Starting phenix.real_space_refine on Tue Mar 12 07:47:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zvj_11458/03_2024/6zvj_11458_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zvj_11458/03_2024/6zvj_11458.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zvj_11458/03_2024/6zvj_11458.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zvj_11458/03_2024/6zvj_11458.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zvj_11458/03_2024/6zvj_11458_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zvj_11458/03_2024/6zvj_11458_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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: 8 Type Number sf(0) Gaussians Fe 8 7.16 5 Zn 3 6.06 5 P 1716 5.49 5 Mg 2 5.21 5 S 393 5.16 5 C 65803 2.51 5 N 20871 2.21 5 O 26224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a GLU 13": "OE1" <-> "OE2" Residue "a GLU 35": "OE1" <-> "OE2" Residue "a GLU 196": "OE1" <-> "OE2" Residue "a GLU 208": "OE1" <-> "OE2" Residue "a GLU 209": "OE1" <-> "OE2" Residue "p PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 198": "OE1" <-> "OE2" Residue "d ARG 68": "NH1" <-> "NH2" Residue "d GLU 268": "OE1" <-> "OE2" Residue "Q GLU 46": "OE1" <-> "OE2" Residue "q GLU 97": "OE1" <-> "OE2" Residue "q GLU 118": "OE1" <-> "OE2" Residue "q GLU 165": "OE1" <-> "OE2" Residue "q ARG 198": "NH1" <-> "NH2" Residue "q ARG 200": "NH1" <-> "NH2" Residue "q PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 251": "OE1" <-> "OE2" Residue "q ARG 252": "NH1" <-> "NH2" Residue "W ARG 2": "NH1" <-> "NH2" Residue "W ARG 23": "NH1" <-> "NH2" Residue "r GLU 43": "OE1" <-> "OE2" Residue "r GLU 91": "OE1" <-> "OE2" Residue "r GLU 118": "OE1" <-> "OE2" Residue "r ARG 170": "NH1" <-> "NH2" Residue "r GLU 205": "OE1" <-> "OE2" Residue "r GLU 208": "OE1" <-> "OE2" Residue "s GLU 42": "OE1" <-> "OE2" Residue "s GLU 50": "OE1" <-> "OE2" Residue "t GLU 134": "OE1" <-> "OE2" Residue "t GLU 135": "OE1" <-> "OE2" Residue "t GLU 164": "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 64": "OE1" <-> "OE2" Residue "f GLU 18": "OE1" <-> "OE2" Residue "f PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 11": "NH1" <-> "NH2" Residue "j GLU 139": "OE1" <-> "OE2" Residue "z ARG 16": "NH1" <-> "NH2" Residue "R GLU 75": "OE1" <-> "OE2" Residue "R ARG 80": "NH1" <-> "NH2" Residue "w GLU 75": "OE1" <-> "OE2" Residue "g ARG 71": "NH1" <-> "NH2" Residue "g GLU 107": "OE1" <-> "OE2" Residue "g ARG 125": "NH1" <-> "NH2" Residue "b GLU 20": "OE1" <-> "OE2" Residue "b ARG 54": "NH1" <-> "NH2" Residue "b GLU 85": "OE1" <-> "OE2" 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 123": "OE1" <-> "OE2" Residue "e GLU 160": "OE1" <-> "OE2" Residue "e GLU 176": "OE1" <-> "OE2" Residue "e GLU 195": "OE1" <-> "OE2" Residue "u PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ARG 36": "NH1" <-> "NH2" Residue "v GLU 37": "OE1" <-> "OE2" Residue "v GLU 58": "OE1" <-> "OE2" Residue "v GLU 87": "OE1" <-> "OE2" Residue "o GLU 71": "OE1" <-> "OE2" Residue "o GLU 110": "OE1" <-> "OE2" Residue "o GLU 118": "OE1" <-> "OE2" Residue "k GLU 7": "OE1" <-> "OE2" Residue "k ARG 14": "NH1" <-> "NH2" Residue "k GLU 109": "OE1" <-> "OE2" Residue "x GLU 13": "OE1" <-> "OE2" Residue "x GLU 32": "OE1" <-> "OE2" Residue "x GLU 44": "OE1" <-> "OE2" Residue "h ARG 19": "NH1" <-> "NH2" Residue "h GLU 45": "OE1" <-> "OE2" Residue "h GLU 96": "OE1" <-> "OE2" Residue "h GLU 107": "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 "V PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 545": "OE1" <-> "OE2" Residue "B ARG 550": "NH1" <-> "NH2" Residue "B GLU 551": "OE1" <-> "OE2" Residue "B GLU 563": "OE1" <-> "OE2" Residue "A ARG 7": "NH1" <-> "NH2" Residue "A ARG 14": "NH1" <-> "NH2" Residue "A ARG 41": "NH1" <-> "NH2" Residue "A GLU 48": "OE1" <-> "OE2" Residue "A GLU 99": "OE1" <-> "OE2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A ARG 210": "NH1" <-> "NH2" 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 PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 547": "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 590": "OE1" <-> "OE2" Residue "A GLU 592": "OE1" <-> "OE2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C GLU 100": "OE1" <-> "OE2" Residue "C GLU 114": "OE1" <-> "OE2" Residue "C GLU 122": "OE1" <-> "OE2" Residue "C GLU 125": "OE1" <-> "OE2" Residue "C ARG 142": "NH1" <-> "NH2" Residue "C GLU 323": "OE1" <-> "OE2" Residue "C GLU 368": "OE1" <-> "OE2" Residue "C ARG 439": "NH1" <-> "NH2" Residue "C ARG 450": "NH1" <-> "NH2" Residue "C GLU 468": "OE1" <-> "OE2" Residue "C GLU 498": "OE1" <-> "OE2" Residue "C ARG 563": "NH1" <-> "NH2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C ARG 708": "NH1" <-> "NH2" Residue "C ARG 719": "NH1" <-> "NH2" Residue "C GLU 731": "OE1" <-> "OE2" Residue "C GLU 861": "OE1" <-> "OE2" Residue "E GLU 99": "OE1" <-> "OE2" Residue "E GLU 176": "OE1" <-> "OE2" Residue "E ARG 369": "NH1" <-> "NH2" Residue "F GLU 145": "OE1" <-> "OE2" Residue "F GLU 167": "OE1" <-> "OE2" Residue "F GLU 188": "OE1" <-> "OE2" Residue "F GLU 193": "OE1" <-> "OE2" Residue "F ARG 210": "NH1" <-> "NH2" Residue "H PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 102": "OE1" <-> "OE2" Residue "H GLU 185": "OE1" <-> "OE2" Residue "H GLU 199": "OE1" <-> "OE2" Residue "H GLU 219": "OE1" <-> "OE2" Residue "H ARG 249": "NH1" <-> "NH2" Residue "H GLU 252": "OE1" <-> "OE2" Residue "H GLU 284": "OE1" <-> "OE2" Residue "H PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 24": "OE1" <-> "OE2" Residue "K GLU 95": "OE1" <-> "OE2" Residue "K GLU 96": "OE1" <-> "OE2" Residue "K GLU 129": "OE1" <-> "OE2" Residue "L GLU 211": "OE1" <-> "OE2" Residue "L ARG 262": "NH1" <-> "NH2" Residue "L GLU 410": "OE1" <-> "OE2" Residue "M GLU 88": "OE1" <-> "OE2" Residue "M GLU 95": "OE1" <-> "OE2" Residue "M TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 166": "NH1" <-> "NH2" Residue "M GLU 170": "OE1" <-> "OE2" Residue "M ARG 206": "NH1" <-> "NH2" Residue "M GLU 233": "OE1" <-> "OE2" Residue "M ARG 278": "NH1" <-> "NH2" Residue "M ARG 330": "NH1" <-> "NH2" Residue "M ARG 340": "NH1" <-> "NH2" Residue "1 ARG 22": "NH1" <-> "NH2" Residue "1 ARG 33": "NH1" <-> "NH2" Residue "1 GLU 82": "OE1" <-> "OE2" Residue "1 ARG 96": "NH1" <-> "NH2" Residue "1 ARG 190": "NH1" <-> "NH2" Residue "1 GLU 211": "OE1" <-> "OE2" Residue "1 GLU 242": "OE1" <-> "OE2" Residue "1 GLU 273": "OE1" <-> "OE2" Residue "1 ARG 306": "NH1" <-> "NH2" Residue "1 ARG 323": "NH1" <-> "NH2" Residue "1 GLU 373": "OE1" <-> "OE2" Residue "1 GLU 380": "OE1" <-> "OE2" Residue "1 ARG 390": "NH1" <-> "NH2" Residue "1 ARG 395": "NH1" <-> "NH2" Residue "1 GLU 466": "OE1" <-> "OE2" Residue "1 GLU 487": "OE1" <-> "OE2" Residue "1 ARG 567": "NH1" <-> "NH2" Residue "1 ARG 568": "NH1" <-> "NH2" Residue "N ARG 34": "NH1" <-> "NH2" Residue "N GLU 75": "OE1" <-> "OE2" Residue "D GLU 23": "OE1" <-> "OE2" Residue "D ARG 26": "NH1" <-> "NH2" Residue "D GLU 172": "OE1" <-> "OE2" Residue "D ARG 183": "NH1" <-> "NH2" Residue "D GLU 189": "OE1" <-> "OE2" Residue "D GLU 200": "OE1" <-> "OE2" Residue "D GLU 214": "OE1" <-> "OE2" Residue "D ARG 218": "NH1" <-> "NH2" Residue "D ARG 271": "NH1" <-> "NH2" Residue "D GLU 302": "OE1" <-> "OE2" Residue "D ARG 329": "NH1" <-> "NH2" Residue "D GLU 345": "OE1" <-> "OE2" Residue "D GLU 352": "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 475": "OE1" <-> "OE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 115020 Number of models: 1 Model: "" Number of chains: 55 Chain: "a" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1706 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain: "p" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1716 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 205} Chain: "d" Number of atoms: 1675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1675 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain: "Q" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 815 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "q" Number of atoms: 2032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2032 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 240} Chain: "W" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 231 Classifications: {'peptide': 24} Modifications used: {'COO': 1} Link IDs: {'TRANS': 23} Chain: "r" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1795 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain: "s" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1400 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain breaks: 3 Chain: "t" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1639 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 191} Chain breaks: 1 Chain: "c" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1500 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "n" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1120 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain breaks: 1 Chain: "m" Number of atoms: 1203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1203 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "i" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 940 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "y" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 626 Classifications: {'peptide': 82} Modifications used: {'COO': 1} 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: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1081 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 134} Chain: "z" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1000 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 116} Chain: "R" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 641 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "T" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 355 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain breaks: 1 Chain: "2" Number of atoms: 36700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1720, 36700 Inner-chain residues flagged as termini: ['pdbres=" U 2 140 "', 'pdbres=" U 2 287 "', 'pdbres=" G 2 330 "', 'pdbres=" C 2 791 "', 'pdbres=" G 2 841 "', 'pdbres=" G 21424 "', 'pdbres=" A 21438 "', 'pdbres=" G 21771 "'] Classifications: {'RNA': 1720} Modifications used: {'5*END': 9, 'rna2p_pur': 142, 'rna2p_pyr': 120, 'rna3p_pur': 769, 'rna3p_pyr': 689} Link IDs: {'rna2p': 261, 'rna3p': 1458} Chain breaks: 1 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: 1746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1746 Classifications: {'peptide': 224} Modifications used: {'COO': 1} 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: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 800 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 87} Chain: "v" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 862 Classifications: {'peptide': 111} Modifications used: {'COO': 1} 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: 1163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1163 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "x" Number of atoms: 1095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1095 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 136} Chain: "h" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 781 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "P" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 558 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "S" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 480 Classifications: {'peptide': 61} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "l" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 451 Classifications: {'peptide': 54} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 52} Chain: "U" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 466 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain breaks: 1 Chain: "V" Number of atoms: 2315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2315 Classifications: {'peptide': 296} Modifications used: {'COO': 1} 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: 5384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 692, 5384 Classifications: {'peptide': 692} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 25, 'TRANS': 666} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 363 Unresolved non-hydrogen angles: 446 Unresolved non-hydrogen dihedrals: 298 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 20, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 206 Chain: "C" Number of atoms: 5073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 5073 Classifications: {'peptide': 625} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 17, 'TRANS': 607} Chain breaks: 4 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2} Unresolved non-hydrogen planarities: 6 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: 3112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 3112 Classifications: {'peptide': 372} Modifications used: {'COO': 1} 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: 4 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: "1" Number of atoms: 4542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4542 Classifications: {'peptide': 576} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 30, 'TRANS': 543} Chain breaks: 1 Chain: "N" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 728 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 3618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3618 Classifications: {'peptide': 447} Modifications used: {'COO': 1} 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} Link IDs: {'TRANS': 77} Chain: "G" Number of atoms: 348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 348 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 1, 'TRANS': 68} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 108 Chain: "J" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 363 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 233 Unresolved non-hydrogen angles: 292 Unresolved non-hydrogen dihedrals: 190 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 116 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} Chain: "1" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 76 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1, 'SF4': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5275 SG CYS Q 23 90.091 168.551 112.336 1.00 9.93 S ATOM 5296 SG CYS Q 26 90.693 167.071 109.023 1.00 10.40 S ATOM 5679 SG CYS Q 74 92.796 165.228 111.408 1.00 9.26 S ATOM 5698 SG CYS Q 77 94.208 167.882 109.353 1.00 12.46 S ATOM 71984 SG CYS U 121 182.896 151.811 34.968 1.00 23.73 S ATOM 72138 SG CYS U 141 179.590 150.383 35.270 1.00 26.75 S ATOM 72157 SG CYS U 144 181.737 153.688 38.220 1.00 27.94 S Time building chain proxies: 42.27, per 1000 atoms: 0.37 Number of scatterers: 115020 At special positions: 0 Unit cell: (225.567, 263.691, 312.405, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 3 29.99 Fe 8 26.01 S 393 16.00 P 1716 15.00 Mg 2 11.99 O 26224 8.00 N 20871 7.00 C 65803 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: 34.85 Conformation dependent library (CDL) restraints added in 10.