=" N3 C 2 638 " -0.008 2.00e-02 2.50e+03 pdb=" C4 C 2 638 " -0.010 2.00e-02 2.50e+03 pdb=" N4 C 2 638 " -0.014 2.00e-02 2.50e+03 pdb=" C5 C 2 638 " -0.003 2.00e-02 2.50e+03 pdb=" C6 C 2 638 " 0.007 2.00e-02 2.50e+03 ... (remaining 14480 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 13515 2.74 - 3.28: 97491 3.28 - 3.82: 212417 3.82 - 4.36: 255803 4.36 - 4.90: 373875 Nonbonded interactions: 953101 Sorted by model distance: nonbonded pdb=" O2' G 2 952 " pdb=" O2 C 2 953 " model vdw 2.199 2.440 nonbonded pdb=" N CYS U 144 " pdb="ZN ZN U 500 " model vdw 2.204 2.310 nonbonded pdb=" O2' A 2 560 " pdb=" OD2 ASP B 488 " model vdw 2.211 2.440 nonbonded pdb=" OP1 G 21338 " pdb=" OG1 THR h 76 " model vdw 2.214 2.440 nonbonded pdb=" OH TYR z 76 " pdb=" OE2 GLU z 86 " model vdw 2.215 2.440 ... (remaining 953096 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.720 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: 13.610 Check model and map are aligned: 1.200 Set scattering table: 0.770 Process input model: 279.580 Find NCS groups from input model: 2.660 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 310.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 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 : 0.010 0.165 114740 Z= 0.627 Angle : 1.047 17.642 163305 Z= 0.533 Chirality : 0.059 0.599 19801 Planarity : 0.007 0.119 14483 Dihedral : 21.463 179.990 54414 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.29 % Favored : 93.70 % Rotamer: Outliers : 0.53 % Allowed : 9.21 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.11 % Twisted Proline : 0.30 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.42 (0.07), residues: 9011 helix: -3.56 (0.05), residues: 3388 sheet: -2.27 (0.14), residues: 1101 loop : -2.53 (0.08), residues: 4522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP W 5 HIS 0.016 0.002 HIS L 432 PHE 0.042 0.003 PHE q 86 TYR 0.033 0.002 TYR l 7 ARG 0.021 0.001 ARG d 121 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18022 Ramachandran restraints generated. 9011 Oldfield, 0 Emsley, 9011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18022 Ramachandran restraints generated. 9011 Oldfield, 0 Emsley, 9011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 8080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 710 time to evaluate : 7.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 216 MET cc_start: 0.8285 (mtt) cc_final: 0.8068 (mtt) REVERT: W 1 MET cc_start: 0.8604 (ttt) cc_final: 0.8396 (ttt) REVERT: n 48 LYS cc_start: 0.7340 (ptmm) cc_final: 0.7081 (ptmt) REVERT: g 16 LYS cc_start: 0.6244 (tptp) cc_final: 0.5474 (mmpt) REVERT: g 145 TYR cc_start: 0.1156 (m-80) cc_final: 0.0420 (m-80) REVERT: u 1 MET cc_start: -0.1930 (ptm) cc_final: -0.2315 (mmm) REVERT: B 487 LYS cc_start: 0.5375 (ttpt) cc_final: 0.5054 (pttt) REVERT: B 510 PHE cc_start: 0.7034 (m-10) cc_final: 0.6781 (m-10) REVERT: B 562 LYS cc_start: 0.3776 (tptt) cc_final: 0.3207 (mmtp) REVERT: C 589 MET cc_start: 0.6250 (tpp) cc_final: 0.5959 (tpt) REVERT: L 304 MET cc_start: 0.0175 (pmm) cc_final: -0.0151 (pmt) REVERT: D 256 MET cc_start: -0.0838 (mtt) cc_final: -0.1309 (mmt) outliers start: 39 outliers final: 23 residues processed: 746 average time/residue: 1.8498 time to fit residues: 1882.2843 Evaluate side-chains 586 residues out of total 8080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 563 time to evaluate : 7.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 157 VAL Chi-restraints excluded: chain d residue 94 ILE Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain q residue 12 VAL Chi-restraints excluded: chain q residue 126 VAL Chi-restraints excluded: chain r residue 20 ASP Chi-restraints excluded: chain r residue 22 ARG Chi-restraints excluded: chain s residue 8 ILE Chi-restraints excluded: chain n residue 120 VAL Chi-restraints excluded: chain f residue 80 ASP Chi-restraints excluded: chain w residue 98 VAL Chi-restraints excluded: chain g residue 42 ILE Chi-restraints excluded: chain g residue 43 GLU Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain b residue 186 VAL Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain V residue 121 VAL Chi-restraints excluded: chain V residue 287 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain F residue 323 PHE Chi-restraints excluded: chain L residue 546 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1085 random chunks: chunk 916 optimal weight: 8.9990 chunk 822 optimal weight: 10.0000 chunk 456 optimal weight: 40.0000 chunk 280 optimal weight: 0.7980 chunk 554 optimal weight: 7.9990 chunk 439 optimal weight: 20.0000 chunk 850 optimal weight: 6.9990 chunk 329 optimal weight: 0.8980 chunk 517 optimal weight: 20.0000 chunk 632 optimal weight: 40.0000 chunk 985 optimal weight: 0.8980 overall best weight: 3.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: p 40 ASN p 149 GLN p 157 GLN p 160 GLN d 235 ASN Q 43 ASN q 8 HIS q 17 HIS q 98 ASN q 112 HIS q 138 HIS q 188 ASN q 224 ASN r 13 GLN r 56 ASN r 163 ASN s 73 GLN s 76 GLN s 114 GLN s 126 HIS ** s 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 64 ASN t 111 GLN t 146 GLN c 132 GLN n 13 GLN n 18 GLN n 83 GLN n 112 HIS m 58 HIS m 105 ASN i 38 ASN i 43 HIS i 79 GLN i 113 GLN y 29 HIS f 15 ASN f 113 HIS j 73 GLN z 22 GLN R 26 GLN R 65 GLN T 44 ASN w 31 ASN w 116 ASN ** g 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 97 GLN b 101 GLN b 179 GLN b 226 GLN ** e 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 65 GLN e 74 ASN e 82 ASN e 137 GLN ** e 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 73 ASN ** v 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 119 GLN ** o 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 19 ASN k 73 ASN k 101 ASN k 105 ASN x 11 GLN x 51 ASN x 128 GLN ** x 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 10 HIS U 91 ASN V 20 GLN V 133 ASN ** V 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 222 ASN V 237 ASN V 305 ASN V 311 GLN ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 ASN B 553 GLN A 47 HIS ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 GLN A 392 ASN A 521 ASN A 549 GLN A 566 GLN A 586 ASN C 69 ASN C 365 ASN ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 ASN ** C 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 HIS C 595 GLN ** C 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 623 GLN C 674 HIS C 678 ASN C 716 HIS C 724 GLN ** C 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 852 GLN C 854 ASN E 33 ASN E 49 ASN E 181 ASN E 302 ASN E 348 HIS E 373 ASN E 395 ASN E 427 ASN F 133 ASN F 182 HIS F 260 ASN F 280 GLN ** F 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 342 ASN F 356 ASN H 58 GLN ** H 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 266 ASN ** H 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 336 GLN H 337 ASN H 345 GLN ** K 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 152 HIS K 169 GLN K 186 GLN L 181 GLN L 239 ASN L 241 ASN L 312 GLN L 363 GLN ** L 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 108 ASN M 146 GLN M 155 ASN ** M 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 273 ASN M 299 GLN M 355 ASN D 62 GLN D 68 GLN ** D 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 GLN D 341 ASN D 351 ASN ** D 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 486 ASN J 158 GLN J 160 ASN Total number of N/Q/H flips: 131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 114740 Z= 0.248 Angle : 0.661 12.202 163305 Z= 0.341 Chirality : 0.042 0.379 19801 Planarity : 0.005 0.112 14483 Dihedral : 22.236 179.647 37081 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.95 % Favored : 95.04 % Rotamer: Outliers : 2.21 % Allowed : 14.88 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.11 % Twisted Proline : 0.30 % 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: -3.12 (0.08), residues: 9011 helix: -1.94 (0.07), residues: 3571 sheet: -1.85 (0.14), residues: 1102 loop : -2.17 (0.09), residues: 4338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 284 HIS 0.011 0.001 HIS L 432 PHE 0.033 0.001 PHE q 86 TYR 0.037 0.001 TYR M 351 ARG 0.007 0.000 ARG a 205 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18022 Ramachandran restraints generated. 9011 Oldfield, 0 Emsley, 9011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18022 Ramachandran restraints generated. 9011 Oldfield, 0 Emsley, 9011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 8080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 621 time to evaluate : 7.235 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: a 44 ASP cc_start: 0.7017 (OUTLIER) cc_final: 0.6736 (m-30) REVERT: W 1 MET cc_start: 0.8624 (ttt) cc_final: 0.8357 (ttt) REVERT: z 74 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7257 (mmp) REVERT: g 16 LYS cc_start: 0.6635 (tptp) cc_final: 0.5645 (mmtt) REVERT: g 86 GLN cc_start: 0.4628 (tm-30) cc_final: 0.4386 (tm-30) REVERT: b 179 GLN cc_start: 0.6291 (OUTLIER) cc_final: 0.6056 (tm-30) REVERT: V 311 GLN cc_start: -0.1185 (OUTLIER) cc_final: -0.2857 (mt0) REVERT: B 487 LYS cc_start: 0.5431 (ttpt) cc_final: 0.5031 (pttt) REVERT: B 489 ILE cc_start: 0.8271 (mt) cc_final: 0.7951 (mm) REVERT: B 522 ASN cc_start: 0.6781 (OUTLIER) cc_final: 0.6430 (p0) REVERT: B 552 LYS cc_start: 0.6161 (tptt) cc_final: 0.4756 (tmtt) REVERT: B 562 LYS cc_start: 0.3541 (tptt) cc_final: 0.3170 (mmtp) REVERT: C 757 ILE cc_start: 0.7168 (OUTLIER) cc_final: 0.6557 (mm) REVERT: C 810 MET cc_start: 0.6300 (OUTLIER) cc_final: 0.6040 (mmm) REVERT: L 304 MET cc_start: 0.0329 (pmm) cc_final: -0.0062 (pmt) REVERT: M 237 ILE cc_start: 0.6804 (OUTLIER) cc_final: 0.6530 (mp) REVERT: D 499 MET cc_start: 0.2461 (mmt) cc_final: 0.1954 (mmt) outliers start: 164 outliers final: 62 residues processed: 723 average time/residue: 1.7618 time to fit residues: 1768.6139 Evaluate side-chains 634 residues out of total 8080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 564 time to evaluate : 7.