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 1 601 " pdb="FE1 SF4 1 601 " - pdb=" SG CYS 1 29 " pdb="FE3 SF4 1 601 " - pdb=" SG CYS 1 61 " pdb="FE2 SF4 1 601 " - pdb=" SG CYS 1 55 " pdb="FE4 SF4 1 601 " - pdb=" SG CYS 1 58 " pdb=" SF4 1 602 " pdb="FE4 SF4 1 602 " - pdb=" SG CYS 1 65 " pdb="FE3 SF4 1 602 " - pdb=" SG CYS 1 25 " pdb="FE2 SF4 1 602 " - pdb=" SG CYS 1 21 " pdb="FE1 SF4 1 602 " - pdb=" SG CYS 1 16 " Number of angles added : 24 Zn2+ tetrahedral coordination pdb=" ZN Q 201 " 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 ZN Q 201 " - pdb=" SG CYS Q 77 " pdb=" ZN U 500 " pdb="ZN ZN U 500 " - pdb=" SG CYS U 141 " pdb="ZN ZN U 500 " - pdb=" SG CYS U 144 " pdb="ZN ZN U 500 " - pdb=" SG CYS U 121 " Number of angles added : 6 19910 Ramachandran restraints generated. 9955 Oldfield, 0 Emsley, 9955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 19108 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 349 helices and 93 sheets defined 48.4% alpha, 14.2% beta 377 base pairs and 900 stacking pairs defined. Time for finding SS restraints: 62.82 Creating SS restraints... Processing helix chain 'a' and resid 5 through 10 removed outlier: 3.901A pdb=" N GLN a 9 " --> pdb=" O LEU a 5 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N MET a 10 " --> pdb=" O ASP a 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 5 through 10' Processing helix chain 'a' and resid 11 through 22 removed outlier: 3.677A pdb=" N GLY a 22 " --> pdb=" O PHE a 18 " (cutoff:3.500A) Processing helix chain 'a' and resid 34 through 39 removed outlier: 4.108A pdb=" N ILE a 38 " --> pdb=" O MET a 34 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TYR a 39 " --> pdb=" O GLU a 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 34 through 39' Processing helix chain 'a' and resid 50 through 68 removed outlier: 4.551A pdb=" N ILE a 68 " --> pdb=" O ALA a 64 " (cutoff:3.500A) Processing helix chain 'a' and resid 80 through 95 removed outlier: 3.953A pdb=" N GLN a 84 " --> pdb=" O ARG a 80 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ARG a 85 " --> pdb=" O ASN a 81 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ALA a 86 " --> pdb=" O THR a 82 " (cutoff:3.500A) Processing helix chain 'a' and resid 126 through 131 removed outlier: 4.077A pdb=" N HIS a 131 " --> pdb=" O PRO a 127 " (cutoff:3.500A) Processing helix chain 'a' and resid 132 through 141 removed outlier: 4.243A pdb=" N SER a 138 " --> pdb=" O LEU a 134 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N TYR a 139 " --> pdb=" O THR a 135 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL a 140 " --> pdb=" O GLU a 136 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN a 141 " --> pdb=" O ALA a 137 " (cutoff:3.500A) Processing helix chain 'a' and resid 167 through 187 removed outlier: 3.630A pdb=" N VAL a 171 " --> pdb=" O GLY a 167 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY a 187 " --> pdb=" O LEU a 183 " (cutoff:3.500A) Processing helix chain 'a' and resid 198 through 204 removed outlier: 4.539A pdb=" N TYR a 202 " --> pdb=" O MET a 198 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR a 204 " --> pdb=" O ASP a 200 " (cutoff:3.500A) Processing helix chain 'a' and resid 206 through 216 removed outlier: 4.789A pdb=" N ALA a 216 " --> pdb=" O LYS a 212 " (cutoff:3.500A) Processing helix chain 'p' and resid 23 through 29 removed outlier: 4.994A pdb=" N LYS p 27 " --> pdb=" O ASP p 23 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N LYS p 28 " --> pdb=" O PRO p 24 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASP p 29 " --> pdb=" O PHE p 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 23 through 29' Processing helix chain 'p' and resid 57 through 64 removed outlier: 4.030A pdb=" N LYS p 63 " --> pdb=" O SER p 59 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N GLY p 64 " --> pdb=" O ASP p 60 " (cutoff:3.500A) Processing helix chain 'p' and resid 70 through 76 removed outlier: 5.083A pdb=" N ASN p 76 " --> pdb=" O ALA p 72 " (cutoff:3.500A) Processing helix chain 'p' and resid 106 through 115 removed outlier: 3.575A pdb=" N MET p 113 " --> pdb=" O LYS p 109 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL p 114 " --> pdb=" O MET p 110 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LYS p 115 " --> pdb=" O CYS p 111 " (cutoff:3.500A) Processing helix chain 'p' and resid 157 through 177 removed outlier: 4.395A pdb=" N VAL p 176 " --> pdb=" O MET p 172 " (cutoff:3.500A) Processing helix chain 'p' and resid 180 through 191 Proline residue: p 190 - end of helix Processing helix chain 'p' and resid 192 through 203 removed outlier: 3.968A pdb=" N GLN p 202 " --> pdb=" O GLU p 198 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N SER p 203 " --> pdb=" O LYS p 199 " (cutoff:3.500A) Processing helix chain 'p' and resid 224 through 233 removed outlier: 4.074A pdb=" N LEU p 228 " --> pdb=" O GLU p 224 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY p 233 " --> pdb=" O MET p 229 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 73 removed outlier: 4.288A pdb=" N ASP d 72 " --> pdb=" O ARG d 68 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N MET d 73 " --> pdb=" O LEU d 69 " (cutoff:3.500A) Processing helix chain 'd' and resid 77 through 85 removed outlier: 4.241A pdb=" N ILE d 81 " --> pdb=" O SER d 77 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE d 84 " --> pdb=" O GLU d 80 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER d 85 " --> pdb=" O ILE d 81 " (cutoff:3.500A) Processing helix chain 'd' and resid 91 through 98 removed outlier: 3.664A pdb=" N ASP d 95 " --> pdb=" O SER d 91 " (cutoff:3.500A) Processing helix chain 'd' and resid 146 through 162 removed outlier: 4.040A pdb=" N ILE d 162 " --> pdb=" O ALA d 158 " (cutoff:3.500A) Processing helix chain 'd' and resid 207 through 218 removed outlier: 4.055A pdb=" N GLY d 218 " --> pdb=" O LEU d 214 " (cutoff:3.500A) Processing helix chain 'd' and resid 232 through 251 removed outlier: 3.568A pdb=" N PHE d 236 " --> pdb=" O THR d 232 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS d 246 " --> pdb=" O ASP d 242 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N THR d 247 " --> pdb=" O ALA d 243 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N TYR d 248 " --> pdb=" O ILE d 244 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N SER d 249 " --> pdb=" O SER d 245 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR d 250 " --> pdb=" O LYS d 246 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU d 251 " --> pdb=" O THR d 247 " (cutoff:3.500A) Processing helix chain 'd' and resid 252 through 257 removed outlier: 3.898A pdb=" N TRP d 256 " --> pdb=" O THR d 252 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N LYS d 257 " --> pdb=" O PRO d 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 252 through 257' Processing helix chain 'd' and resid 264 through 270 removed outlier: 4.006A pdb=" N THR d 270 " --> pdb=" O TYR d 266 " (cutoff:3.500A) Processing helix chain 'Q' and resid 46 through 57 removed outlier: 4.795A pdb=" N ARG Q 51 " --> pdb=" O ALA Q 47 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ASP Q 52 " --> pdb=" O ALA Q 48 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER Q 54 " --> pdb=" O VAL Q 50 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA Q 56 " --> pdb=" O ASP Q 52 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER Q 57 " --> pdb=" O ILE Q 53 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 82 removed outlier: 3.990A pdb=" N ILE Q 79 " --> pdb=" O VAL Q 75 " (cutoff:3.500A) Processing helix chain 'Q' and resid 88 through 93 removed outlier: 5.267A pdb=" N LYS Q 93 " --> pdb=" O ARG Q 89 " (cutoff:3.500A) Processing helix chain 'q' and resid 43 through 50 Processing helix chain 'q' and resid 57 through 68 removed outlier: 3.845A pdb=" N VAL q 61 " --> pdb=" O THR q 57 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS q 62 " --> pdb=" O GLY q 58 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLN q 67 " --> pdb=" O LYS q 63 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ARG q 68 " --> pdb=" O ILE q 64 " (cutoff:3.500A) Processing helix chain 'q' and resid 115 through 120 removed outlier: 5.479A pdb=" N LYS q 120 " --> pdb=" O PRO q 116 " (cutoff:3.500A) Processing helix chain 'q' and resid 221 through 226 removed outlier: 3.881A pdb=" N ILE q 225 " --> pdb=" O ARG q 221 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N PHE q 226 " --> pdb=" O LEU q 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 221 through 226' Processing helix chain 'q' and resid 247 through 256 Processing helix chain 'W' and resid 2 through 24 removed outlier: 3.790A pdb=" N GLN W 22 " --> pdb=" O ARG W 18 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG W 23 " --> pdb=" O LYS W 19 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N SER W 24 " --> pdb=" O MET W 20 " (cutoff:3.500A) Processing helix chain 'r' and resid 20 through 29 removed outlier: 4.185A pdb=" N LEU r 24 " --> pdb=" O ASP r 20 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG r 25 " --> pdb=" O GLU r 21 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N THR r 26 " --> pdb=" O ARG r 22 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N PHE r 27 " --> pdb=" O LYS r 23 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR r 28 " --> pdb=" O LEU r 24 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N GLU r 29 " --> pdb=" O ARG r 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 20 through 29' Processing helix chain 'r' and resid 137 through 146 removed outlier: 3.727A pdb=" N ILE r 141 " --> pdb=" O ARG r 137 " (cutoff:3.500A) Processing helix chain 'r' and resid 152 through 157 removed outlier: 4.732A pdb=" N TYR r 156 " --> pdb=" O ASP r 152 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL r 157 " --> pdb=" O VAL r 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 152 through 157' Processing helix chain 'r' and resid 181 through 221 removed outlier: 3.502A pdb=" N LEU r 185 " --> pdb=" O THR r 181 " (cutoff:3.500A) Processing helix chain 's' and resid 18 through 31 removed outlier: 3.702A pdb=" N GLY s 22 " --> pdb=" O GLU s 18 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU s 30 " --> pdb=" O ALA s 26 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU s 31 " --> pdb=" O LEU s 27 " (cutoff:3.500A) Processing helix chain 's' and resid 65 through 77 removed outlier: 4.675A pdb=" N LYS s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ILE s 75 " --> pdb=" O SER s 71 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN s 76 " --> pdb=" O PHE s 72 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N VAL s 77 " --> pdb=" O GLN s 73 " (cutoff:3.500A) Processing helix chain 's' and resid 78 through 87 Processing helix chain 's' and resid 117 through 122 removed outlier: 3.801A pdb=" N THR s 121 " --> pdb=" O PRO s 117 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N LEU s 122 " --> pdb=" O ARG s 118 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 117 through 122' Processing helix chain 's' and resid 123 through 135 removed outlier: 4.561A pdb=" N VAL s 134 " --> pdb=" O LEU s 130 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N PHE s 135 " --> pdb=" O GLU s 131 " (cutoff:3.500A) Processing helix chain 's' and resid 159 through 167 removed outlier: 4.302A pdb=" N GLN s 163 " --> pdb=" O ASP s 159 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ASN s 164 " --> pdb=" O LYS s 160 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASN s 165 " --> pdb=" O ALA s 161 " (cutoff:3.500A) Processing helix chain 's' and resid 169 through 181 Processing helix chain 't' and resid 87 through 94 removed outlier: 4.060A pdb=" N VAL t 91 " --> pdb=" O ASN t 87 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LYS t 94 " --> pdb=" O LEU t 90 " (cutoff:3.500A) Processing helix chain 't' and resid 106 through 117 removed outlier: 3.561A pdb=" N TYR t 117 " --> pdb=" O TYR t 113 " (cutoff:3.500A) Processing helix chain 't' and resid 130 through 138 removed outlier: 4.032A pdb=" N ILE t 136 " --> pdb=" O GLU t 132 " (cutoff:3.500A) Processing helix chain 't' and resid 142 through 157 removed outlier: 3.577A pdb=" N LYS t 148 " --> pdb=" O LYS t 144 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LYS t 154 " --> pdb=" O ASP t 150 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ASN t 155 " --> pdb=" O GLU t 151 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ALA t 156 " --> pdb=" O ARG t 152 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N LYS t 157 " --> pdb=" O LYS t 153 " (cutoff:3.500A) Processing helix chain 't' and resid 159 through 169 removed outlier: 4.537A pdb=" N GLN t 165 " --> pdb=" O LEU t 161 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLN t 168 " --> pdb=" O GLU t 164 " (cutoff:3.500A) Processing helix chain 't' and resid 192 through 206 removed outlier: 3.891A pdb=" N GLU t 196 " --> pdb=" O GLY t 192 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS t 206 " --> pdb=" O ILE t 202 " (cutoff:3.500A) Processing helix chain 'c' and resid 21 through 36 Processing helix chain 'c' and resid 39 through 63 removed outlier: 3.856A pdb=" N VAL c 43 " --> pdb=" O ASN c 39 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL c 46 " --> pdb=" O GLU c 42 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N THR c 62 " --> pdb=" O ARG c 58 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LEU c 63 " --> pdb=" O GLU c 59 " (cutoff:3.500A) Processing helix chain 'c' and resid 67 through 85 removed outlier: 4.307A pdb=" N ASN c 75 " --> pdb=" O LEU c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 93 through 100 removed outlier: 3.936A pdb=" N ILE c 97 " --> pdb=" O LYS c 93 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU c 98 " --> pdb=" O LEU c 94 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY c 99 " --> pdb=" O ASP c 95 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU c 100 " --> pdb=" O TYR c 