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 87 VAL Chi-restraints excluded: chain a residue 97 THR Chi-restraints excluded: chain a residue 157 VAL Chi-restraints excluded: chain a residue 200 ASP Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain d residue 104 ASP Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 89 ARG Chi-restraints excluded: chain q residue 12 VAL Chi-restraints excluded: chain W residue 10 MET Chi-restraints excluded: chain r residue 22 ARG Chi-restraints excluded: chain s residue 8 ILE Chi-restraints excluded: chain c residue 95 ASP Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain n residue 120 VAL Chi-restraints excluded: chain f residue 25 VAL Chi-restraints excluded: chain j residue 112 VAL Chi-restraints excluded: chain z residue 74 MET Chi-restraints excluded: chain z residue 100 LYS Chi-restraints excluded: chain z residue 101 LYS Chi-restraints excluded: chain w residue 55 THR Chi-restraints excluded: chain w residue 99 ASP Chi-restraints excluded: chain w residue 130 THR Chi-restraints excluded: chain g residue 34 VAL Chi-restraints excluded: chain g residue 42 ILE Chi-restraints excluded: chain g residue 46 THR Chi-restraints excluded: chain g residue 118 THR Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain b residue 107 TYR Chi-restraints excluded: chain b residue 154 ASP Chi-restraints excluded: chain b residue 179 GLN Chi-restraints excluded: chain b residue 186 VAL Chi-restraints excluded: chain e residue 26 ASP Chi-restraints excluded: chain e residue 30 ILE Chi-restraints excluded: chain e residue 69 VAL Chi-restraints excluded: chain k residue 131 VAL Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain l residue 54 LYS Chi-restraints excluded: chain V residue 65 PHE Chi-restraints excluded: chain V residue 102 VAL Chi-restraints excluded: chain V residue 287 THR Chi-restraints excluded: chain V residue 311 GLN Chi-restraints excluded: chain B residue 522 ASN Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain C residue 810 MET Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 385 ASP Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 271 GLN Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain F residue 323 PHE Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain K residue 126 ASP Chi-restraints excluded: chain K residue 186 GLN Chi-restraints excluded: chain L residue 431 VAL Chi-restraints excluded: chain M residue 195 ASP Chi-restraints excluded: chain M residue 231 PHE Chi-restraints excluded: chain M residue 237 ILE Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 413 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1085 random chunks: chunk 547 optimal weight: 0.2980 chunk 305 optimal weight: 6.9990 chunk 820 optimal weight: 20.0000 chunk 670 optimal weight: 50.0000 chunk 271 optimal weight: 7.9990 chunk 987 optimal weight: 9.9990 chunk 1066 optimal weight: 50.0000 chunk 879 optimal weight: 20.0000 chunk 978 optimal weight: 6.9990 chunk 336 optimal weight: 60.0000 chunk 791 optimal weight: 5.9990 overall best weight: 5.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: q 36 HIS r 163 ASN s 76 GLN s 114 GLN ** s 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 111 GLN ** c 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 62 GLN ** i 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 35 ASN f 92 ASN w 116 ASN g 142 GLN b 179 GLN ** e 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 32 HIS ** v 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 119 GLN ** o 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 29 GLN ** V 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 191 HIS V 237 ASN V 296 GLN V 311 GLN ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 GLN ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 302 ASN ** F 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 GLN ** H 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 244 GLN ** H 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 454 GLN ** L 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 65 ASN M 258 ASN M 362 ASN ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 ASN D 73 HIS ** D 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN ** D 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 114740 Z= 0.347 Angle : 0.673 11.687 163305 Z= 0.344 Chirality : 0.043 0.372 19801 Planarity : 0.005 0.110 14483 Dihedral : 22.155 179.931 37065 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.58 % Favored : 94.41 % Rotamer: Outliers : 2.81 % Allowed : 16.64 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.11 % Twisted Proline : 0.30 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.08), residues: 9011 helix: -1.19 (0.08), residues: 3580 sheet: -1.87 (0.14), residues: 1198 loop : -1.95 (0.09), residues: 4233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP u 69 HIS 0.009 0.001 HIS L 432 PHE 0.033 0.002 PHE q 86 TYR 0.040 0.001 TYR u 12 ARG 0.009 0.000 ARG C 65 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18022 Ramachandran restraints generated. 9011 Oldfield, 0 Emsley, 9011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18022 Ramachandran restraints generated. 9011 Oldfield, 0 Emsley, 9011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 8080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 587 time to evaluate : 7.294 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: a 44 ASP cc_start: 0.7127 (OUTLIER) cc_final: 0.6838 (m-30) REVERT: p 180 ASP cc_start: 0.7504 (OUTLIER) cc_final: 0.6918 (p0) REVERT: d 216 MET cc_start: 0.7982 (mtt) cc_final: 0.7750 (mtt) REVERT: W 1 MET cc_start: 0.8666 (ttt) cc_final: 0.8407 (ttt) REVERT: y 62 MET cc_start: 0.8367 (ptp) cc_final: 0.8153 (ptp) REVERT: z 74 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7225 (mmp) REVERT: g 16 LYS cc_start: 0.6691 (tptp) cc_final: 0.5708 (mmpt) REVERT: b 189 MET cc_start: 0.6435 (tpp) cc_final: 0.6179 (tpt) REVERT: e 137 GLN cc_start: 0.6209 (OUTLIER) cc_final: 0.5767 (tm-30) REVERT: u 16 PHE cc_start: 0.4424 (OUTLIER) cc_final: 0.3442 (m-80) REVERT: B 487 LYS cc_start: 0.5464 (ttpt) cc_final: 0.5040 (pttt) REVERT: B 562 LYS cc_start: 0.3500 (tptt) cc_final: 0.3289 (tptp) REVERT: C 96 ILE cc_start: 0.5646 (OUTLIER) cc_final: 0.5291 (mp) REVERT: C 757 ILE cc_start: 0.7140 (OUTLIER) cc_final: 0.6514 (mm) REVERT: H 104 MET cc_start: 0.3787 (mmm) cc_final: 0.3548 (mmm) REVERT: H 197 MET cc_start: 0.5147 (mmm) cc_final: 0.4779 (mpm) REVERT: L 304 MET cc_start: 0.0276 (pmm) cc_final: -0.0143 (pmt) REVERT: M 237 ILE cc_start: 0.6713 (OUTLIER) cc_final: 0.6436 (mp) REVERT: D 199 LEU cc_start: -0.5933 (OUTLIER) cc_final: -0.6165 (mp) REVERT: D 256 MET cc_start: -0.0360 (OUTLIER) cc_final: -0.0580 (mmt) outliers start: 208 outliers final: 96 residues processed: 733 average time/residue: 1.6789 time to fit residues: 1725.1270 Evaluate side-chains 666 residues out of total 8080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 560 time to evaluate : 7.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 87 VAL Chi-restraints excluded: chain a residue 97 THR Chi-restraints excluded: chain a residue 157 VAL Chi-restraints excluded: chain a residue 200 ASP Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 180 ASP Chi-restraints excluded: chain d residue 94 ILE Chi-restraints excluded: chain d residue 104 ASP Chi-restraints excluded: chain d residue 224 THR Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 63 VAL Chi-restraints excluded: chain q residue 12 VAL Chi-restraints excluded: chain q residue 21 ASP Chi-restraints excluded: chain q residue 126 VAL Chi-restraints excluded: chain r residue 22 ARG Chi-restraints excluded: chain r residue 163 ASN Chi-restraints excluded: chain s residue 8 ILE Chi-restraints excluded: chain t residue 155 ASN Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 149 VAL Chi-restraints excluded: chain n residue 120 VAL Chi-restraints excluded: chain m residue 83 ASP Chi-restraints excluded: chain i residue 81 VAL Chi-restraints excluded: chain i residue 85 CYS Chi-restraints excluded: chain f residue 4 MET Chi-restraints excluded: chain f residue 25 VAL Chi-restraints excluded: chain f residue 80 ASP Chi-restraints excluded: chain j residue 112 VAL Chi-restraints excluded: chain z residue 74 MET Chi-restraints excluded: chain z residue 100 LYS Chi-restraints excluded: chain w residue 4 VAL Chi-restraints excluded: chain w residue 55 THR Chi-restraints excluded: chain w residue 98 VAL Chi-restraints excluded: chain w residue 130 THR Chi-restraints excluded: chain g residue 42 ILE Chi-restraints excluded: chain g residue 46 THR Chi-restraints excluded: chain g residue 118 THR Chi-restraints excluded: chain b residue 17 PHE Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain b residue 107 TYR Chi-restraints excluded: chain b residue 122 VAL Chi-restraints excluded: chain b residue 137 VAL Chi-restraints excluded: chain b residue 154 ASP Chi-restraints excluded: chain b residue 186 VAL Chi-restraints excluded: chain e residue 26 ASP Chi-restraints excluded: chain e residue 30 ILE Chi-restraints excluded: chain e residue 68 ILE Chi-restraints excluded: chain e residue 69 VAL Chi-restraints excluded: chain e residue 137 GLN Chi-restraints excluded: chain u residue 16 PHE Chi-restraints excluded: chain h residue 22 ILE Chi-restraints excluded: chain h residue 97 ILE Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain S residue 21 THR Chi-restraints excluded: chain S residue 27 CYS Chi-restraints excluded: chain l residue 38 MET Chi-restraints excluded: chain l residue 49 ASP Chi-restraints excluded: chain l residue 54 LYS Chi-restraints excluded: chain V residue 65 PHE Chi-restraints excluded: chain V residue 102 VAL Chi-restraints excluded: chain V residue 192 THR Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain C residue 839 THR Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 385 ASP Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 271 GLN Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain F residue 323 PHE Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain L residue 192 TYR Chi-restraints excluded: chain L residue 431 VAL Chi-restraints excluded: chain L residue 486 PHE Chi-restraints excluded: chain M residue 195 ASP Chi-restraints excluded: chain M residue 231 PHE Chi-restraints excluded: chain M residue 237 ILE Chi-restraints excluded: chain M residue 334 VAL Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 73 HIS Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 413 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1085 random chunks: chunk 975 optimal weight: 40.0000 chunk 742 optimal weight: 9.9990 chunk 512 optimal weight: 40.0000 chunk 109 optimal weight: 6.9990 chunk 471 optimal weight: 20.0000 chunk 662 optimal weight: 30.0000 chunk 990 optimal weight: 8.9990 chunk 1048 optimal weight: 50.0000 chunk 517 optimal weight: 50.0000 chunk 938 optimal weight: 50.0000 chunk 282 optimal weight: 6.9990 overall best weight: 10.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: p 124 HIS Q 8 ASN s 76 GLN s 114 GLN ** s 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 143 ASN ** c 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 113 GLN y 82 ASN w 116 ASN g 142 GLN ** e 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 119 GLN ** o 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 10 ASN x 51 ASN ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN B 520 GLN B 543 ASN ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 GLN ** A 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 365 ASN ** C 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 678 ASN ** C 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 ASN E 416 GLN F 95 HIS ** F 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 ASN ** H 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 GLN ** L 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 116 ASN M 199 GLN ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 HIS D 191 GLN ** D 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN ** D 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.173 114740 Z= 0.599 Angle : 0.793 11.921 163305 Z= 0.398 Chirality : 0.050 0.362 19801 Planarity : 0.006 0.107 14483 Dihedral : 22.222 179.989 37064 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.14 % Favored : 93.85 % Rotamer: Outliers : 3.52 % Allowed : 18.25 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.11 % Twisted Proline : 0.30 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.08), residues: 9011 helix: -0.90 (0.08), residues: 3583 sheet: -1.84 (0.14), residues: 1219 loop : -1.89 (0.09), residues: 4209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP u 69 HIS 0.015 0.001 HIS D 73 PHE 0.039 0.002 PHE q 86 TYR 0.036 0.002 TYR u 12 ARG 0.011 0.001 ARG c 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18022 Ramachandran restraints generated. 9011 Oldfield, 0 Emsley, 9011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18022 Ramachandran restraints generated. 9011 Oldfield, 0 Emsley, 9011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 829 residues out of total 8080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 568 time to evaluate : 7.353 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 44 ASP cc_start: 0.7230 (OUTLIER) cc_final: 0.6896 (m-30) REVERT: p 180 ASP cc_start: 0.7400 (OUTLIER) cc_final: 0.7174 (p0) REVERT: d 216 MET cc_start: 0.7980 (mtt) cc_final: 0.7773 (mtt) REVERT: W 1 MET cc_start: 0.8694 (ttt) cc_final: 0.8416 (ttt) REVERT: z 74 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.7333 (mmp) REVERT: g 16 LYS cc_start: 0.6714 (tptp) cc_final: 0.5853 (mmpt) REVERT: e 137 GLN cc_start: 0.6050 (OUTLIER) cc_final: 0.5642 (tm-30) REVERT: u 16 PHE cc_start: 0.5103 (OUTLIER) cc_final: 0.4574 (m-80) REVERT: V 311 GLN cc_start: -0.1078 (OUTLIER) cc_final: -0.2893 (mt0) REVERT: B 487 LYS cc_start: 0.5512 (ttpt) cc_final: 0.5037 (pttt) REVERT: B 522 ASN cc_start: 0.6025 (p0) cc_final: 0.5773 (p0) REVERT: C 96 ILE cc_start: 0.5788 (OUTLIER) cc_final: 0.5425 (mp) REVERT: C 582 TRP cc_start: 0.7548 (OUTLIER) cc_final: 0.7056 (t-100) REVERT: C 757 ILE cc_start: 0.7243 (OUTLIER) cc_final: 0.6621 (mm) REVERT: E 362 MET cc_start: 0.3609 (pp-130) cc_final: 0.3326 (pp-130) REVERT: F 213 ILE cc_start: 0.4213 (OUTLIER) cc_final: 0.3880 (mp) REVERT: H 104 MET cc_start: 0.3716 (mmm) cc_final: 0.3467 (mmm) REVERT: L 304 MET cc_start: 0.0600 (pmm) cc_final: 0.0153 (pmt) REVERT: L 432 HIS cc_start: 0.4234 (OUTLIER) cc_final: 0.4007 (p90) REVERT: M 113 MET cc_start: -0.1288 (pmt) cc_final: -0.2388 (pp-130) REVERT: M 237 ILE cc_start: 0.6748 (OUTLIER) cc_final: 0.6424 (mp) REVERT: M 277 MET cc_start: 0.4127 (tpp) cc_final: 0.3901 (tpp) REVERT: D 180 MET cc_start: 0.1726 (OUTLIER) cc_final: 0.1208 (mtt) REVERT: D 256 MET cc_start: -0.0073 (OUTLIER) cc_final: -0.1635 (mmt) REVERT: D 499 MET cc_start: 0.2384 (mmt) cc_final: 0.1680 (mmt) outliers start: 261 outliers final: 145 residues processed: 766 average time/residue: 1.6322 time to fit residues: 1767.5139 Evaluate side-chains 706 residues out of total 8080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 547 time to evaluate : 7.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 87 VAL Chi-restraints excluded: chain a residue 97 THR Chi-restraints excluded: chain a residue 107 THR Chi-restraints excluded: chain a residue 157 VAL Chi-restraints excluded: chain a residue 200 ASP Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 91 VAL Chi-restraints excluded: chain p residue 119 THR Chi-restraints excluded: chain p residue 180 ASP Chi-restraints excluded: chain d residue 94 ILE Chi-restraints excluded: chain d residue 104 ASP Chi-restraints excluded: chain d residue 110 MET Chi-restraints excluded: chain d residue 224 THR Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 46 GLU Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 63 VAL Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain q residue 12 VAL Chi-restraints excluded: chain q residue 21 ASP Chi-restraints excluded: chain q residue 126 VAL Chi-restraints excluded: chain q residue 139 LEU Chi-restraints excluded: chain q residue 171 ASP Chi-restraints excluded: chain r residue 22 ARG Chi-restraints excluded: chain r residue 49 VAL Chi-restraints excluded: chain r residue 151 ASP Chi-restraints excluded: chain r residue 184 VAL Chi-restraints excluded: chain s residue 8 ILE Chi-restraints excluded: chain s residue 64 VAL Chi-restraints excluded: chain s residue 76 GLN Chi-restraints excluded: chain s residue 92 VAL Chi-restraints excluded: chain t residue 155 ASN Chi-restraints excluded: chain t residue 160 SER Chi-restraints excluded: chain t residue 189 VAL Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 149 VAL Chi-restraints excluded: chain c residue 151 LEU Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain n residue 120 VAL Chi-restraints excluded: chain m residue 83 ASP Chi-restraints excluded: chain i residue 67 ASP Chi-restraints excluded: chain i residue 81 VAL Chi-restraints excluded: chain i residue 85 CYS Chi-restraints excluded: chain i residue 98 ARG Chi-restraints excluded: chain f residue 4 MET Chi-restraints excluded: chain f residue 25 VAL Chi-restraints excluded: chain f residue 80 ASP Chi-restraints excluded: chain j residue 112 VAL Chi-restraints excluded: chain z residue 6 THR Chi-restraints excluded: chain z residue 74 MET Chi-restraints excluded: chain z residue 100 LYS Chi-restraints excluded: chain z residue 101 LYS Chi-restraints excluded: chain z residue 102 THR Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain w residue 4 VAL Chi-restraints excluded: chain w residue 55 THR Chi-restraints excluded: chain w residue 56 HIS Chi-restraints excluded: chain w residue 63 ARG Chi-restraints excluded: chain w residue 92 ASP Chi-restraints excluded: chain w residue 98 VAL Chi-restraints excluded: chain w residue 130 THR Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 42 ILE Chi-restraints excluded: chain g residue 46 THR Chi-restraints excluded: chain g residue 118 THR Chi-restraints excluded: chain g residue 142 GLN Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain b residue 107 TYR Chi-restraints excluded: chain b residue 122 VAL Chi-restraints excluded: chain b residue 137 VAL Chi-restraints excluded: chain b residue 154 ASP Chi-restraints excluded: chain b residue 186 VAL Chi-restraints excluded: chain e residue 26 ASP Chi-restraints excluded: chain e residue 30 ILE Chi-restraints excluded: chain e residue 68 ILE Chi-restraints excluded: chain e residue 69 VAL Chi-restraints excluded: chain e residue 137 GLN Chi-restraints excluded: chain e residue 185 SER Chi-restraints excluded: chain u residue 16 PHE Chi-restraints excluded: chain u residue 40 VAL Chi-restraints excluded: chain u residue 69 TRP Chi-restraints excluded: chain v residue 119 GLN Chi-restraints excluded: chain k residue 131 VAL Chi-restraints excluded: chain k residue 138 THR Chi-restraints excluded: chain h residue 24 LEU Chi-restraints excluded: chain h residue 60 THR Chi-restraints excluded: chain h residue 89 ILE Chi-restraints excluded: chain h residue 97 ILE Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain S residue 15 THR Chi-restraints excluded: chain S residue 27 CYS Chi-restraints excluded: chain l residue 38 MET Chi-restraints excluded: chain l residue 49 ASP Chi-restraints excluded: chain l residue 54 LYS Chi-restraints excluded: chain U residue 131 PHE Chi-restraints excluded: chain V residue 65 PHE Chi-restraints excluded: chain V residue 92 LEU Chi-restraints excluded: chain V residue 102 VAL Chi-restraints excluded: chain V residue 174 VAL Chi-restraints excluded: chain V residue 287 THR Chi-restraints excluded: chain V residue 311 GLN Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 470 PHE Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 518 HIS Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 582 TRP Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain C residue 839 THR Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 385 ASP Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 323 PHE Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain H residue 333 PHE Chi-restraints excluded: chain L residue 192 TYR Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 417 CYS Chi-restraints excluded: chain L residue 431 VAL Chi-restraints excluded: chain L residue 432 HIS Chi-restraints excluded: chain L residue 486 PHE Chi-restraints excluded: chain M residue 195 ASP Chi-restraints excluded: chain M residue 231 PHE Chi-restraints excluded: chain M residue 237 ILE Chi-restraints excluded: chain M residue 334 VAL Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 413 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1085 random chunks: chunk 873 optimal weight: 2.9990 chunk 595 optimal weight: 8.9990 chunk 15 optimal weight: 0.3980 chunk 780 optimal weight: 100.0000 chunk 432 optimal weight: 4.9990 chunk 894 optimal weight: 50.0000 chunk 724 optimal weight: 0.1980 chunk 1 optimal weight: 2.9990 chunk 535 optimal weight: 20.0000 chunk 941 optimal weight: 9.9990 chunk 264 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: p 202 GLN s 76 GLN s 114 GLN ** s 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 116 ASN g 80 GLN g 142 GLN e 36 GLN ** e 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 51 ASN ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 28 HIS ** V 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 GLN B 543 ASN A 80 GLN ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 386 ASN C 460 GLN C 472 HIS ** C 579 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 678 ASN E 49 ASN F 140 ASN ** F 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 345 GLN ** L 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 116 ASN M 199 GLN M 272 GLN M 355 ASN ** D 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN ** D 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 114740 Z= 0.160 Angle : 0.607 11.443 163305 Z= 0.309 Chirality : 0.039 0.373 19801 Planarity : 0.004 0.106 14483 Dihedral : 22.089 179.633 37064 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.85 % Favored : 95.14 % Rotamer: Outliers : 2.87 % Allowed : 20.03 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.11 % Twisted Proline : 0.30 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.09), residues: 9011 helix: -0.48 (0.09), residues: 3582 sheet: -1.61 (0.14), residues: 1221 loop : -1.68 (0.09), residues: 4208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP E 370 HIS 0.009 0.001 HIS L 432 PHE 0.033 0.001 PHE q 86 TYR 0.022 0.001 TYR K 150 ARG 0.011 0.000 ARG j 140 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18022 Ramachandran restraints generated. 