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 93 through 100' Processing helix chain 'c' and resid 101 through 109 removed outlier: 4.787A pdb=" N PHE c 105 " --> pdb=" O LYS c 101 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU c 106 " --> pdb=" O ILE c 102 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU c 107 " --> pdb=" O GLU c 103 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG c 108 " --> pdb=" O ASP c 104 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG c 109 " --> pdb=" O PHE c 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 101 through 109' Processing helix chain 'c' and resid 110 through 118 removed outlier: 3.629A pdb=" N LEU c 117 " --> pdb=" O GLN c 113 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY c 118 " --> pdb=" O VAL c 114 " (cutoff:3.500A) Processing helix chain 'c' and resid 122 through 133 removed outlier: 3.545A pdb=" N GLN c 132 " --> pdb=" O VAL c 128 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG c 133 " --> pdb=" O LEU c 129 " (cutoff:3.500A) Processing helix chain 'c' and resid 150 through 157 removed outlier: 4.728A pdb=" N LYS c 155 " --> pdb=" O LEU c 151 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N HIS c 156 " --> pdb=" O ASP c 152 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ILE c 157 " --> pdb=" O SER c 153 " (cutoff:3.500A) Processing helix chain 'c' and resid 171 through 180 removed outlier: 3.790A pdb=" N LYS c 179 " --> pdb=" O ARG c 175 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N LYS c 180 " --> pdb=" O LYS c 176 " (cutoff:3.500A) Processing helix chain 'n' and resid 47 through 53 removed outlier: 3.589A pdb=" N ILE n 51 " --> pdb=" O PRO n 47 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY n 53 " --> pdb=" O GLU n 49 " (cutoff:3.500A) Processing helix chain 'm' and resid 29 through 44 removed outlier: 4.639A pdb=" N LYS m 43 " --> pdb=" O LYS m 39 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N GLY m 44 " --> pdb=" O LEU m 40 " (cutoff:3.500A) Processing helix chain 'm' and resid 46 through 57 removed outlier: 3.580A pdb=" N ILE m 50 " --> pdb=" O THR m 46 " (cutoff:3.500A) Processing helix chain 'm' and resid 62 through 68 removed outlier: 3.597A pdb=" N VAL m 66 " --> pdb=" O GLN m 62 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY m 68 " --> pdb=" O ARG m 64 " (cutoff:3.500A) Processing helix chain 'm' and resid 70 through 79 removed outlier: 3.696A pdb=" N LYS m 78 " --> pdb=" O ILE m 74 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY m 79 " --> pdb=" O LEU m 75 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 106 removed outlier: 4.410A pdb=" N ARG m 104 " --> pdb=" O LYS m 100 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN m 105 " --> pdb=" O HIS m 101 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ARG m 106 " --> pdb=" O LEU m 102 " (cutoff:3.500A) Processing helix chain 'm' and resid 108 through 133 removed outlier: 3.612A pdb=" N LYS m 112 " --> pdb=" O ASP m 108 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N PHE m 113 " --> pdb=" O LYS m 109 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR m 131 " --> pdb=" O ARG m 127 " (cutoff:3.500A) Processing helix chain 'm' and resid 145 through 150 removed outlier: 3.645A pdb=" N LEU m 149 " --> pdb=" O THR m 145 " (cutoff:3.500A) removed outlier: 3.900A 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 57 through 63 removed outlier: 4.393A pdb=" N LYS i 61 " --> pdb=" O THR i 57 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL i 62 " --> pdb=" O GLY i 58 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LYS i 63 " --> pdb=" O GLY i 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 57 through 63' Processing helix chain 'i' and resid 64 through 69 removed outlier: 5.269A pdb=" N SER i 69 " --> pdb=" O ASP i 65 " (cutoff:3.500A) Processing helix chain 'i' and resid 70 through 89 removed outlier: 3.567A pdb=" N ALA i 74 " --> pdb=" O SER i 70 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU i 87 " --> pdb=" O GLN i 83 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU i 88 " --> pdb=" O ARG i 84 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLY i 89 " --> pdb=" O CYS i 85 " (cutoff:3.500A) Processing helix chain 'i' and resid 110 through 123 removed outlier: 4.504A pdb=" N SER i 114 " --> pdb=" O PRO i 110 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA i 115 " --> pdb=" O GLY i 111 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA i 120 " --> pdb=" O LEU i 116 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLY i 123 " --> pdb=" O LEU i 119 " (cutoff:3.500A) Processing helix chain 'y' and resid 56 through 63 removed outlier: 3.954A pdb=" N MET y 62 " --> pdb=" O ALA y 58 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY y 63 " --> pdb=" O ILE y 59 " (cutoff:3.500A) Processing helix chain 'y' and resid 64 through 77 removed outlier: 3.678A pdb=" N SER y 68 " --> pdb=" O GLU y 64 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP y 76 " --> pdb=" O LEU y 72 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY y 77 " --> pdb=" O ALA y 73 " (cutoff:3.500A) Processing helix chain 'f' and resid 5 through 21 removed outlier: 3.809A pdb=" N ASP f 9 " --> pdb=" O ASN f 5 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG f 20 " --> pdb=" O ASN f 16 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY f 21 " --> pdb=" O ALA f 17 " (cutoff:3.500A) Processing helix chain 'f' and resid 31 through 45 removed outlier: 4.075A pdb=" N VAL f 35 " --> pdb=" O SER f 31 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG f 36 " --> pdb=" O LYS f 32 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS f 44 " --> pdb=" O VAL f 40 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY f 45 " --> pdb=" O MET f 41 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 94 removed outlier: 3.559A pdb=" N LEU f 86 " --> pdb=" O GLN f 82 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N GLU f 87 " --> pdb=" O LEU f 83 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N LYS f 88 " --> pdb=" O LYS f 84 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN f 92 " --> pdb=" O LYS f 88 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU f 94 " --> pdb=" O GLN f 90 " (cutoff:3.500A) Processing helix chain 'f' and resid 112 through 120 removed outlier: 3.566A pdb=" N ARG f 117 " --> pdb=" O HIS f 113 " (cutoff:3.500A) Processing helix chain 'j' and resid 9 through 25 removed outlier: 4.219A pdb=" N ASP j 19 " --> pdb=" O SER j 15 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N TRP j 22 " --> pdb=" O ARG j 18 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N HIS j 23 " --> pdb=" O ASP j 19 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASP j 24 " --> pdb=" O GLN j 20 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N LYS j 25 " --> pdb=" O LYS j 21 " (cutoff:3.500A) Processing helix chain 'j' and resid 26 through 31 Processing helix chain 'j' and resid 33 through 39 removed outlier: 3.832A pdb=" N LYS j 37 " --> pdb=" O GLY j 33 " (cutoff:3.500A) Processing helix chain 'j' and resid 89 through 94 removed outlier: 4.601A pdb=" N PHE j 93 " --> pdb=" O GLY j 89 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ILE j 94 " --> pdb=" O CYS j 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 89 through 94' Processing helix chain 'j' and resid 129 through 136 removed outlier: 3.724A pdb=" N GLY j 136 " --> pdb=" O ALA j 132 " (cutoff:3.500A) Processing helix chain 'z' and resid 36 through 49 removed outlier: 3.500A pdb=" N LYS z 49 " --> pdb=" O ALA z 45 " (cutoff:3.500A) Processing helix chain 'z' and resid 78 through 86 Processing helix chain 'z' and resid 87 through 95 removed outlier: 4.097A pdb=" N HIS z 94 " --> pdb=" O ARG z 90 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY z 95 " --> pdb=" O LEU z 91 " (cutoff:3.500A) Processing helix chain 'z' and resid 103 through 118 removed outlier: 4.923A pdb=" N ARG z 107 " --> pdb=" O SER z 103 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS z 115 " --> pdb=" O LYS z 111 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LYS z 116 " --> pdb=" O ASN z 112 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL z 117 " --> pdb=" O ARG z 113 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ARG z 118 " --> pdb=" O MET z 114 " (cutoff:3.500A) Processing helix chain 'z' and resid 120 through 126 removed outlier: 3.979A pdb=" N ASN z 124 " --> pdb=" O THR z 120 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLY z 126 " --> pdb=" O LYS z 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 11 through 19 removed outlier: 4.463A pdb=" N LYS R 18 " --> pdb=" O GLU R 14 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N HIS R 19 " --> pdb=" O GLU R 15 " (cutoff:3.500A) Processing helix chain 'T' and resid 10 through 16 removed outlier: 5.008A pdb=" N GLY T 14 " --> pdb=" O GLY T 10 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN T 15 " --> pdb=" O LYS T 11 " (cutoff:3.500A) Processing helix chain 'T' and resid 30 through 42 removed outlier: 3.833A pdb=" N ARG T 34 " --> pdb=" O GLY T 30 " (cutoff:3.500A) Processing helix chain 'w' and resid 6 through 20 removed outlier: 4.333A pdb=" N ALA w 13 " --> pdb=" O VAL w 9 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG w 14 " --> pdb=" O LYS w 10 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LYS w 19 " --> pdb=" O VAL w 15 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TYR w 20 " --> pdb=" O ILE w 16 " (cutoff:3.500A) Processing helix chain 'w' and resid 27 through 39 removed outlier: 3.574A pdb=" N ASN w 31 " --> pdb=" O ASP w 27 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG w 33 " --> pdb=" O HIS w 29 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLU w 36 " --> pdb=" O LYS w 32 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLU w 37 " --> pdb=" O ARG w 33 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE w 38 " --> pdb=" O VAL w 34 " (cutoff:3.500A) Processing helix chain 'w' and resid 43 through 62 removed outlier: 3.996A pdb=" N ARG w 47 " --> pdb=" O SER w 43 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLN w 62 " --> pdb=" O MET w 58 " (cutoff:3.500A) Processing helix chain 'w' and resid 70 through 80 removed outlier: 4.602A pdb=" N GLN w 74 " --> pdb=" O SER w 70 " (cutoff:3.500A) Processing helix chain 'w' and resid 99 through 110 removed outlier: 3.913A pdb=" N LYS w 103 " --> pdb=" O ASP w 99 " (cutoff:3.500A) Processing helix chain 'g' and resid 47 through 53 removed outlier: 4.249A pdb=" N LEU g 51 " --> pdb=" O LEU g 47 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU g 52 " --> pdb=" O GLN g 48 " (cutoff:3.500A) Processing helix chain 'g' and resid 59 through 64 removed outlier: 3.934A pdb=" N PHE g 63 " --> pdb=" O GLY g 59 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA g 64 " --> pdb=" O LYS g 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 59 through 64' Processing helix chain 'g' and resid 76 through 99 removed outlier: 3.816A pdb=" N GLN g 80 " --> pdb=" O GLY g 76 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN g 86 " --> pdb=" O TYR g 82 " (cutoff:3.500A) Processing helix chain 'g' and resid 101 through 116 removed outlier: 3.506A pdb=" N LYS g 105 " --> pdb=" O ASP g 101 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN g 114 " --> pdb=" O ASP g 110 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N TYR g 115 " --> pdb=" O ILE g 111 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP g 116 " --> pdb=" O LEU g 112 " (cutoff:3.500A) Processing helix chain 'b' and resid 6 through 29 Processing helix chain 'b' and resid 54 through 60 removed outlier: 3.975A pdb=" N VAL b 58 " --> pdb=" O ARG b 54 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLY b 60 " --> pdb=" O GLN b 56 " (cutoff:3.500A) Processing helix chain 'b' and resid 63 through 78 removed outlier: 3.580A pdb=" N ARG b 67 " --> pdb=" O GLY b 63 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE b 77 " --> pdb=" O VAL b 73 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY b 78 " --> pdb=" O GLN b 74 " (cutoff:3.500A) Processing helix chain 'b' and resid 93 through 98 removed outlier: 3.964A pdb=" N CYS b 97 " --> pdb=" O THR b 93 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ALA b 98 " --> pdb=" O ARG b 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 93 through 98' Processing helix chain 'b' and resid 99 through 112 Processing helix chain 'b' and resid 114 through 130 removed outlier: 3.710A pdb=" N GLY b 130 " --> pdb=" O ILE b 126 " (cutoff:3.500A) Processing helix chain 'b' and resid 161 through 167 removed outlier: 4.939A pdb=" N ASN b 165 " --> pdb=" O GLY b 161 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TYR b 166 " --> pdb=" O ASP b 162 " (cutoff:3.500A) Processing helix chain 'e' and resid 32 through 40 removed outlier: 4.206A pdb=" N GLN e 36 " --> pdb=" O ASP e 32 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ASP e 37 " --> pdb=" O ILE e 33 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N TYR e 38 " --> pdb=" O SER e 34 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ALA e 40 " --> pdb=" O GLN e 36 " (cutoff:3.500A) Processing helix chain 'e' and resid 61 through 67 removed outlier: 5.041A pdb=" N GLN e 65 " --> pdb=" O PHE e 61 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N CYS e 66 " --> pdb=" O ARG e 62 " (cutoff:3.500A) Proline residue: e 67 - end of helix No H-bonds generated for 'chain 'e' and resid 61 through 67' Processing helix chain 'e' and resid 68 through 78 removed outlier: 3.671A pdb=" N MET e 76 " --> pdb=" O LEU e 72 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N MET e 77 " --> pdb=" O THR e 73 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N MET e 78 " --> pdb=" O ASN e 74 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 104 removed outlier: 4.285A pdb=" N THR e 89 " --> pdb=" O LYS e 85 " (cutoff:3.500A) Processing helix chain 'e' and resid 107 through 120 removed outlier: 3.630A pdb=" N VAL e 111 " --> pdb=" O ASN e 107 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY e 120 " --> pdb=" O ILE e 116 " (cutoff:3.500A) Processing helix chain 'e' and resid 142 through 165 removed outlier: 4.320A pdb=" N GLY e 157 " --> pdb=" O LEU e 153 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA e 158 " --> pdb=" O LEU e 154 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG e 159 " --> pdb=" O CYS e 155 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLU e 160 " --> pdb=" O THR e 156 