9011 Oldfield, 0 Emsley, 9011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18022 Ramachandran restraints generated. 9011 Oldfield, 0 Emsley, 9011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 8080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 603 time to evaluate : 7.321 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: a 44 ASP cc_start: 0.7085 (OUTLIER) cc_final: 0.6728 (m-30) REVERT: W 1 MET cc_start: 0.8568 (ttt) cc_final: 0.8317 (ttt) REVERT: w 18 GLU cc_start: 0.5037 (mm-30) cc_final: 0.4735 (mm-30) REVERT: g 16 LYS cc_start: 0.6702 (tptp) cc_final: 0.5786 (mmpt) REVERT: u 16 PHE cc_start: 0.5114 (OUTLIER) cc_final: 0.4624 (m-80) REVERT: B 487 LYS cc_start: 0.5361 (ttpt) cc_final: 0.4955 (pttt) REVERT: B 501 ARG cc_start: 0.3125 (tpp80) cc_final: 0.2898 (tpp-160) REVERT: B 520 GLN cc_start: 0.6807 (tp40) cc_final: 0.6383 (tp-100) REVERT: B 522 ASN cc_start: 0.5621 (p0) cc_final: 0.4809 (p0) REVERT: B 524 ASP cc_start: 0.4962 (m-30) cc_final: 0.4538 (m-30) REVERT: B 544 PHE cc_start: 0.6216 (m-10) cc_final: 0.5895 (m-10) REVERT: A 315 MET cc_start: 0.7217 (mpt) cc_final: 0.6920 (mpt) REVERT: A 318 MET cc_start: 0.5458 (ppp) cc_final: 0.4722 (ppp) REVERT: C 582 TRP cc_start: 0.7243 (OUTLIER) cc_final: 0.6855 (t-100) REVERT: E 362 MET cc_start: 0.3634 (pp-130) cc_final: 0.3005 (pp-130) REVERT: F 213 ILE cc_start: 0.3924 (OUTLIER) cc_final: 0.3579 (mp) REVERT: L 304 MET cc_start: 0.0604 (pmm) cc_final: 0.0156 (pmt) REVERT: L 432 HIS cc_start: 0.4359 (OUTLIER) cc_final: 0.3910 (p90) REVERT: M 113 MET cc_start: -0.0947 (pmt) cc_final: -0.2433 (pp-130) REVERT: M 237 ILE cc_start: 0.6551 (OUTLIER) cc_final: 0.6190 (mp) REVERT: D 256 MET cc_start: -0.0415 (OUTLIER) cc_final: -0.1803 (mmt) REVERT: D 499 MET cc_start: 0.2253 (mmt) cc_final: 0.1652 (mmt) outliers start: 213 outliers final: 96 residues processed: 754 average time/residue: 1.7240 time to fit residues: 1823.1960 Evaluate side-chains 661 residues out of total 8080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 558 time to evaluate : 7.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 157 VAL Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 91 VAL Chi-restraints excluded: chain d residue 104 ASP Chi-restraints excluded: chain d residue 110 MET Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 63 VAL Chi-restraints excluded: chain q residue 12 VAL Chi-restraints excluded: chain q residue 126 VAL Chi-restraints excluded: chain r residue 22 ARG Chi-restraints excluded: chain r residue 49 VAL Chi-restraints excluded: chain s residue 8 ILE Chi-restraints excluded: chain t residue 155 ASN Chi-restraints excluded: chain t residue 160 SER Chi-restraints excluded: chain c residue 95 ASP Chi-restraints excluded: chain n residue 120 VAL Chi-restraints excluded: chain i residue 85 CYS Chi-restraints excluded: chain j residue 15 SER Chi-restraints excluded: chain j residue 112 VAL Chi-restraints excluded: chain z residue 100 LYS Chi-restraints excluded: chain z residue 101 LYS Chi-restraints excluded: chain w residue 17 ILE Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 39 LEU Chi-restraints excluded: chain g residue 118 THR Chi-restraints excluded: chain b residue 17 PHE Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain b residue 107 TYR Chi-restraints excluded: chain b residue 122 VAL Chi-restraints excluded: chain b residue 137 VAL Chi-restraints excluded: chain b residue 154 ASP Chi-restraints excluded: chain e residue 26 ASP Chi-restraints excluded: chain e residue 30 ILE Chi-restraints excluded: chain e residue 69 VAL Chi-restraints excluded: chain e residue 185 SER Chi-restraints excluded: chain u residue 16 PHE Chi-restraints excluded: chain u residue 40 VAL Chi-restraints excluded: chain h residue 24 LEU Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain S residue 27 CYS Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain V residue 65 PHE Chi-restraints excluded: chain V residue 92 LEU Chi-restraints excluded: chain V residue 102 VAL Chi-restraints excluded: chain V residue 192 THR Chi-restraints excluded: chain V residue 287 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 582 TRP Chi-restraints excluded: chain C residue 698 MET Chi-restraints excluded: chain C residue 839 THR Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 276 ASP Chi-restraints excluded: chain E residue 385 ASP Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain F residue 323 PHE Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain H residue 333 PHE Chi-restraints excluded: chain K residue 22 ASN Chi-restraints excluded: chain K residue 182 ASP Chi-restraints excluded: chain L residue 192 TYR Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 417 CYS Chi-restraints excluded: chain L residue 431 VAL Chi-restraints excluded: chain L residue 432 HIS Chi-restraints excluded: chain L residue 486 PHE Chi-restraints excluded: chain M residue 195 ASP Chi-restraints excluded: chain M residue 231 PHE Chi-restraints excluded: chain M residue 237 ILE Chi-restraints excluded: chain M residue 334 VAL Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 413 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1085 random chunks: chunk 352 optimal weight: 8.9990 chunk 944 optimal weight: 8.9990 chunk 207 optimal weight: 10.0000 chunk 615 optimal weight: 7.9990 chunk 258 optimal weight: 6.9990 chunk 1049 optimal weight: 7.9990 chunk 871 optimal weight: 10.0000 chunk 486 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 347 optimal weight: 40.0000 chunk 551 optimal weight: 8.9990 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 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 216 ASN r 163 ASN s 114 GLN ** s 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 111 GLN ** c 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 116 ASN g 142 GLN ** e 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 119 GLN ** o 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 237 ASN ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 365 ASN ** C 579 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 116 ASN M 199 GLN ** D 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN ** D 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.117 114740 Z= 0.437 Angle : 0.705 11.142 163305 Z= 0.355 Chirality : 0.045 0.347 19801 Planarity : 0.005 0.105 14483 Dihedral : 22.072 179.895 37061 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.76 % Favored : 94.23 % Rotamer: Outliers : 3.09 % Allowed : 21.18 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.11 % Twisted Proline : 0.30 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.09), residues: 9011 helix: -0.40 (0.09), residues: 3587 sheet: -1.58 (0.14), residues: 1197 loop : -1.70 (0.09), residues: 4227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP u 69 HIS 0.011 0.001 HIS o 54 PHE 0.034 0.002 PHE q 86 TYR 0.029 0.002 TYR b 120 ARG 0.010 0.001 ARG w 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18022 Ramachandran restraints generated. 9011 Oldfield, 0 Emsley, 9011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18022 Ramachandran restraints generated. 9011 Oldfield, 0 Emsley, 9011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 8080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 565 time to evaluate : 7.112 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: a 44 ASP cc_start: 0.7147 (OUTLIER) cc_final: 0.6839 (m-30) REVERT: d 216 MET cc_start: 0.7973 (mtt) cc_final: 0.7768 (mtt) REVERT: W 1 MET cc_start: 0.8659 (ttt) cc_final: 0.8393 (ttt) REVERT: g 16 LYS cc_start: 0.6719 (tptp) cc_final: 0.5863 (mmpt) REVERT: u 16 PHE cc_start: 0.5100 (OUTLIER) cc_final: 0.4661 (m-80) REVERT: B 487 LYS cc_start: 0.5384 (ttpt) cc_final: 0.4934 (pttt) REVERT: B 519 TRP cc_start: 0.6214 (OUTLIER) cc_final: 0.4291 (m100) REVERT: B 520 GLN cc_start: 0.6808 (tp40) cc_final: 0.6341 (tp-100) REVERT: B 522 ASN cc_start: 0.5807 (p0) cc_final: 0.4648 (p0) REVERT: B 550 ARG cc_start: 0.5618 (mmt90) cc_final: 0.5385 (mtt-85) REVERT: A 315 MET cc_start: 0.7233 (mpt) cc_final: 0.6960 (mpt) REVERT: A 318 MET cc_start: 0.5613 (ppp) cc_final: 0.4980 (ppp) REVERT: C 582 TRP cc_start: 0.7342 (OUTLIER) cc_final: 0.6854 (t-100) REVERT: C 757 ILE cc_start: 0.7166 (OUTLIER) cc_final: 0.6561 (mm) REVERT: E 362 MET cc_start: 0.3863 (pp-130) cc_final: 0.2988 (pp-130) REVERT: F 213 ILE cc_start: 0.3926 (OUTLIER) cc_final: 0.3593 (mp) REVERT: L 304 MET cc_start: 0.0699 (pmm) cc_final: 0.0171 (pmt) REVERT: L 432 HIS cc_start: 0.4351 (OUTLIER) cc_final: 0.3931 (p90) REVERT: M 113 MET cc_start: -0.0983 (pmt) cc_final: -0.2422 (pp-130) REVERT: M 237 ILE cc_start: 0.6562 (OUTLIER) cc_final: 0.6204 (mp) REVERT: D 256 MET cc_start: -0.0276 (OUTLIER) cc_final: -0.1759 (mmt) outliers start: 229 outliers final: 147 residues processed: 737 average time/residue: 1.6832 time to fit residues: 1758.2939 Evaluate side-chains 701 residues out of total 8080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 545 time to evaluate : 7.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 87 VAL Chi-restraints excluded: chain a residue 97 THR Chi-restraints excluded: chain a residue 157 VAL Chi-restraints excluded: chain a residue 200 ASP Chi-restraints excluded: chain p residue 77 ASP Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 91 VAL Chi-restraints excluded: chain d residue 94 ILE Chi-restraints excluded: chain d residue 104 ASP Chi-restraints excluded: chain d residue 110 MET Chi-restraints excluded: chain d residue 224 THR Chi-restraints excluded: chain d residue 249 SER Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 63 VAL Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain q residue 12 VAL Chi-restraints excluded: chain q residue 21 ASP Chi-restraints excluded: chain q residue 126 VAL Chi-restraints excluded: chain q residue 171 ASP Chi-restraints excluded: chain W residue 10 MET Chi-restraints excluded: chain r residue 22 ARG Chi-restraints excluded: chain r residue 49 VAL Chi-restraints excluded: chain r residue 163 ASN Chi-restraints excluded: chain s residue 8 ILE Chi-restraints excluded: chain s residue 92 VAL Chi-restraints excluded: chain s residue 184 ASP Chi-restraints excluded: chain t residue 155 ASN Chi-restraints excluded: chain t residue 160 SER Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 149 VAL Chi-restraints excluded: chain c residue 151 LEU Chi-restraints excluded: chain n residue 120 VAL Chi-restraints excluded: chain n residue 143 LEU Chi-restraints excluded: chain m residue 32 ASP Chi-restraints excluded: chain m residue 83 ASP Chi-restraints excluded: chain i residue 67 ASP Chi-restraints excluded: chain i residue 85 CYS Chi-restraints excluded: chain i residue 98 ARG Chi-restraints excluded: chain j residue 15 SER Chi-restraints excluded: chain j residue 112 VAL Chi-restraints excluded: chain z residue 6 THR Chi-restraints excluded: chain z residue 100 LYS Chi-restraints excluded: chain z residue 101 LYS Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain w residue 4 VAL Chi-restraints excluded: chain w residue 17 ILE Chi-restraints excluded: chain w residue 55 THR Chi-restraints excluded: chain w residue 56 HIS Chi-restraints excluded: chain w residue 98 VAL Chi-restraints excluded: chain w residue 130 THR Chi-restraints excluded: chain g residue 11 GLN Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 39 LEU Chi-restraints excluded: chain g residue 42 ILE Chi-restraints excluded: chain g residue 46 THR Chi-restraints excluded: chain g residue 142 GLN Chi-restraints excluded: chain b residue 17 PHE Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain b residue 107 TYR Chi-restraints excluded: chain b residue 122 VAL Chi-restraints excluded: chain b residue 137 VAL Chi-restraints excluded: chain b residue 154 ASP Chi-restraints excluded: chain b residue 186 VAL Chi-restraints excluded: chain e residue 26 ASP Chi-restraints excluded: chain e residue 30 ILE Chi-restraints excluded: chain e residue 37 ASP Chi-restraints excluded: chain e residue 68 ILE Chi-restraints excluded: chain e residue 69 VAL Chi-restraints excluded: chain e residue 128 ILE Chi-restraints excluded: chain e residue 185 SER Chi-restraints excluded: chain u residue 16 PHE Chi-restraints excluded: chain u residue 38 LYS Chi-restraints excluded: chain u residue 40 VAL Chi-restraints excluded: chain u residue 69 TRP Chi-restraints excluded: chain v residue 119 GLN Chi-restraints excluded: chain k residue 131 VAL Chi-restraints excluded: chain k residue 138 THR Chi-restraints excluded: chain h residue 24 LEU Chi-restraints excluded: chain h residue 87 ARG Chi-restraints excluded: chain h residue 89 ILE Chi-restraints excluded: chain h residue 97 ILE Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain S residue 27 CYS Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain l residue 38 MET Chi-restraints excluded: chain l residue 49 ASP Chi-restraints excluded: chain V residue 65 PHE Chi-restraints excluded: chain V residue 92 LEU Chi-restraints excluded: chain V residue 102 VAL Chi-restraints excluded: chain V residue 192 THR Chi-restraints excluded: chain V residue 287 THR Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 519 TRP Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 582 TRP Chi-restraints excluded: chain C residue 698 MET Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain C residue 839 THR Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 276 ASP Chi-restraints excluded: chain E residue 385 ASP Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 156 MET Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain H residue 333 PHE Chi-restraints excluded: chain K residue 22 ASN Chi-restraints excluded: chain K residue 182 ASP Chi-restraints excluded: chain L residue 192 TYR Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 417 CYS Chi-restraints excluded: chain L residue 431 VAL Chi-restraints excluded: chain L residue 432 HIS Chi-restraints excluded: chain L residue 486 PHE Chi-restraints excluded: chain M residue 142 THR Chi-restraints excluded: chain M residue 195 ASP Chi-restraints excluded: chain M residue 231 PHE Chi-restraints excluded: chain M residue 237 ILE Chi-restraints excluded: chain M residue 334 VAL Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain J residue 155 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1085 random chunks: chunk 1012 optimal weight: 20.0000 chunk 118 optimal weight: 7.9990 chunk 598 optimal weight: 0.0040 chunk 766 optimal weight: 50.0000 chunk 593 optimal weight: 10.0000 chunk 883 optimal weight: 20.0000 chunk 586 optimal weight: 40.0000 chunk 1045 optimal weight: 30.0000 chunk 654 optimal weight: 30.0000 chunk 637 optimal weight: 8.9990 chunk 482 optimal weight: 0.9990 overall best weight: 5.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 163 ASN s 76 GLN s 114 GLN ** s 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 116 ASN ** e 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 119 GLN ** o 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 237 ASN B 477 ASN ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 ASN ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 579 HIS ** C 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 678 ASN C 858 GLN E 49 ASN F 160 HIS ** F 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 116 ASN ** D 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN ** D 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 114740 Z= 0.339 Angle : 0.671 11.777 163305 Z= 0.338 Chirality : 0.043 0.332 19801 Planarity : 0.005 0.105 14483 Dihedral : 22.065 179.670 37059 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.64 % Favored : 94.35 % Rotamer: Outliers : 3.21 % Allowed : 21.65 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.11 % Twisted Proline : 0.30 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.09), residues: 9011 helix: -0.27 (0.09), residues: 3596 sheet: -1.55 (0.14), residues: 1191 loop : -1.66 (0.09), residues: 4224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP E 370 HIS 0.013 0.001 HIS o 54 PHE 0.033 0.001 PHE q 86 TYR 0.040 0.001 TYR u 12 ARG 0.011 0.000 ARG w 23 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18022 Ramachandran restraints generated. 9011 Oldfield, 0 Emsley, 9011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18022 Ramachandran restraints generated. 9011 Oldfield, 0 Emsley, 9011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 8080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 561 time to evaluate : 7.353 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: a 44 ASP cc_start: 0.7184 (OUTLIER) cc_final: 0.6878 (m-30) REVERT: W 1 MET cc_start: 0.8632 (ttt) cc_final: 0.8273 (ttt) REVERT: j 76 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8506 (ptpt) REVERT: g 16 LYS cc_start: 0.6704 (tptp) cc_final: 0.5879 (mmpt) REVERT: u 16 PHE cc_start: 0.5036 (OUTLIER) cc_final: 0.4728 (m-80) REVERT: B 487 LYS cc_start: 0.5443 (ttpt) cc_final: 0.4960 (pttt) REVERT: B 510 PHE cc_start: 0.6951 (m-80) cc_final: 0.6749 (m-10) REVERT: B 519 TRP cc_start: 0.6210 (OUTLIER) cc_final: 0.4236 (m100) REVERT: B 524 ASP cc_start: 0.4609 (m-30) cc_final: 0.3968 (t70) REVERT: B 544 PHE cc_start: 0.6232 (m-10) cc_final: 0.5899 (m-10) REVERT: C 96 ILE cc_start: 0.5738 (OUTLIER) cc_final: 0.5375 (mp) REVERT: C 582 TRP cc_start: 0.7457 (OUTLIER) cc_final: 0.6932 (t60) REVERT: C 757 ILE cc_start: 0.7103 (OUTLIER) cc_final: 0.6595 (mm) REVERT: C 807 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7363 (mm) REVERT: E 362 MET cc_start: 0.3810 (pp-130) cc_final: 0.2782 (pp-130) REVERT: F 213 ILE cc_start: 0.4233 (OUTLIER) cc_final: 0.3843 (mp) REVERT: H 247 MET cc_start: 0.5103 (mmm) cc_final: 0.4692 (mmm) REVERT: L 304 MET cc_start: 0.0455 (pmm) cc_final: -0.0213 (pmt) REVERT: L 432 HIS cc_start: 0.4394 (OUTLIER) cc_final: 0.3925 (p90) REVERT: M 90 LEU cc_start: 0.1921 (OUTLIER) cc_final: 0.1689 (tm) REVERT: M 113 MET cc_start: -0.0952 (pmt) cc_final: -0.2293 (pp-130) REVERT: M 297 MET cc_start: 0.3407 (mmm) cc_final: 0.3189 (mmm) REVERT: D 256 MET cc_start: -0.0315 (OUTLIER) cc_final: -0.1748 (mmt) outliers start: 238 outliers final: 151 residues processed: 740 average time/residue: 1.6688 time to fit residues: 1747.1539 Evaluate side-chains 705 residues out of total 8080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 542 time to evaluate : 7.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 97 THR Chi-restraints excluded: chain a residue 157 VAL Chi-restraints excluded: chain a residue 200 ASP Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 91 VAL Chi-restraints excluded: chain d residue 94 ILE Chi-restraints excluded: chain d residue 104 ASP Chi-restraints excluded: chain d residue 110 MET Chi-restraints excluded: chain d residue 249 SER Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 63 VAL Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain q residue 12 VAL Chi-restraints excluded: chain q residue 21 ASP Chi-restraints excluded: chain q residue 24 THR Chi-restraints excluded: chain q residue 40 GLU Chi-restraints excluded: chain q residue 126 VAL Chi-restraints excluded: chain W residue 10 MET Chi-restraints excluded: chain r residue 22 ARG Chi-restraints excluded: chain r residue 49 VAL Chi-restraints excluded: chain s residue 8 ILE Chi-restraints excluded: chain s residue 92 VAL Chi-restraints excluded: chain s residue 184 ASP Chi-restraints excluded: chain t residue 155 ASN Chi-restraints excluded: chain t residue 160 SER Chi-restraints excluded: chain t residue 186 ASP Chi-restraints excluded: chain c residue 61 LEU Chi-restraints excluded: chain c residue 95 ASP Chi-restraints excluded: chain c residue 151 LEU Chi-restraints excluded: chain c residue 152 ASP Chi-restraints excluded: chain n residue 120 VAL Chi-restraints excluded: chain n residue 143 LEU Chi-restraints excluded: chain m residue 83 ASP Chi-restraints excluded: chain i residue 67 ASP Chi-restraints excluded: chain i residue 81 VAL Chi-restraints excluded: chain i residue 98 ARG Chi-restraints excluded: chain j residue 15 SER Chi-restraints excluded: chain j residue 76 LYS Chi-restraints excluded: chain j residue 112 VAL Chi-restraints excluded: chain z residue 6 THR Chi-restraints excluded: chain z residue 100 LYS Chi-restraints excluded: chain z residue 101 LYS Chi-restraints excluded: chain z residue 102 THR Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain w residue 9 VAL Chi-restraints excluded: chain w residue 