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ARG e 164 " --> pdb=" O GLU e 160 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ASN e 165 " --> pdb=" O ALA e 161 " (cutoff:3.500A) Processing helix chain 'e' and resid 168 through 183 removed outlier: 3.630A pdb=" N CYS e 172 " --> pdb=" O THR e 168 " (cutoff:3.500A) Processing helix chain 'e' and resid 187 through 204 removed outlier: 4.157A pdb=" N ALA e 200 " --> pdb=" O LEU e 196 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ARG e 204 " --> pdb=" O ALA e 200 " (cutoff:3.500A) Processing helix chain 'u' and resid 4 through 19 Processing helix chain 'u' and resid 41 through 56 removed outlier: 3.515A pdb=" N VAL u 45 " --> pdb=" O PRO u 41 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ARG u 55 " --> pdb=" O SER u 51 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY u 56 " --> pdb=" O LEU u 52 " (cutoff:3.500A) Processing helix chain 'u' and resid 72 through 83 removed outlier: 3.508A pdb=" N LEU u 83 " --> pdb=" O LEU u 79 " (cutoff:3.500A) Processing helix chain 'v' and resid 15 through 29 removed outlier: 5.204A pdb=" N VAL v 21 " --> pdb=" O ALA v 17 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU v 22 " --> pdb=" O LEU v 18 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS v 23 " --> pdb=" O GLN v 19 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N THR v 24 " --> pdb=" O GLU v 20 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ILE v 27 " --> pdb=" O LYS v 23 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N HIS v 28 " --> pdb=" O THR v 24 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASP v 29 " --> pdb=" O ALA v 25 " (cutoff:3.500A) Processing helix chain 'v' and resid 34 through 45 removed outlier: 3.721A pdb=" N ALA v 38 " --> pdb=" O GLY v 34 " (cutoff:3.500A) Processing helix chain 'v' and resid 63 through 73 removed outlier: 4.110A pdb=" N CYS v 69 " --> pdb=" O VAL v 65 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ALA v 70 " --> pdb=" O GLU v 66 " (cutoff:3.500A) Processing helix chain 'v' and resid 81 through 90 removed outlier: 3.928A pdb=" N LEU v 85 " --> pdb=" O ASP v 81 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N GLY v 90 " --> pdb=" O GLY v 86 " (cutoff:3.500A) Processing helix chain 'v' and resid 120 through 126 removed outlier: 3.924A pdb=" N ILE v 124 " --> pdb=" O ALA v 120 " (cutoff:3.500A) Processing helix chain 'o' and resid 21 through 28 removed outlier: 5.818A pdb=" N ASP o 27 " --> pdb=" O ASP o 23 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N MET o 28 " --> pdb=" O GLN o 24 " (cutoff:3.500A) Processing helix chain 'o' and resid 29 through 37 removed outlier: 4.486A pdb=" N GLN o 35 " --> pdb=" O GLU o 31 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU o 36 " --> pdb=" O GLN o 32 " (cutoff:3.500A) Processing helix chain 'o' and resid 38 through 48 Processing helix chain 'o' and resid 50 through 67 removed outlier: 3.624A pdb=" N GLU o 66 " --> pdb=" O LYS o 62 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ALA o 67 " --> pdb=" O ALA o 63 " (cutoff:3.500A) Processing helix chain 'o' and resid 115 through 121 removed outlier: 4.516A pdb=" N PHE o 119 " --> pdb=" O TYR o 115 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N SER o 120 " --> pdb=" O LEU o 116 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ILE o 121 " --> pdb=" O GLY o 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 115 through 121' Processing helix chain 'k' and resid 25 through 32 removed outlier: 4.499A pdb=" N THR k 31 " --> pdb=" O ALA k 27 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ALA k 32 " --> pdb=" O PHE k 28 " (cutoff:3.500A) Processing helix chain 'k' and resid 37 through 49 removed outlier: 4.162A pdb=" N VAL k 43 " --> pdb=" O ARG k 39 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP k 49 " --> pdb=" O LEU k 45 " (cutoff:3.500A) Processing helix chain 'k' and resid 60 through 74 removed outlier: 3.531A pdb=" N VAL k 64 " --> pdb=" O THR k 60 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASN k 73 " --> pdb=" O THR k 69 " (cutoff:3.500A) Proline residue: k 74 - end of helix Processing helix chain 'k' and resid 100 through 118 removed outlier: 4.339A pdb=" N ASP k 104 " --> pdb=" O ALA k 100 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN k 105 " --> pdb=" O ASN k 101 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG k 118 " --> pdb=" O LEU k 114 " (cutoff:3.500A) Processing helix chain 'k' and resid 119 through 128 removed outlier: 3.991A pdb=" N LEU k 123 " --> pdb=" O ALA k 119 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY k 128 " --> pdb=" O ARG k 124 " (cutoff:3.500A) Processing helix chain 'x' and resid 5 through 10 removed outlier: 4.052A pdb=" N VAL x 9 " --> pdb=" O THR x 5 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ASN x 10 " --> pdb=" O VAL x 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 5 through 10' Processing helix chain 'x' and resid 11 through 26 removed outlier: 4.509A pdb=" N VAL x 15 " --> pdb=" O GLN x 11 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ARG x 16 " --> pdb=" O GLN x 12 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N GLY x 26 " --> pdb=" O LEU x 22 " (cutoff:3.500A) Processing helix chain 'x' and resid 51 through 67 Processing helix chain 'x' and resid 71 through 80 removed outlier: 3.746A pdb=" N LYS x 77 " --> pdb=" O GLY x 73 " (cutoff:3.500A) Processing helix chain 'x' and resid 96 through 111 removed outlier: 3.788A pdb=" N ALA x 100 " --> pdb=" O SER x 96 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU x 110 " --> pdb=" O ALA x 106 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LYS x 111 " --> pdb=" O LEU x 107 " (cutoff:3.500A) Processing helix chain 'x' and resid 124 through 142 removed outlier: 3.613A pdb=" N LEU x 131 " --> pdb=" O GLY x 127 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE x 134 " --> pdb=" O ASP x 130 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA x 140 " --> pdb=" O GLY x 136 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA x 141 " --> pdb=" O GLN x 137 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ASN x 142 " --> pdb=" O VAL x 138 " (cutoff:3.500A) Processing helix chain 'h' and resid 28 through 47 removed outlier: 4.062A pdb=" N LEU h 32 " --> pdb=" O ASN h 28 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS h 46 " --> pdb=" O GLY h 42 " (cutoff:3.500A) Processing helix chain 'h' and resid 94 through 106 removed outlier: 3.726A pdb=" N VAL h 98 " --> pdb=" O PRO h 94 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LYS h 99 " --> pdb=" O SER h 95 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N GLN h 100 " --> pdb=" O GLU h 96 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ILE h 101 " --> pdb=" O ILE h 97 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR h 102 " --> pdb=" O VAL h 98 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N SER h 103 " --> pdb=" O LYS h 99 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ILE h 104 " --> pdb=" O GLN h 100 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N SER h 105 " --> pdb=" O ILE h 101 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ILE h 106 " --> pdb=" O THR h 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 94 through 106' Processing helix chain 'P' and resid 53 through 66 removed outlier: 5.388A pdb=" N LYS P 57 " --> pdb=" O ALA P 53 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL P 62 " --> pdb=" O LEU P 58 " (cutoff:3.500A) Proline residue: P 63 - end of helix removed outlier: 5.598A pdb=" N LYS P 66 " --> pdb=" O VAL P 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 77 removed outlier: 3.909A pdb=" N VAL P 73 " --> pdb=" O THR P 69 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N SER P 74 " --> pdb=" O PRO P 70 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLU P 75 " --> pdb=" O ALA P 71 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ARG P 76 " --> pdb=" O VAL P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 80 through 95 removed outlier: 3.509A pdb=" N ALA P 84 " --> pdb=" O ARG P 80 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU P 92 " --> pdb=" O LEU P 88 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N SER P 93 " --> pdb=" O GLN P 89 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS P 94 " --> pdb=" O GLU P 90 " (cutoff:3.500A) Processing helix chain 'l' and resid 4 through 9 removed outlier: 7.417A pdb=" N TRP l 8 " --> pdb=" O GLN l 4 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N SER l 9 " --> pdb=" O GLN l 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 4 through 9' Processing helix chain 'l' and resid 15 through 20 removed outlier: 3.684A pdb=" N ARG l 19 " --> pdb=" O GLY l 15 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N SER l 20 " --> pdb=" O GLN l 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 15 through 20' Processing helix chain 'l' and resid 39 through 47 removed outlier: 3.736A pdb=" N TYR l 46 " --> pdb=" O CYS l 42 " (cutoff:3.500A) Processing helix chain 'U' and resid 100 through 107 removed outlier: 4.840A pdb=" N LYS U 104 " --> pdb=" O LEU U 100 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR U 105 " --> pdb=" O ALA U 101 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N TYR U 106 " --> pdb=" O VAL U 102 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LYS U 107 " --> pdb=" O LEU U 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 100 through 107' Processing helix chain 'B' and resid 196 through 213 removed outlier: 4.794A pdb=" N GLU B 201 " --> pdb=" O PRO B 197 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LYS B 202 " --> pdb=" O ASP B 198 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS B 213 " --> pdb=" O LYS B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 251 removed outlier: 4.570A pdb=" N ALA B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL B 247 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP B 251 " --> pdb=" O VAL B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 464 removed outlier: 4.213A pdb=" N ILE B 464 " --> pdb=" O LYS B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 722 removed outlier: 3.969A pdb=" N ILE B 717 " --> pdb=" O SER B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 744 removed outlier: 4.276A pdb=" N LEU B 737 " --> pdb=" O GLN B 733 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS B 744 " --> pdb=" O SER B 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 22 removed outlier: 4.551A pdb=" N ALA A 11 " --> pdb=" O ARG A 7 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LEU A 12 " --> pdb=" O PRO A 8 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS A 13 " --> pdb=" O GLU A 9 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU A 17 " --> pdb=" O LYS A 13 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU A 20 " --> pdb=" O ASN A 16 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL A 21 " --> pdb=" O GLU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 38 removed outlier: 4.430A pdb=" N ALA A 27 " --> pdb=" O LYS A 23 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A 31 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N MET A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER A 37 " --> pdb=" O ASP A 33 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N LYS A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 62 removed outlier: 4.817A pdb=" N GLU A 48 " --> pdb=" O GLN A 44 " (cutoff:3.500A) Proline residue: A 49 - end of helix removed outlier: 3.610A pdb=" N LYS A 53 " --> pdb=" O PRO A 49 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASP A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.768A pdb=" N ALA A 67 " --> pdb=" O LYS A 63 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS A 68 " --> pdb=" O SER A 64 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A 69 " --> pdb=" O HIS A 65 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLN A 79 " --> pdb=" O LYS A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 116 removed outlier: 4.015A pdb=" N LEU A 86 " --> pdb=" O ASN A 82 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS A 100 " --> pdb=" O MET A 96 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 113 " --> pdb=" O GLN A 109 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A 116 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.596A pdb=" N VAL A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A 128 " --> pdb=" O PRO A 124 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 131 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 146 removed outlier: 3.530A pdb=" N THR A 141 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG A 143 " --> pdb=" O ASP A 139 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 165 removed outlier: 3.884A pdb=" N CYS A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 164 " --> pdb=" O CYS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 189 removed outlier: 3.703A pdb=" N GLN A 179 " --> pdb=" O HIS A 175 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS A 183 " --> pdb=" O GLN A 179 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 211 removed outlier: 3.637A pdb=" N PHE A 194 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN A 200 " --> pdb=" O LYS A 196 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN A 207 " --> pdb=" O MET A 203 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 244 removed outlier: 3.594A pdb=" N GLN A 226 " --> pdb=" O ASN A 222 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 235 " --> pdb=" O GLU A 231 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN A 236 " --> pdb=" O THR A 232 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER A 242 " --> pdb=" O ASP A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 264 removed outlier: 3.686A pdb=" N GLY A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 259 " --> pdb=" O ASP A 255 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER A 261 " --> pdb=" O HIS A 257 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N LYS A 264 " --> pdb=" O PHE A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 287 removed outlier: 3.621A pdb=" N MET A 272 " --> pdb=" O LYS A 268 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASN A 274 " --> pdb=" O GLN A 270 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A 280 " --> pdb=" O TYR A 276 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY A 287 " --> pdb=" O PHE A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 308 removed outlier: 4.273A pdb=" N HIS A 292 " --> pdb=" O ASN A 288 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N HIS A 301 " --> pdb=" O HIS A 297 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ARG A 304 " --> pdb=" O TYR A 300 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLU A 305 " --> pdb=" O HIS A 301 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N MET A 306 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ARG A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS A 308 " --> pdb=" O ARG A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 329 removed outlier: 4.271A pdb=" N MET A 315 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR A 320 " --> pdb=" O GLN A 316 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ARG A 321 " --> pdb=" O ARG A 317 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL A 322 " --> pdb=" O MET A 318 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 324 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE A 329 " --> pdb=" O ALA A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 343 removed outlier: 4.717A pdb=" N ALA A 339 " --> pdb=" O ARG A 335 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASP A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 360 removed outlier: 3.946A pdb=" N LYS A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLN A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ARG A 353 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ARG A 354 " --> pdb=" O GLU A 350 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU A 355 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU A 359 " --> pdb=" O LEU A 355 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY A 360 " --> pdb=" O ALA A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 378 removed outlier: 3.514A pdb=" N ASN A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ASP A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N MET A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL A 375 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N PHE A 377 " --> pdb=" O ASP A 373 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN A 378 " --> pdb=" O MET A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 384 removed outlier: 3.724A pdb=" N VAL A 383 " --> pdb=" O VAL A 379 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 379 through 384' Processing helix chain 'A' and resid 385 through 394 removed outlier: 4.895A pdb=" N ASP A 389 " --> pdb=" O PRO A 385 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N LEU A 390 " --> pdb=" O GLU A 386 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N TYR A 391 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ASN A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 418 removed outlier: 5.891A pdb=" N CYS A 404 " --> pdb=" O PRO A 400 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLU A 405 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR A 408 " --> pdb=" O CYS A 404 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLN A 417 " --> pdb=" O TRP A 413 " (cutoff:3.500A) Proline residue: A 418 - end of helix Processing helix chain 'A' and resid 424 through 447 removed outlier: 4.081A pdb=" N VAL A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) Proline residue: A 429 - end of helix removed outlier: 4.613A pdb=" N GLN A 432 " --> pdb=" O VAL A 428 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN A 434 " --> pdb=" O GLN A 430 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU A 437 " --> pdb=" O ASN A 433 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLN A 445 " --> pdb=" O GLN A 441 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE A 446 " --> pdb=" O GLN A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 460 removed outlier: 3.706A pdb=" N LEU A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER A 457 " --> pdb=" O SER A 453 " (cutoff:3.500A) Proline residue: A 460 - end of helix Processing helix chain 'A' and resid 463 through 477 removed outlier: 3.596A pdb=" N ARG A 469 " --> pdb=" O PHE A 465 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 472 " --> pdb=" O GLU A 468 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP A 473 " --> pdb=" O ARG A 469 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 475 " --> pdb=" O ILE A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 522 removed outlier: 4.274A pdb=" N ARG A 520 " --> pdb=" O SER A 516 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ASN A 521 " --> pdb=" O GLU A 517 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLN A 522 " --> pdb=" O GLN A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 538 removed outlier: 3.515A pdb=" N LEU A 530 " --> pdb=" O MET A 526 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA A 531 " --> pdb=" O SER A 527 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU A 535 " --> pdb=" O ALA A 531 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL A 536 " --> pdb=" O LYS A 532 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE A 537 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LYS A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 566 removed outlier: 3.618A pdb=" N LEU A 543 " --> pdb=" O PRO A 539 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN A 544 " --> pdb=" O ALA A 540 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU A 545 " --> pdb=" O HIS A 541 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 558 " --> pdb=" O VAL A 554 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ARG A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LYS A 563 " --> pdb=" O LYS A 559 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLU A 564 " --> pdb=" O ASN A 560 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N HIS A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLN A 566 " --> pdb=" O ARG A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 601 removed outlier: 3.603A pdb=" N GLU A 576 " --> pdb=" O ARG A 572 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU A 580 " --> pdb=" O GLU A 576 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 592 " --> pdb=" O GLN A 588 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG A 597 " --> pdb=" O GLU A 593 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU A 598 " --> pdb=" O LEU A 594 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU A 601 " --> pdb=" O ARG A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 640 removed outlier: 3.502A pdb=" N GLU A 615 " --> pdb=" O ARG A 611 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG A 623 " --> pdb=" O ARG A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 685 Proline residue: A 666 - end of helix removed outlier: 4.535A pdb=" N GLN A 685 " --> pdb=" O LYS A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 725 Processing helix chain 'C' and resid 51 through 74 removed outlier: 3.867A pdb=" N ARG C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE C 57 " --> pdb=" O LYS C 53 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN C 62 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LEU C 63 " --> pdb=" O GLU C 59 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS C 72 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE C 73 " --> pdb=" O ASN C 69 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 94 removed outlier: 3.524A pdb=" N CYS C 79 " --> pdb=" O ASP C 75 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE C 83 " --> pdb=" O CYS C 79 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU C 84 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LYS C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA C 93 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LYS C 94 " --> pdb=" O TYR C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 124 removed outlier: 4.308A pdb=" N ILE C 107 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE C 109 " --> pdb=" O PHE C 105 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASP C 123 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS C 124 " --> pdb=" O LEU C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 149 removed outlier: 4.269A pdb=" N SER C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN C 143 " --> pdb=" O SER C 139 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LYS C 147 " --> pdb=" O GLN C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 341 removed outlier: 3.838A pdb=" N VAL C 329 " --> pdb=" O THR C 325 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE C 330 " --> pdb=" O HIS C 326 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LYS C 331 " --> pdb=" O ALA C 327 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLN C 338 " --> pdb=" O ASN C 334 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA C 339 " --> pdb=" O GLU C 335 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG C 340 " --> pdb=" O ILE C 336 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY C 341 " --> pdb=" O LEU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 363 removed outlier: 4.713A pdb=" N ILE C 351 " --> pdb=" O ARG C 347 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU C 352 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU C 354 " --> pdb=" O GLN C 350 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU C 357 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN C 359 " --> pdb=" O GLN C 355 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N GLU C 363 " --> pdb=" O GLN C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 387 removed outlier: 3.832A pdb=" N ILE C 371 " --> pdb=" O GLY C 367 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS C 373 " --> pdb=" O GLY C 369 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS C 375 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE C 376 " --> pdb=" O VAL C 372 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASN C 377 " --> pdb=" O LYS C 373 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE C 378 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE C 379 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP C 384 " --> pdb=" O ALA C 380 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ASN C 386 " --> pdb=" O LEU C 382 " (cutoff:3.500A) Proline residue: C 387 - end of helix Processing helix chain 'C' and resid 394 through 416 removed outlier: 4.339A pdb=" N LYS C 400 " --> pdb=" O GLU C 396 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU C 402 " --> pdb=" O TRP C 398 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASP C 403 " --> pdb=" O GLY C 399 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU C 408 " --> pdb=" O CYS C 404 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP C 410 " --> pdb=" O ASN C 406 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE C 411 " --> pdb=" O GLU C 407 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE C 413 " --> pdb=" O MET C 409 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA C 414 " --> pdb=" O ASP C 410 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN C 415 " --> pdb=" O ILE C 411 " (cutoff:3.500A) Proline residue: C 416 - end of helix Processing helix chain 'C' and resid 443 through 463 removed outlier: 4.737A pdb=" N LEU C 447 " --> pdb=" O CYS C 443 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL C 448 " --> pdb=" O ILE C 444 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU C 453 " --> pdb=" O GLU C 449 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE C 458 " --> pdb=" O GLU C 454 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET C 459 " --> pdb=" O PHE C 455 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN C 460 " --> pdb=" O THR C 456 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASN C 461 " --> pdb=" O LYS C 457 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR C 462 " --> pdb=" O ILE C 458 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ASP C 463 " --> pdb=" O MET C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 491 removed outlier: 3.995A pdb=" N GLU C 471 " --> pdb=" O GLN C 467 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS C 474 " --> pdb=" O VAL C 470 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ASP C 475 " --> pdb=" O GLU C 471 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N GLU C 476 " --> pdb=" O HIS C 472 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ALA C 477 " --> pdb=" O LEU C 473 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N GLN C 478 " --> pdb=" O LYS C 474 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLU C 491 " --> pdb=" O GLN C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 511 removed outlier: 3.748A pdb=" N VAL C 499 " --> pdb=" O THR C 495 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG C 501 " --> pdb=" O GLU C 497 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE C 502 " --> pdb=" O GLU C 498 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU C 505 " --> pdb=" O ARG C 501 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE C 507 " --> pdb=" O TYR C 503 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS C 509 " --> pdb=" O LEU C 505 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR C 510 " --> pdb=" O ARG C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 559 removed outlier: 3.939A pdb=" N MET C 548 " --> pdb=" O SER C 544 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU C 549 " --> pdb=" O ALA C 545 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS C 553 " --> pdb=" O GLU C 549 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR C 554 " --> pdb=" O ARG C 550 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE C 555 " --> pdb=" O LEU C 551 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS C 558 " --> pdb=" O TYR C 554 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASP C 559 " --> pdb=" O ILE C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 580 removed outlier: 4.344A pdb=" N ARG C 565 " --> pdb=" O THR C 561 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR C 566 " --> pdb=" O ASP C 562 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA C 568 " --> pdb=" O ILE C 564 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N HIS C 572 " --> pdb=" O ALA C 568 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N SER C 580 " --> pdb=" O HIS C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 593 removed outlier: 5.536A pdb=" N ALA C 585 " --> pdb=" O ARG C 581 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET C 589 " --> pdb=" O ALA C 585 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS C 593 " --> pdb=" O MET C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 602 removed outlier: 5.945A pdb=" N GLN C 599 " --> pdb=" O GLN C 595 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N HIS C 600 " --> pdb=" O ASP C 596 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ALA C 601 " --> pdb=" O ASN C 597 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ASP C 602 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 624 removed outlier: 4.500A pdb=" N LEU C 608 " --> pdb=" O PRO C 604 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN C 623 " --> pdb=" O CYS C 619 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY C 624 " --> pdb=" O ALA C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 638 removed outlier: 4.180A pdb=" N HIS C 630 " --> pdb=" O THR C 626 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN C 631 " --> pdb=" O LYS C 627 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA C 632 " --> pdb=" O ASP C 628 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ASP C 635 " --> pdb=" O ASN C 631 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ILE C 636 " --> pdb=" O ALA C 632 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLN C 637 " --> pdb=" O LEU C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 647 removed outlier: 4.140A pdb=" N LEU C 645 " --> pdb=" O ARG C 641 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU C 646 " --> pdb=" O ALA C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 670 removed outlier: 4.483A pdb=" N ARG C 667 " --> pdb=" O GLU C 663 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG C 668 " --> pdb=" O LYS C 664 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG C 669 " --> pdb=" O VAL C 665 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN C 670 " --> pdb=" O GLU C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 678 through 702 removed outlier: 3.759A pdb=" N LEU C 687 " --> pdb=" O GLU C 683 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE C 695 " --> pdb=" O MET C 691 " (cutoff:3.500A) Proline residue: C 696 - end of helix removed outlier: 3.896A pdb=" N ALA C 699 " --> pdb=" O ILE C 695 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS C 701 " --> pdb=" O TYR C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 711 through 724 removed outlier: 3.504A pdb=" N HIS C 715 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG C 723 " --> pdb=" O ARG C 719 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLN C 724 " --> pdb=" O VAL C 720 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 747 removed outlier: 3.530A pdb=" N HIS C 736 " --> pdb=" O SER C 732 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL C 737 " --> pdb=" O MET C 733 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA C 743 " --> pdb=" O ALA C 739 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS C 745 " --> pdb=" O SER C 741 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY C 747 " --> pdb=" O ALA C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 757 removed outlier: 3.718A pdb=" N CYS C 752 " --> pdb=" O ASP C 748 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE C 756 " --> pdb=" O CYS C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 765 removed outlier: 5.981A pdb=" N ASN C 762 " --> pdb=" O ASN C 758 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLY C 763 " --> pdb=" O GLU C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 800 removed outlier: 4.349A pdb=" N VAL C 775 " --> pdb=" O GLU C 771 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU C 779 " --> pdb=" O VAL C 775 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL C 780 " --> pdb=" O ARG C 776 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU C 786 " --> pdb=" O LYS C 782 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR C 791 " --> pdb=" O SER C 787 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER C 796 " --> pdb=" O LEU C 792 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N SER C 797 " --> pdb=" O PHE C 793 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL C 798 " --> pdb=" O THR C 794 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR C 799 " --> pdb=" O TYR C 795 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ASP C 800 " --> pdb=" O SER C 796 " (cutoff:3.500A) Processing helix chain 'C' and resid 803 through 812 removed outlier: 3.951A pdb=" N PHE C 811 " --> pdb=" O LEU C 807 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU C 812 " --> pdb=" O SER C 808 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 829 Processing helix chain 'C' and resid 850 through 878 removed outlier: 3.653A pdb=" N LEU C 855 " --> pdb=" O ALA C 851 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA C 856 " --> pdb=" O GLN C 852 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLU C 861 " --> pdb=" O LEU C 857 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL C 873 " --> pdb=" O ASN C 869 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE C 874 " --> pdb=" O ASN C 870 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP C 875 " --> pdb=" O GLU C 871 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS C 876 " --> pdb=" O ARG C 872 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 15 removed outlier: 3.586A pdb=" N ALA E 11 " --> pdb=" O THR E 7 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N HIS E 12 " --> pdb=" O THR E 8 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE E 13 " --> pdb=" O ARG E 9 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU E 14 " --> pdb=" O ILE E 10 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ASP E 15 " --> pdb=" O ALA E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 30 removed outlier: 4.836A pdb=" N PHE E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) Proline residue: E 21 - end of helix removed outlier: 3.929A pdb=" N PHE E 25 " --> pdb=" O PRO E 21 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU E 26 " --> pdb=" O LEU E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 49 removed outlier: 4.004A pdb=" N GLN E 39 " --> pdb=" O LYS E 35 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP E 43 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU E 44 " --> pdb=" O GLY E 40 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP E 47 " --> pdb=" O ASP E 43 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASN E 49 " --> pdb=" O LEU E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 62 removed outlier: 3.660A pdb=" N ASP E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR E 58 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS E 59 " --> pdb=" O MET E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 90 removed outlier: 4.244A pdb=" N ARG E 71 " --> pdb=" O PRO E 67 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR E 76 " --> pdb=" O GLU E 72 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL E 78 " --> pdb=" O ARG E 74 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU E 81 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN E 83 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 3.588A 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 99 through 104 removed outlier: 5.198A pdb=" N GLN E 103 " --> pdb=" O GLU E 99 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET E 104 " --> pdb=" O THR E 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 99 through 104' Processing helix chain 'E' and resid 110 through 121 removed outlier: 3.651A pdb=" N LYS E 120 " --> pdb=" O TYR E 116 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N HIS E 121 " --> pdb=" O LEU E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 142 removed outlier: 3.920A pdb=" N LEU E 128 " --> pdb=" O ARG E 124 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP E 129 " --> pdb=" O GLN E 125 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR E 130 " --> pdb=" O GLU E 126 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE E 137 " --> pdb=" O ARG E 133 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N CYS E 141 " --> pdb=" O PHE E 137 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY E 142 " --> pdb=" O GLN E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 158 removed outlier: 4.183A pdb=" N ALA E 148 " --> pdb=" O TYR E 144 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU E 149 " --> pdb=" O SER E 145 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N TYR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU E 151 " --> pdb=" O ALA E 147 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR E 152 " --> pdb=" O ALA E 148 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU E 157 " --> pdb=" O PHE E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 178 removed outlier: 3.575A pdb=" N ALA E 174 " --> pdb=" O TRP E 170 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE E 177 " --> pdb=" O LEU E 173 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU E 178 " --> pdb=" O ALA E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 199 removed outlier: 3.516A pdb=" N GLU E 187 " --> pdb=" O ASP E 183 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU E 194 " --> pdb=" O THR E 190 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP E 197 " --> pdb=" O LYS E 193 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASN E 199 " --> pdb=" O THR E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 222 removed outlier: 3.771A pdb=" N TRP E 213 " --> pdb=" O GLN E 209 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU E 214 " --> pdb=" O GLN E 210 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE E 215 " --> pdb=" O ARG E 211 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N HIS E 216 " --> pdb=" O THR E 212 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU E 219 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE E 220 " --> pdb=" O HIS E 216 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL E 221 " --> pdb=" O TRP E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 235 removed outlier: 4.757A pdb=" N ASN E 231 " --> pdb=" O LYS E 227 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ASP E 234 " --> pdb=" O ASP E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 249 removed outlier: 3.759A pdb=" N ALA E 245 " --> pdb=" O GLN E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 264 removed outlier: 4.782A pdb=" N TYR E 256 " --> pdb=" O HIS E 252 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL E 261 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE E 262 " --> pdb=" O THR E 258 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR E 263 " --> pdb=" O THR E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 285 removed outlier: 4.899A pdb=" N LYS E 275 " --> pdb=" O ARG E 271 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ASP E 276 " --> pdb=" O GLN E 272 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS E 279 " --> pdb=" O LYS E 275 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL E 280 " --> pdb=" O ASP E 276 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE E 281 " --> pdb=" O LEU E 277 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN E 282 " --> pdb=" O VAL E 278 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN E 283 " --> pdb=" O LYS E 279 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU E 284 " --> pdb=" O VAL E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 301 removed outlier: 3.842A pdb=" N VAL E 296 " --> pdb=" O ILE E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 319 removed outlier: 3.706A pdb=" N LYS E 310 " --> pdb=" O ASP E 306 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU E 316 " --> pdb=" O LEU E 312 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N SER E 317 " --> pdb=" O ARG E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 348 removed outlier: 3.900A pdb=" N ILE E 333 " --> pdb=" O LEU E 329 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU E 334 " --> pdb=" O GLU E 330 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN E 335 " --> pdb=" O ASP E 331 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE E 344 " --> pdb=" O ILE E 340 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE E 347 " --> pdb=" O THR E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 352 through 361 removed outlier: 3.783A pdb=" N LEU E 356 " --> pdb=" O SER E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 379 removed outlier: 3.596A pdb=" N VAL E 372 " --> pdb=" O GLU E 368 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASN E 377 " --> pdb=" O ASN E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 430 removed outlier: 3.529A pdb=" N ILE E 405 " --> pdb=" O TYR E 401 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU E 406 " --> pdb=" O GLN E 402 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N LYS E 407 " --> pdb=" O GLN E 403 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N SER E 410 " --> pdb=" O GLU E 406 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU E 411 " --> pdb=" O LYS E 407 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE E 413 " --> pdb=" O LYS E 409 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLN E 416 " --> pdb=" O SER E 412 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE E 422 " --> pdb=" O LEU E 418 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU E 423 " --> pdb=" O ALA E 419 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LYS E 424 " --> pdb=" O MET E 420 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU E 426 " --> pdb=" O ILE E 422 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ASN E 427 " --> pdb=" O GLU E 423 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN E 428 " --> pdb=" O LYS E 424 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN E 429 " --> pdb=" O LYS E 425 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N SER E 430 " --> pdb=" O LEU E 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 109 removed outlier: 4.520A pdb=" N LEU F 99 " --> pdb=" O HIS F 95 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA F 100 " --> pdb=" O PRO F 96 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER F 101 " --> pdb=" O VAL F 97 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG F 108 " --> pdb=" O ASP F 104 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ARG F 109 " --> pdb=" O SER F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 164 removed outlier: 3.740A pdb=" N LYS F 154 " --> pdb=" O MET F 150 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN F 155 " --> pdb=" O GLU F 151 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR F 157 " --> pdb=" O ALA F 153 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL F 163 " --> pdb=" O