17 ILE Chi-restraints excluded: chain w residue 55 THR Chi-restraints excluded: chain w residue 56 HIS Chi-restraints excluded: chain w residue 98 VAL Chi-restraints excluded: chain g residue 11 GLN Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 39 LEU Chi-restraints excluded: chain g residue 42 ILE Chi-restraints excluded: chain g residue 46 THR Chi-restraints excluded: chain g residue 118 THR Chi-restraints excluded: chain b residue 8 LYS Chi-restraints excluded: chain b residue 17 PHE Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain b residue 107 TYR Chi-restraints excluded: chain b residue 122 VAL Chi-restraints excluded: chain b residue 137 VAL Chi-restraints excluded: chain b residue 154 ASP Chi-restraints excluded: chain b residue 186 VAL Chi-restraints excluded: chain e residue 26 ASP Chi-restraints excluded: chain e residue 30 ILE Chi-restraints excluded: chain e residue 37 ASP Chi-restraints excluded: chain e residue 68 ILE Chi-restraints excluded: chain e residue 69 VAL Chi-restraints excluded: chain e residue 185 SER Chi-restraints excluded: chain u residue 16 PHE Chi-restraints excluded: chain u residue 38 LYS Chi-restraints excluded: chain u residue 40 VAL Chi-restraints excluded: chain k residue 131 VAL Chi-restraints excluded: chain h residue 24 LEU Chi-restraints excluded: chain h residue 60 THR Chi-restraints excluded: chain h residue 87 ARG Chi-restraints excluded: chain h residue 97 ILE Chi-restraints excluded: chain h residue 101 ILE Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain S residue 27 CYS Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain l residue 49 ASP Chi-restraints excluded: chain V residue 65 PHE Chi-restraints excluded: chain V residue 92 LEU Chi-restraints excluded: chain V residue 192 THR Chi-restraints excluded: chain V residue 228 TYR Chi-restraints excluded: chain V residue 287 THR Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 519 TRP Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 582 TRP Chi-restraints excluded: chain C residue 698 MET Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain C residue 839 THR Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 276 ASP Chi-restraints excluded: chain E residue 385 ASP Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain F residue 323 PHE Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 197 MET Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain H residue 333 PHE Chi-restraints excluded: chain K residue 3 MET Chi-restraints excluded: chain K residue 22 ASN Chi-restraints excluded: chain K residue 182 ASP Chi-restraints excluded: chain L residue 192 TYR Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 417 CYS Chi-restraints excluded: chain L residue 431 VAL Chi-restraints excluded: chain L residue 432 HIS Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 486 PHE Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 142 THR Chi-restraints excluded: chain M residue 195 ASP Chi-restraints excluded: chain M residue 231 PHE Chi-restraints excluded: chain M residue 237 ILE Chi-restraints excluded: chain M residue 334 VAL Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 413 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1085 random chunks: chunk 646 optimal weight: 10.0000 chunk 417 optimal weight: 50.0000 chunk 624 optimal weight: 50.0000 chunk 315 optimal weight: 5.9990 chunk 205 optimal weight: 0.3980 chunk 202 optimal weight: 0.8980 chunk 664 optimal weight: 20.0000 chunk 712 optimal weight: 2.9990 chunk 517 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 822 optimal weight: 0.9980 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 163 ASN s 76 GLN s 114 GLN ** s 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 116 ASN ** e 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 74 ASN e 83 ASN ** e 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 119 GLN o 53 GLN ** o 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 GLN B 543 ASN ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 GLN C 365 ASN ** C 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 678 ASN ** C 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 ASN ** F 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 116 ASN ** D 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN ** D 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 114740 Z= 0.185 Angle : 0.622 13.380 163305 Z= 0.313 Chirality : 0.039 0.371 19801 Planarity : 0.004 0.104 14483 Dihedral : 21.977 179.616 37059 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.24 % Favored : 94.75 % Rotamer: Outliers : 2.75 % Allowed : 22.57 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.11 % Twisted Proline : 0.30 % Twisted General : 0.01 % 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: -1.48 (0.09), residues: 9011 helix: -0.11 (0.09), residues: 3594 sheet: -1.39 (0.14), residues: 1201 loop : -1.58 (0.09), residues: 4216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP E 370 HIS 0.011 0.001 HIS o 54 PHE 0.032 0.001 PHE F 307 TYR 0.022 0.001 TYR b 120 ARG 0.011 0.000 ARG w 23 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18022 Ramachandran restraints generated. 9011 Oldfield, 0 Emsley, 9011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18022 Ramachandran restraints generated. 9011 Oldfield, 0 Emsley, 9011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 8080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 577 time to evaluate : 7.409 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: a 44 ASP cc_start: 0.7174 (OUTLIER) cc_final: 0.6887 (m-30) REVERT: W 1 MET cc_start: 0.8615 (ttt) cc_final: 0.8321 (ttt) REVERT: g 16 LYS cc_start: 0.6701 (tptp) cc_final: 0.5785 (mmpt) REVERT: B 471 SER cc_start: 0.2497 (p) cc_final: 0.1961 (p) REVERT: B 487 LYS cc_start: 0.5381 (ttpt) cc_final: 0.4921 (pttp) REVERT: B 492 ARG cc_start: 0.6937 (mmm-85) cc_final: 0.6697 (ttm110) REVERT: B 510 PHE cc_start: 0.6997 (m-80) cc_final: 0.6765 (m-10) REVERT: B 524 ASP cc_start: 0.4956 (m-30) cc_final: 0.4589 (t0) REVERT: A 318 MET cc_start: 0.5947 (ppp) cc_final: 0.5689 (ppp) REVERT: C 582 TRP cc_start: 0.7378 (OUTLIER) cc_final: 0.6687 (t60) REVERT: C 709 MET cc_start: 0.5147 (tpp) cc_final: 0.4918 (tpt) REVERT: C 807 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.7238 (mm) REVERT: E 362 MET cc_start: 0.3960 (pp-130) cc_final: 0.3058 (pp-130) REVERT: F 213 ILE cc_start: 0.4114 (OUTLIER) cc_final: 0.3749 (mp) REVERT: L 304 MET cc_start: 0.0429 (pmm) cc_final: -0.0244 (pmt) REVERT: L 432 HIS cc_start: 0.4168 (OUTLIER) cc_final: 0.3652 (p90) REVERT: M 90 LEU cc_start: 0.1882 (OUTLIER) cc_final: 0.1634 (tm) REVERT: M 113 MET cc_start: -0.1082 (pmt) cc_final: -0.2301 (pp-130) REVERT: D 256 MET cc_start: -0.0449 (OUTLIER) cc_final: -0.1833 (mmt) REVERT: D 499 MET cc_start: 0.2281 (mmt) cc_final: 0.1802 (mtt) outliers start: 204 outliers final: 136 residues processed: 732 average time/residue: 1.6808 time to fit residues: 1734.2041 Evaluate side-chains 692 residues out of total 8080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 549 time to evaluate : 7.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 97 THR Chi-restraints excluded: chain a residue 157 VAL Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 91 VAL Chi-restraints excluded: chain d residue 104 ASP Chi-restraints excluded: chain d residue 110 MET Chi-restraints excluded: chain d residue 224 THR Chi-restraints excluded: chain d residue 249 SER Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 63 VAL Chi-restraints excluded: chain q residue 12 VAL Chi-restraints excluded: chain q residue 21 ASP Chi-restraints excluded: chain q residue 126 VAL Chi-restraints excluded: chain r residue 22 ARG Chi-restraints excluded: chain r residue 49 VAL Chi-restraints excluded: chain s residue 8 ILE Chi-restraints excluded: chain s residue 184 ASP Chi-restraints excluded: chain t residue 69 SER Chi-restraints excluded: chain t residue 160 SER Chi-restraints excluded: chain c residue 61 LEU Chi-restraints excluded: chain c residue 95 ASP Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 149 VAL Chi-restraints excluded: chain c residue 152 ASP Chi-restraints excluded: chain n residue 120 VAL Chi-restraints excluded: chain m residue 22 VAL Chi-restraints excluded: chain i residue 67 ASP Chi-restraints excluded: chain i residue 98 ARG Chi-restraints excluded: chain j residue 15 SER Chi-restraints excluded: chain j residue 112 VAL Chi-restraints excluded: chain z residue 100 LYS Chi-restraints excluded: chain z residue 101 LYS Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain w residue 9 VAL Chi-restraints excluded: chain w residue 17 ILE Chi-restraints excluded: chain w residue 55 THR Chi-restraints excluded: chain w residue 56 HIS Chi-restraints excluded: chain w residue 98 VAL Chi-restraints excluded: chain w residue 123 THR Chi-restraints excluded: chain w residue 130 THR Chi-restraints excluded: chain g residue 11 GLN Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 39 LEU Chi-restraints excluded: chain g residue 46 THR Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain b residue 8 LYS Chi-restraints excluded: chain b residue 17 PHE Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain b residue 107 TYR Chi-restraints excluded: chain b residue 122 VAL Chi-restraints excluded: chain b residue 137 VAL Chi-restraints excluded: chain b residue 186 VAL Chi-restraints excluded: chain e residue 26 ASP Chi-restraints excluded: chain e residue 30 ILE Chi-restraints excluded: chain e residue 37 ASP Chi-restraints excluded: chain e residue 68 ILE Chi-restraints excluded: chain e residue 69 VAL Chi-restraints excluded: chain e residue 128 ILE Chi-restraints excluded: chain e residue 185 SER Chi-restraints excluded: chain u residue 38 LYS Chi-restraints excluded: chain u residue 40 VAL Chi-restraints excluded: chain v residue 119 GLN Chi-restraints excluded: chain k residue 131 VAL Chi-restraints excluded: chain h residue 24 LEU Chi-restraints excluded: chain h residue 97 ILE Chi-restraints excluded: chain h residue 101 ILE Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain S residue 27 CYS Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain l residue 49 ASP Chi-restraints excluded: chain V residue 65 PHE Chi-restraints excluded: chain V residue 92 LEU Chi-restraints excluded: chain V residue 192 THR Chi-restraints excluded: chain V residue 228 TYR Chi-restraints excluded: chain V residue 287 THR Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 582 TRP Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain C residue 839 THR Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 276 ASP Chi-restraints excluded: chain E residue 385 ASP Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 156 MET Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 197 MET Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain H residue 254 SER Chi-restraints excluded: chain H residue 333 PHE Chi-restraints excluded: chain K residue 22 ASN Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 182 ASP Chi-restraints excluded: chain L residue 224 VAL Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 417 CYS Chi-restraints excluded: chain L residue 431 VAL Chi-restraints excluded: chain L residue 432 HIS Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 486 PHE Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 142 THR Chi-restraints excluded: chain M residue 195 ASP Chi-restraints excluded: chain M residue 231 PHE Chi-restraints excluded: chain M residue 237 ILE Chi-restraints excluded: chain M residue 334 VAL Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 457 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1085 random chunks: chunk 951 optimal weight: 10.0000 chunk 1001 optimal weight: 5.9990 chunk 914 optimal weight: 10.0000 chunk 974 optimal weight: 30.0000 chunk 586 optimal weight: 0.9990 chunk 424 optimal weight: 50.0000 chunk 765 optimal weight: 9.9990 chunk 299 optimal weight: 7.9990 chunk 880 optimal weight: 7.9990 chunk 921 optimal weight: 5.9990 chunk 971 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 163 ASN s 76 GLN s 114 GLN ** s 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 111 GLN ** c 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 116 ASN ** e 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 119 GLN ** o 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 GLN B 543 ASN ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 GLN ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 715 HIS ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 322 GLN ** H 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 116 ASN M 299 GLN ** D 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN ** D 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 114740 Z= 0.351 Angle : 0.687 16.099 163305 Z= 0.344 Chirality : 0.043 0.321 19801 Planarity : 0.005 0.103 14483 Dihedral : 21.987 179.818 37059 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.66 % Favored : 94.33 % Rotamer: Outliers : 2.60 % Allowed : 22.94 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.11 % Twisted Proline : 0.30 % Twisted General : 0.01 % 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: -1.46 (0.09), residues: 9011 helix: -0.11 (0.09), residues: 3602 sheet: -1.36 (0.15), residues: 1163 loop : -1.57 (0.09), residues: 4246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP E 370 HIS 0.013 0.001 HIS o 54 PHE 0.031 0.001 PHE q 86 TYR 0.029 0.001 TYR b 120 ARG 0.008 0.000 ARG w 23 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18022 Ramachandran restraints generated. 9011 Oldfield, 0 Emsley, 9011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18022 Ramachandran restraints generated. 9011 Oldfield, 0 Emsley, 9011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 8080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 555 time to evaluate : 7.572 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: a 44 ASP cc_start: 0.7179 (OUTLIER) cc_final: 0.6882 (m-30) REVERT: W 1 MET cc_start: 0.8631 (ttt) cc_final: 0.8336 (ttt) REVERT: j 76 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8492 (ptpt) REVERT: g 16 LYS cc_start: 0.6702 (tptp) cc_final: 0.5866 (mmpt) REVERT: B 471 SER cc_start: 0.2341 (p) cc_final: 0.1678 (p) REVERT: B 487 LYS cc_start: 0.5450 (ttpt) cc_final: 0.4943 (pttp) REVERT: B 511 ASN cc_start: 0.5570 (p0) cc_final: 0.5278 (m-40) REVERT: B 524 ASP cc_start: 0.5135 (m-30) cc_final: 0.4857 (t0) REVERT: A 323 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7785 (mm) REVERT: C 582 TRP cc_start: 0.7438 (OUTLIER) cc_final: 0.6570 (t60) REVERT: C 807 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.7234 (mm) REVERT: E 362 MET cc_start: 0.4047 (pp-130) cc_final: 0.3160 (pp-130) REVERT: F 213 ILE cc_start: 0.3966 (OUTLIER) cc_final: 0.3748 (mp) REVERT: L 304 MET cc_start: 0.0362 (pmm) cc_final: -0.0325 (pmt) REVERT: L 432 HIS cc_start: 0.4050 (OUTLIER) cc_final: 0.3532 (p90) REVERT: M 90 LEU cc_start: 0.1967 (OUTLIER) cc_final: 0.1702 (tm) REVERT: M 113 MET cc_start: -0.1076 (pmt) cc_final: -0.2284 (pp-130) REVERT: M 297 MET cc_start: 0.4874 (mmm) cc_final: 0.4650 (mpm) REVERT: M 320 MET cc_start: 0.4568 (OUTLIER) cc_final: 0.4294 (ppp) REVERT: D 256 MET cc_start: -0.0334 (OUTLIER) cc_final: -0.1782 (mmt) REVERT: D 499 MET cc_start: 0.2256 (mmt) cc_final: 0.1825 (mtt) outliers start: 193 outliers final: 145 residues processed: 708 average time/residue: 1.7451 time to fit residues: 1755.4144 Evaluate side-chains 698 residues out of total 8080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 543 time to evaluate : 7.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 2 SER Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 87 VAL Chi-restraints excluded: chain a residue 97 THR Chi-restraints excluded: chain a residue 157 VAL Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 91 VAL Chi-restraints excluded: chain d residue 94 ILE Chi-restraints excluded: chain d residue 104 ASP Chi-restraints excluded: chain d residue 110 MET Chi-restraints excluded: chain d residue 215 MET Chi-restraints excluded: chain d residue 224 THR Chi-restraints excluded: chain d residue 249 SER Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 63 VAL Chi-restraints excluded: chain q residue 12 VAL Chi-restraints excluded: chain q residue 21 ASP Chi-restraints excluded: chain q residue 126 VAL Chi-restraints excluded: chain q residue 171 ASP Chi-restraints excluded: chain r residue 22 ARG Chi-restraints excluded: chain r residue 49 VAL Chi-restraints excluded: chain s residue 8 ILE Chi-restraints excluded: chain s residue 184 ASP Chi-restraints excluded: chain t residue 69 SER Chi-restraints excluded: chain t residue 155 ASN Chi-restraints excluded: chain t residue 160 SER Chi-restraints excluded: chain c residue 61 LEU Chi-restraints excluded: chain c residue 95 ASP Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 149 VAL Chi-restraints excluded: chain c residue 152 ASP Chi-restraints excluded: chain n residue 120 VAL Chi-restraints excluded: chain m residue 22 VAL Chi-restraints excluded: chain m residue 32 ASP Chi-restraints excluded: chain m residue 83 ASP Chi-restraints excluded: chain i residue 67 ASP Chi-restraints excluded: chain i residue 86 LYS Chi-restraints excluded: chain i residue 98 ARG Chi-restraints excluded: chain i residue 107 THR Chi-restraints excluded: chain j residue 15 SER Chi-restraints excluded: chain j residue 76 LYS Chi-restraints excluded: chain j residue 112 VAL Chi-restraints excluded: chain z residue 101 LYS Chi-restraints excluded: chain z residue 102 THR Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain w residue 9 VAL Chi-restraints excluded: chain w residue 17 ILE Chi-restraints excluded: chain w residue 55 THR Chi-restraints excluded: chain w residue 56 HIS Chi-restraints excluded: chain w residue 98 VAL Chi-restraints excluded: chain w residue 123 THR Chi-restraints excluded: chain w residue 130 THR Chi-restraints excluded: chain g residue 11 GLN Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 39 LEU Chi-restraints excluded: chain g residue 46 THR Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain b residue 8 LYS Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain b residue 107 TYR Chi-restraints excluded: chain b residue 122 VAL Chi-restraints excluded: chain b residue 137 VAL Chi-restraints excluded: chain b residue 186 VAL Chi-restraints excluded: chain e residue 26 ASP Chi-restraints excluded: chain e residue 30 ILE Chi-restraints excluded: chain e residue 37 ASP Chi-restraints excluded: chain e residue 68 ILE Chi-restraints excluded: chain e residue 69 VAL Chi-restraints excluded: chain e residue 128 ILE Chi-restraints excluded: chain e residue 185 SER Chi-restraints excluded: chain u residue 38 LYS Chi-restraints excluded: chain u residue 40 VAL Chi-restraints excluded: chain o residue 46 ASN Chi-restraints excluded: chain k residue 131 VAL Chi-restraints excluded: chain h residue 97 ILE Chi-restraints excluded: chain h residue 101 ILE Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain S residue 27 CYS Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain l residue 49 ASP Chi-restraints excluded: chain V residue 65 PHE Chi-restraints excluded: chain V residue 92 LEU Chi-restraints excluded: chain V residue 192 THR Chi-restraints excluded: chain V residue 228 TYR Chi-restraints excluded: chain V residue 287 THR Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 582 TRP Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain C residue 839 THR Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 276 ASP Chi-restraints excluded: chain E residue 385 ASP Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 156 MET Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain H residue 254 SER Chi-restraints excluded: chain H residue 333 PHE Chi-restraints excluded: chain K residue 22 ASN Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 182 ASP Chi-restraints excluded: chain L residue 224 VAL Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 417 CYS Chi-restraints excluded: chain L residue 431 VAL Chi-restraints excluded: chain L residue 432 HIS Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 486 PHE Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 142 THR Chi-restraints excluded: chain M residue 195 ASP Chi-restraints excluded: chain M residue 231 PHE Chi-restraints excluded: chain M residue 237 ILE Chi-restraints excluded: chain M residue 320 MET Chi-restraints excluded: chain M residue 334 VAL Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 457 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1085 random chunks: chunk 639 optimal weight: 50.0000 chunk 1030 optimal weight: 8.9990 chunk 628 optimal weight: 9.9990 chunk 488 optimal weight: 2.9990 chunk 716 optimal weight: 5.9990 chunk 1080 optimal weight: 50.0000 chunk 994 optimal weight: 6.9990 chunk 860 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 664 optimal weight: 8.9990 chunk 527 optimal weight: 40.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 163 ASN s 76 GLN s 114 GLN ** s 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 116 ASN ** e 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 119 GLN ** o 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 237 ASN ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 GLN ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 365 ASN ** C 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 116 ASN ** D 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN ** D 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 114740 Z= 0.352 Angle : 0.700 15.050 163305 Z= 0.349 Chirality : 0.043 0.307 19801 Planarity : 0.005 0.102 14483 Dihedral : 22.007 179.635 37059 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.86 % Favored : 94.13 % Rotamer: Outliers : 2.35 % Allowed : 23.28 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.11 % Twisted Proline : 0.30 % Twisted General : 0.01 % 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: -1.48 (0.09), residues: 9011 helix: -0.13 (0.09), residues: 3611 sheet: -1.40 (0.14), residues: 1173 loop : -1.57 (0.09), residues: 4227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP E 370 HIS 0.013 0.001 HIS o 54 PHE 0.040 0.002 PHE B 544 TYR 0.034 0.001 TYR b 120 ARG 0.018 0.000 ARG B 492 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18022 Ramachandran restraints generated. 9011 Oldfield, 0 Emsley, 9011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18022 Ramachandran restraints generated. 9011 Oldfield, 0 Emsley, 9011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 8080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 549 time to evaluate : 7.514 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: a 44 ASP cc_start: 0.7174 (OUTLIER) cc_final: 0.6883 (m-30) REVERT: W 1 MET cc_start: 0.8635 (ttt) cc_final: 0.8339 (ttt) REVERT: j 76 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8498 (ptpt) REVERT: g 16 LYS cc_start: 0.6696 (tptp) cc_final: 0.5852 (mmpt) REVERT: B 471 SER cc_start: 0.3000 (p) cc_final: 0.2452 (p) REVERT: B 487 LYS cc_start: 0.5188 (ttpt) cc_final: 0.4719 (pttp) REVERT: B 524 ASP cc_start: 0.5276 (m-30) cc_final: 0.4934 (t0) REVERT: A 318 MET cc_start: 0.6457 (ppp) cc_final: 0.6181 (ppp) REVERT: C 582 TRP cc_start: 0.7466 (OUTLIER) cc_final: 0.6527 (t60) REVERT: C 709 MET cc_start: 0.4892 (tpp) cc_final: 0.4608 (tpt) REVERT: C 757 ILE cc_start: 0.7222 (OUTLIER) cc_final: 0.6650 (mm) REVERT: C 807 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7258 (mm) REVERT: E 362 MET cc_start: 0.3934 (pp-130) cc_final: 0.3250 (pp-130) REVERT: F 213 ILE cc_start: 0.4111 (OUTLIER) cc_final: 0.3871 (mp) REVERT: L 304 MET cc_start: 0.0442 (pmm) cc_final: -0.0272 (pmt) REVERT: L 349 MET cc_start: -0.0972 (mtm) cc_final: -0.1282 (ttt) REVERT: L 432 HIS cc_start: 0.3937 (OUTLIER) cc_final: 0.3447 (p90) REVERT: M 64 MET cc_start: 0.4220 (pmt) cc_final: 0.3699 (pmm) REVERT: M 90 LEU cc_start: 0.1963 (OUTLIER) cc_final: 0.1708 (tm) REVERT: M 113 MET cc_start: -0.1067 (pmt) cc_final: -0.2252 (pp-130) REVERT: M 297 MET cc_start: 0.4559 (mmm) cc_final: 0.4293 (mmm) REVERT: D 256 MET cc_start: -0.0290 (OUTLIER) cc_final: -0.1673 (mmt) REVERT: D 499 MET cc_start: 0.2140 (mmt) cc_final: 0.1863 (mtt) outliers start: 174 outliers final: 148 residues processed: 690 average time/residue: 1.6530 time to fit residues: 1611.0111 Evaluate side-chains 699 residues out of total 8080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 542 time to evaluate : 7.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 2 SER Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 38 ILE Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 87 VAL Chi-restraints excluded: chain a residue 97 THR Chi-restraints excluded: chain a residue 157 VAL Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 91 VAL Chi-restraints excluded: chain d residue 94 ILE Chi-restraints excluded: chain d residue 104 ASP Chi-restraints excluded: chain d residue 110 MET Chi-restraints excluded: chain d residue 215 MET Chi-restraints excluded: chain d residue 224 THR Chi-restraints excluded: chain d residue 249 SER Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 63 VAL Chi-restraints excluded: chain q residue 12 VAL Chi-restraints excluded: chain q residue 21 ASP Chi-restraints excluded: chain q residue 24 THR Chi-restraints excluded: chain q residue 126 VAL Chi-restraints excluded: chain q residue 171 ASP Chi-restraints excluded: chain r residue 22 ARG Chi-restraints excluded: chain r residue 49 VAL Chi-restraints excluded: chain r residue 151 ASP Chi-restraints excluded: chain s residue 8 ILE Chi-restraints excluded: chain s residue 92 VAL Chi-restraints excluded: chain s residue 184 ASP Chi-restraints excluded: chain t residue 69 SER Chi-restraints excluded: chain t residue 160 SER Chi-restraints excluded: chain c residue 61 LEU Chi-restraints excluded: chain c residue 95 ASP Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 149 VAL Chi-restraints excluded: chain c residue 151 LEU Chi-restraints excluded: chain c residue 152 ASP Chi-restraints excluded: chain n residue 120 VAL Chi-restraints excluded: chain m residue 22 VAL Chi-restraints excluded: chain m residue 32 ASP Chi-restraints excluded: chain i residue 67 ASP Chi-restraints excluded: chain i residue 98 ARG Chi-restraints excluded: chain j residue 15 SER Chi-restraints excluded: chain j residue 76 LYS Chi-restraints excluded: chain j residue 112 VAL Chi-restraints excluded: chain z residue 101 LYS Chi-restraints excluded: chain z residue 102 THR Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain w residue 4 VAL Chi-restraints excluded: chain w residue 9 VAL Chi-restraints excluded: chain w residue 17 ILE Chi-restraints excluded: chain w residue 56 HIS Chi-restraints excluded: chain w residue 98 VAL Chi-restraints excluded: chain w residue 108 LEU Chi-restraints excluded: chain w residue 123 THR Chi-restraints excluded: chain w residue 130 THR Chi-restraints excluded: chain g residue 11 GLN Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 39 LEU Chi-restraints excluded: chain g residue 42 ILE Chi-restraints excluded: chain g residue 46 THR Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain b residue 8 LYS Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain b residue 107 TYR Chi-restraints excluded: chain b residue 122 VAL Chi-restraints excluded: chain b residue 137 VAL Chi-restraints excluded: chain b residue 186 VAL Chi-restraints excluded: chain e residue 26 ASP Chi-restraints excluded: chain e residue 30 ILE Chi-restraints excluded: chain e residue 37 ASP Chi-restraints excluded: chain e residue 68 ILE Chi-restraints excluded: chain e residue 69 VAL Chi-restraints excluded: chain e residue 128 ILE Chi-restraints excluded: chain e residue 185 SER Chi-restraints excluded: chain u residue 38 LYS Chi-restraints excluded: chain u residue 40 VAL Chi-restraints excluded: chain v residue 119 GLN Chi-restraints excluded: chain o residue 46 ASN Chi-restraints excluded: chain k residue 131 VAL Chi-restraints excluded: chain h residue 22 ILE Chi-restraints excluded: chain h residue 89 ILE Chi-restraints excluded: chain h residue 97 ILE Chi-restraints excluded: chain h residue 101 ILE Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain S residue 27 CYS Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain l residue 49 ASP Chi-restraints excluded: chain V residue 65 PHE Chi-restraints excluded: chain V residue 92 LEU Chi-restraints excluded: chain V residue 192 THR Chi-restraints excluded: chain V residue 228 TYR Chi-restraints excluded: chain V residue 287 THR Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 582 TRP Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain C residue 839 THR Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 276 ASP Chi-restraints excluded: chain E residue 385 ASP Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 156 MET Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain H residue 254 SER Chi-restraints excluded: chain H residue 333 PHE Chi-restraints excluded: chain K residue 22 ASN Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 182 ASP Chi-restraints excluded: chain L residue 224 VAL Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 417 CYS Chi-restraints excluded: chain L residue 431 VAL Chi-restraints excluded: chain L residue 432 HIS Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 486 PHE Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 142 THR Chi-restraints excluded: chain M residue 195 ASP Chi-restraints excluded: chain M residue 231 PHE Chi-restraints excluded: chain M residue 237 ILE Chi-restraints excluded: chain M residue 261 ASP Chi-restraints excluded: chain M residue 334 VAL Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 457 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1085 random chunks: chunk 683 optimal weight: 9.9990 chunk 916 optimal weight: 9.9990 chunk 263 optimal weight: 4.9990 chunk 793 optimal weight: 9.9990 chunk 127 optimal weight: 7.9990 chunk 239 optimal weight: 8.9990 chunk 862 optimal weight: 20.0000 chunk 360 optimal weight: 5.9990 chunk 885 optimal weight: 50.0000 chunk 109 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: r 163 ASN s 76 GLN s 114 GLN ** s 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 116 ASN ** e 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 84 HIS ** v 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 119 GLN ** o 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 237 ASN ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 368 HIS ** L 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 116 ASN ** D 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN ** D 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.129439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.110249 restraints weight = 292788.157| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 2.69 r_work: 0.3264 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 114740 Z= 0.314 Angle : 0.686 15.008 163305 Z= 0.343 Chirality : 0.042 0.300 19801 Planarity : 0.004 0.102 14483 Dihedral : 21.995 179.530 37059 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.84 % Favored : 94.15 % Rotamer: Outliers : 2.51 % Allowed : 23.16 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.81 % Cis-general : 0.11 % Twisted Proline : 0.30 % Twisted General : 0.01 % 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: -1.42 (0.09), residues: 9011 helix: -0.08 (0.09), residues: 3608 sheet: -1.35 (0.15), residues: 1157 loop : -1.54 (0.09), residues: 4246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP k 82 HIS 0.013 0.001 HIS o 54 PHE 0.031 0.001 PHE q 86 TYR 0.050 0.001 TYR u 12 ARG 0.008 0.000 ARG B 548 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27042.26 seconds wall clock time: 473 minutes 47.02 seconds (28427.02 seconds total)