LEU F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 194 removed outlier: 4.350A pdb=" N VAL F 184 " --> pdb=" O THR F 180 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE F 186 " --> pdb=" O HIS F 182 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N HIS F 187 " --> pdb=" O SER F 183 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR F 189 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR F 190 " --> pdb=" O ILE F 186 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER F 191 " --> pdb=" O HIS F 187 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG F 192 " --> pdb=" O GLU F 188 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU F 193 " --> pdb=" O TYR F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 254 removed outlier: 4.180A pdb=" N ASP F 250 " --> pdb=" O ARG F 246 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LEU F 251 " --> pdb=" O ILE F 247 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE F 252 " --> pdb=" O GLY F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 296 removed outlier: 3.707A pdb=" N GLN F 271 " --> pdb=" O SER F 267 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER F 284 " --> pdb=" O GLN F 280 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR F 285 " --> pdb=" O ASP F 281 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL F 286 " --> pdb=" O ALA F 282 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP F 292 " --> pdb=" O GLN F 288 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER F 295 " --> pdb=" O GLU F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 315 removed outlier: 4.525A pdb=" N VAL F 304 " --> pdb=" O ALA F 300 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE F 307 " --> pdb=" O THR F 303 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET F 309 " --> pdb=" O GLY F 305 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER F 310 " --> pdb=" O ARG F 306 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL F 312 " --> pdb=" O LEU F 308 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL F 315 " --> pdb=" O LEU F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 357 removed outlier: 4.030A pdb=" N PHE F 323 " --> pdb=" O VAL F 319 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR F 325 " --> pdb=" O ASP F 321 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET F 326 " --> pdb=" O ASP F 322 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER F 329 " --> pdb=" O THR F 325 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN F 347 " --> pdb=" O LEU F 343 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N LEU F 357 " --> pdb=" O LYS F 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 55 removed outlier: 4.639A pdb=" N VAL H 46 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU H 47 " --> pdb=" O GLY H 43 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS H 48 " --> pdb=" O LEU H 44 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR H 53 " --> pdb=" O ILE H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 111 removed outlier: 3.655A pdb=" N MET H 103 " --> pdb=" O TYR H 99 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET H 104 " --> pdb=" O GLN H 100 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG H 105 " --> pdb=" O MET H 101 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL H 110 " --> pdb=" O SER H 106 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN H 111 " --> pdb=" O LEU H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 145 removed outlier: 3.736A pdb=" N LEU H 134 " --> pdb=" O THR H 130 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N TYR H 140 " --> pdb=" O SER H 136 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA H 143 " --> pdb=" O SER H 139 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE H 144 " --> pdb=" O TYR H 140 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU H 145 " --> pdb=" O GLN H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 160 removed outlier: 3.616A pdb=" N THR H 157 " --> pdb=" O ASP H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 180 removed outlier: 4.164A pdb=" N CYS H 177 " --> pdb=" O LEU H 173 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU H 179 " --> pdb=" O GLU H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 191 removed outlier: 3.951A pdb=" N LYS H 188 " --> pdb=" O PRO H 184 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS H 189 " --> pdb=" O GLU H 185 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN H 191 " --> pdb=" O LEU H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 198 removed outlier: 4.297A pdb=" N MET H 197 " --> pdb=" O THR H 193 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N PHE H 198 " --> pdb=" O PHE H 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 193 through 198' Processing helix chain 'H' and resid 208 through 222 removed outlier: 3.692A pdb=" N ASN H 212 " --> pdb=" O SER H 208 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS H 220 " --> pdb=" O TRP H 216 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS H 221 " --> pdb=" O GLU H 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 235 through 289 removed outlier: 4.227A pdb=" N LEU H 239 " --> pdb=" O SER H 235 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG H 249 " --> pdb=" O LEU H 245 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS H 269 " --> pdb=" O ARG H 265 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN H 272 " --> pdb=" O SER H 268 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN H 283 " --> pdb=" O GLN H 279 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU H 284 " --> pdb=" O ARG H 280 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N MET H 286 " --> pdb=" O GLN H 282 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN H 287 " --> pdb=" O GLN H 283 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG H 288 " --> pdb=" O GLU H 284 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLN H 289 " --> pdb=" O ASN H 285 " (cutoff:3.500A) Processing helix chain 'H' and resid 313 through 349 removed outlier: 5.417A pdb=" N LEU H 317 " --> pdb=" O ARG H 313 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA H 320 " --> pdb=" O SER H 316 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN H 329 " --> pdb=" O THR H 325 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS H 331 " --> pdb=" O CYS H 327 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA H 335 " --> pdb=" O LYS H 331 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN H 336 " --> pdb=" O GLU H 332 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS H 340 " --> pdb=" O GLN H 336 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA H 346 " --> pdb=" O PHE H 342 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU H 349 " --> pdb=" O GLN H 345 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 12 removed outlier: 4.530A pdb=" N GLN K 6 " --> pdb=" O ALA K 2 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET K 7 " --> pdb=" O MET K 3 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN K 10 " --> pdb=" O GLN K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 39 removed outlier: 5.119A pdb=" N THR K 28 " --> pdb=" O GLU K 24 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ARG K 31 " --> pdb=" O ALA K 27 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA K 37 " --> pdb=" O VAL K 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 57 removed outlier: 4.097A pdb=" N LEU K 51 " --> pdb=" O ASN K 47 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR K 54 " --> pdb=" O VAL K 50 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN K 55 " --> pdb=" O LEU K 51 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE K 56 " --> pdb=" O LYS K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 78 removed outlier: 4.261A pdb=" N GLN K 68 " --> pdb=" O THR K 64 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE K 69 " --> pdb=" O VAL K 65 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU K 70 " --> pdb=" O THR K 66 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU K 71 " --> pdb=" O ALA K 67 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR K 75 " --> pdb=" O LEU K 71 " (cutoff:3.500A) Proline residue: K 78 - end of helix Processing helix chain 'K' and resid 80 through 89 removed outlier: 4.712A pdb=" N LEU K 84 " --> pdb=" O THR K 80 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N CYS K 87 " --> pdb=" O THR K 83 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE K 89 " --> pdb=" O CYS K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 95 removed outlier: 4.131A pdb=" N GLN K 94 " --> pdb=" O ASP K 90 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU K 95 " --> pdb=" O GLN K 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 90 through 95' Processing helix chain 'K' and resid 96 through 112 removed outlier: 7.459A pdb=" N GLN K 101 " --> pdb=" O ARG K 97 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY K 106 " --> pdb=" O ILE K 102 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASP K 107 " --> pdb=" O LEU K 103 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU K 108 " --> pdb=" O TYR K 104 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU K 109 " --> pdb=" O LEU K 105 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU K 110 " --> pdb=" O GLY K 106 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N THR K 111 " --> pdb=" O ASP K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 118 removed outlier: 4.443A pdb=" N PHE K 117 " --> pdb=" O HIS K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 132 removed outlier: 5.360A pdb=" N THR K 132 " --> pdb=" O LEU K 128 " (cutoff:3.500A) Processing helix chain 'K' and resid 133 through 150 removed outlier: 3.553A pdb=" N HIS K 144 " --> pdb=" O LYS K 140 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY K 147 " --> pdb=" O CYS K 143 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ILE K 148 " --> pdb=" O HIS K 144 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N THR K 149 " --> pdb=" O VAL K 145 " (cutoff:3.500A) Processing helix chain 'K' and resid 154 through 163 removed outlier: 3.560A pdb=" N MET K 161 " --> pdb=" O LEU K 157 " (cutoff:3.500A) Processing helix chain 'K' and resid 166 through 178 removed outlier: 5.025A pdb=" N VAL K 172 " --> pdb=" O SER K 168 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS K 176 " --> pdb=" O VAL K 172 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR K 177 " --> pdb=" O TRP K 173 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLY K 178 " --> pdb=" O MET K 174 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 218 removed outlier: 4.029A pdb=" N VAL K 210 " --> pdb=" O ASP K 206 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N SER K 212 " --> pdb=" O ASP K 208 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ILE K 213 " --> pdb=" O SER K 209 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA K 215 " --> pdb=" O SER K 211 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N SER K 216 " --> pdb=" O SER K 212 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER K 217 " --> pdb=" O ILE K 213 " (cutoff:3.500A) Processing helix chain 'K' and resid 17 through 22 removed outlier: 3.531A pdb=" N ARG K 20 " --> pdb=" O GLY K 17 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYR K 21 " --> pdb=" O ILE K 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 200 removed outlier: 3.607A pdb=" N ILE L 187 " --> pdb=" O LEU L 183 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE L 190 " --> pdb=" O ILE L 186 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR L 192 " --> pdb=" O ASP L 188 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLN L 193 " --> pdb=" O GLU L 189 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER L 196 " --> pdb=" O TYR L 192 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER L 198 " --> pdb=" O PHE L 194 " (cutoff:3.500A) Processing helix chain 'L' and resid 208 through 218 removed outlier: 4.912A pdb=" N ILE L 212 " --> pdb=" O SER L 208 " (cutoff:3.500A) Processing helix chain 'L' and resid 223 through 247 removed outlier: 4.000A pdb=" N ASN L 229 " --> pdb=" O HIS L 225 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL L 230 " --> pdb=" O SER L 226 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N HIS L 232 " --> pdb=" O LEU L 228 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN L 241 " --> pdb=" O LYS L 237 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG L 242 " --> pdb=" O SER L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 251 through 258 Processing helix chain 'L' and resid 260 through 267 removed outlier: 4.144A pdb=" N SER L 264 " --> pdb=" O TYR L 260 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR L 266 " --> pdb=" O ARG L 262 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS L 267 " --> pdb=" O HIS L 263 " (cutoff:3.500A) Processing helix chain 'L' and resid 276 through 291 removed outlier: 4.117A pdb=" N LEU L 280 " --> pdb=" O GLY L 276 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ALA L 290 " --> pdb=" O ASP L 286 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ILE L 291 " --> pdb=" O TYR L 287 " (cutoff:3.500A) Processing helix chain 'L' and resid 295 through 303 removed outlier: 5.173A pdb=" N SER L 303 " --> pdb=" O LEU L 299 " (cutoff:3.500A) Processing helix chain 'L' and resid 308 through 327 removed outlier: 3.681A pdb=" N VAL L 313 " --> pdb=" O PRO L 309 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR L 314 " --> pdb=" O GLU L 310 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TYR L 316 " --> pdb=" O GLN L 312 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR L 317 " --> pdb=" O VAL L 313 " (cutoff:3.500A) Processing helix chain 'L' and resid 329 through 341 removed outlier: 3.812A pdb=" N ILE L 333 " --> pdb=" O TYR L 329 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ARG L 334 " --> pdb=" O GLN L 330 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE L 336 " --> pdb=" O ALA L 332 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE L 339 " --> pdb=" O VAL L 335 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU L 340 " --> pdb=" O PHE L 336 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU L 341 " --> pdb=" O ALA L 337 " (cutoff:3.500A) Processing helix chain 'L' and resid 356 through 376 removed outlier: 3.705A pdb=" N ILE L 360 " --> pdb=" O LYS L 356 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU L 365 " --> pdb=" O ASN L 361 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR L 376 " --> pdb=" O ALA L 372 " (cutoff:3.500A) Processing helix chain 'L' and resid 379 through 386 removed outlier: 5.836A pdb=" N ASP L 383 " --> pdb=" O PRO L 379 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N GLU L 384 " --> pdb=" O MET L 380 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER L 385 " --> pdb=" O ARG L 381 " (cutoff:3.500A) Processing helix chain 'L' and resid 389 through 404 removed outlier: 3.717A pdb=" N LYS L 393 " --> pdb=" O GLN L 389 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR L 394 " --> pdb=" O LEU L 390 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS L 397 " --> pdb=" O LYS L 393 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU L 399 " --> pdb=" O GLY L 395 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG L 400 " --> pdb=" O ASP L 396 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET L 401 " --> pdb=" O LYS L 397 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLN L 402 " --> pdb=" O MET L 398 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N LYS L 403 " --> pdb=" O LEU L 399 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY L 404 " --> pdb=" O ARG L 400 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 422 removed outlier: 4.151A pdb=" N GLU L 410 " --> pdb=" O PRO L 406 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU L 412 " --> pdb=" O VAL L 408 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR L 415 " --> pdb=" O GLU L 411 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER L 416 " --> pdb=" O LEU L 412 " (cutoff:3.500A) Proline residue: L 418 - end of helix removed outlier: 5.068A pdb=" N LEU L 421 " --> pdb=" O CYS L 417 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER L 422 " --> pdb=" O PRO L 418 " (cutoff:3.500A) Processing helix chain 'L' and resid 434 through 462 removed outlier: 6.979A pdb=" N GLU L 438 " --> pdb=" O ASN L 434 " (cutoff:3.500A) Proline residue: L 439 - end of helix removed outlier: 3.618A pdb=" N GLN L 443 " --> pdb=" O PRO L 439 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LYS L 445 " --> pdb=" O LEU L 441 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N VAL L 446 " --> pdb=" O GLN L 442 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP L 449 " --> pdb=" O LYS L 445 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU L 450 " --> pdb=" O VAL L 446 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL L 451 " --> pdb=" O PHE L 447 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN L 453 " --> pdb=" O ASP L 449 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA L 455 " --> pdb=" O VAL L 451 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN L 456 " --> pdb=" O GLN L 452 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU L 457 " --> pdb=" O GLN L 453 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER L 458 " --> pdb=" O GLN L 454 " (cutoff:3.500A) Processing helix chain 'L' and resid 471 through 483 removed outlier: 3.528A pdb=" N ALA L 476 " --> pdb=" O VAL L 472 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU L 483 " --> pdb=" O LEU L 479 " (cutoff:3.500A) Processing helix chain 'L' and resid 488 through 498 removed outlier: 5.200A pdb=" N VAL L 492 " --> pdb=" O ILE L 488 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N HIS L 495 " --> pdb=" O LEU L 491 " (cutoff:3.500A) Processing helix chain 'L' and resid 523 through 552 removed outlier: 5.268A pdb=" N MET L 527 " --> pdb=" O ILE L 523 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE L 530 " --> pdb=" O ASP L 526 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE L 544 " --> pdb=" O GLY L 540 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN L 546 " --> pdb=" O PHE L 542 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE L 547 " --> pdb=" O PHE L 543 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU L 552 " --> pdb=" O HIS L 548 " (cutoff:3.500A) Processing helix chain 'M' and resid 11 through 26 removed outlier: 4.541A pdb=" N ALA M 15 " --> pdb=" O GLU M 11 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA M 16 " --> pdb=" O GLU M 12 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER M 24 " --> pdb=" O ALA M 20 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS M 25 " --> pdb=" O TYR M 21 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY M 26 " --> pdb=" O LEU M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 53 removed outlier: 4.021A pdb=" N CYS M 49 " --> pdb=" O ILE M 45 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASP M 50 " --> pdb=" O ILE M 46 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N VAL M 51 " --> pdb=" O GLU M 47 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N CYS M 52 " --> pdb=" O ALA M 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 74 removed outlier: 4.999A pdb=" N MET M 64 " --> pdb=" O VAL M 60 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N VAL M 67 " --> pdb=" O VAL M 63 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ILE M 73 " --> pdb=" O SER M 69 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N LEU M 74 " --> pdb=" O LEU M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 97 removed outlier: 3.525A pdb=" N GLU M 88 " --> pdb=" O GLU M 84 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N PHE M 93 " --> pdb=" O LYS M 89 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ARG M 94 " --> pdb=" O LEU M 90 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLU M 95 " --> pdb=" O VAL M 91 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY M 96 " --> pdb=" O LYS M 92 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLU M 97 " --> pdb=" O PHE M 93 " (cutoff:3.500A) Processing helix chain 'M' and resid 99 through 114 removed outlier: 3.518A pdb=" N ASN M 108 " --> pdb=" O GLN M 104 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N MET M 113 " --> pdb=" O LEU M 109 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASP M 114 " --> pdb=" O PHE M 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 117 through 134 removed outlier: 4.580A pdb=" N TYR M 121 " --> pdb=" O THR M 117 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N THR M 122 " --> pdb=" O PRO M 118 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER M 133 " --> pdb=" O LYS M 129 " (cutoff:3.500A) Processing helix chain 'M' and resid 143 through 155 removed outlier: 3.532A pdb=" N ARG M 148 " --> pdb=" O LEU M 144 " (cutoff:3.500A) Processing helix chain 'M' and resid 157 through 176 removed outlier: 3.598A pdb=" N GLU M 170 " --> pdb=" O ARG M 166 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N CYS M 175 " --> pdb=" O ALA M 171 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LYS M 176 " --> pdb=" O LEU M 172 " (cutoff:3.500A) Processing helix chain 'M' and resid 178 through 192 removed outlier: 3.687A pdb=" N SER M 182 " --> pdb=" O SER M 178 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LYS M 183 " --> pdb=" O ASP M 179 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TYR M 192 " --> pdb=" O LEU M 188 " (cutoff:3.500A) Processing helix chain 'M' and resid 193 through 201 removed outlier: 5.178A pdb=" N SER M 198 " --> pdb=" O GLU M 194 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLN M 199 " --> pdb=" O ASP M 195 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ALA M 200 " --> pdb=" O ASN M 196 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ARG M 201 " --> pdb=" O ALA M 197 " (cutoff:3.500A) Processing helix chain 'M' and resid 202 through 215 removed outlier: 4.375A pdb=" N ILE M 208 " --> pdb=" O ALA M 204 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS M 213 " --> pdb=" O VAL M 209 " (cutoff:3.500A) Proline residue: M 215 - end of helix Processing helix chain 'M' and resid 219 through 226 removed outlier: 4.714A pdb=" N LEU M 223 " --> pdb=" O LEU M 219 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU M 224 " --> pdb=" O PHE M 220 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR M 225 " --> pdb=" O ASP M 221 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LEU M 226 " --> pdb=" O HIS M 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 219 through 226' Processing helix chain 'M' and resid 227 through 233 removed outlier: 3.949A pdb=" N PHE M 231 " --> pdb=" O LYS M 227 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLU M 233 " --> pdb=" O VAL M 229 " (cutoff:3.500A) Processing helix chain 'M' and resid 236 through 246 removed outlier: 4.809A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU M 241 " --> pdb=" O ILE M 237 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR M 242 " --> pdb=" O HIS M 238 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE M 243 " --> pdb=" O ASP M 239 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SER M 246 " --> pdb=" O THR M 242 " (cutoff:3.500A) Processing helix chain 'M' and resid 248 through 260 removed outlier: 3.590A pdb=" N TYR M 252 " --> pdb=" O LYS M 248 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS M 254 " --> pdb=" O ALA M 250 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE M 255 " --> pdb=" O SER M 251 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLN M 257 " --> pdb=" O VAL M 253 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN M 259 " --> pdb=" O PHE M 255 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS M 260 " --> pdb=" O TYR M 256 " (cutoff:3.500A) Processing helix chain 'M' and resid 269 through 290 removed outlier: 3.923A pdb=" N ASN M 273 " --> pdb=" O LEU M 269 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE M 282 " --> pdb=" O ARG M 278 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU M 288 " --> pdb=" O GLY M 284 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LYS M 290 " --> pdb=" O ALA M 286 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 301 removed outlier: 4.716A pdb=" N MET M 297 " --> pdb=" O SER M 293 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN M 298 " --> pdb=" O PHE M 294 " (cutoff:3.500A) Processing helix chain 'M' and resid 307 through 319 removed outlier: 3.900A pdb=" N PHE M 311 " --> pdb=" O ASP M 307 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE M 313 " --> pdb=" O GLU M 309 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR M 318 " --> pdb=" O ASP M 314 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LYS M 319 " --> pdb=" O ALA M 315 " (cutoff:3.500A) Processing helix chain 'M' and resid 343 through 372 removed outlier: 3.864A pdb=" N LEU M 350 " --> pdb=" O GLN M 346 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP M 352 " --> pdb=" O GLN M 348 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA M 356 " --> pdb=" O ASP M 352 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL M 364 " --> pdb=" O ASN M 360 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU M 369 " --> pdb=" O LYS M 365 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU M 371 " --> pdb=" O SER M 367 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N SER M 372 " --> pdb=" O LEU M 368 " (cutoff:3.500A) Processing helix chain '1' and resid 12 through 17 removed outlier: 4.810A pdb=" N CYS 1 16 " --> pdb=" O ASN 1 12 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N LYS 1 17 " --> pdb=" O HIS 1 13 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 12 through 17' Processing helix chain '1' and resid 23 through 29 removed outlier: 3.664A pdb=" N LYS 1 27 " --> pdb=" O GLN 1 23 " (cutoff:3.500A) Processing helix chain '1' and resid 30 through 35 Processing helix chain '1' and resid 59 through 65 removed outlier: 4.560A pdb=" N LYS 1 63 " --> pdb=" O GLY 1 59 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS 1 64 " --> pdb=" O ILE 1 60 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N CYS 1 65 " --> pdb=" O CYS 1 61 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 59 through 65' Processing helix chain '1' and resid 115 through 125 removed outlier: 4.063A pdb=" N LEU 1 120 " --> pdb=" O LYS 1 116 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE 1 122 " --> pdb=" O THR 1 118 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU 1 123 " --> pdb=" O ALA 1 119 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLY 1 125 " --> pdb=" O LYS 1 121 " (cutoff:3.500A) Processing helix chain '1' and resid 139 through 148 removed outlier: 3.675A pdb=" N TYR 1 146 " --> pdb=" O GLU 1 142 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ARG 1 148 " --> pdb=" O LEU 1 144 " (cutoff:3.500A) Processing helix chain '1' and resid 150 through 162 removed outlier: 4.752A pdb=" N ASN 1 154 " --> pdb=" O SER 1 150 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N THR 1 157 " --> pdb=" O GLN 1 153 " (cutoff:3.500A) Processing helix chain '1' and resid 176 through 181 removed outlier: 4.663A pdb=" N LYS 1 181 " --> pdb=" O PRO 1 177 " (cutoff:3.500A) Processing helix chain '1' and resid 183 through 192 removed outlier: 4.415A pdb=" N LYS 1 191 " --> pdb=" O ILE 1 187 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP 1 192 " --> pdb=" O LEU 1 188 " (cutoff:3.500A) Processing helix chain '1' and resid 197 through 205 removed outlier: 5.338A pdb=" N CYS 1 201 " --> pdb=" O GLN 1 197 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLN 1 202 " --> pdb=" O ALA 1 198 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU 1 204 " --> pdb=" O VAL 1 200 " (cutoff:3.500A) Processing helix chain '1' and resid 206 through 211 removed outlier: 7.434A pdb=" N LYS 1 210 " --> pdb=" O LEU 1 206 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLU 1 211 " --> pdb=" O THR 1 207 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 206 through 211' Processing helix chain '1' and resid 218 through 234 removed outlier: 3.749A pdb=" N ALA 1 226 " --> pdb=" O LEU 1 222 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL 1 230 " --> pdb=" O ALA 1 226 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS 1 231 " --> pdb=" O CYS 1 227 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLN 1 233 " --> pdb=" O VAL 1 229 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N LYS 1 234 " --> pdb=" O VAL 1 230 " (cutoff:3.500A) Processing helix chain '1' and resid 248 through 263 removed outlier: 3.671A pdb=" N ARG 1 260 " --> pdb=" O ALA 1 256 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE 1 263 " --> pdb=" O ILE 1 259 " (cutoff:3.500A) Processing helix chain '1' and resid 275 through 283 removed outlier: 6.392A pdb=" N LEU 1 279 " --> pdb=" O ASP 1 275 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ASP 1 280 " --> pdb=" O LEU 1 276 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N TYR 1 281 " --> pdb=" O SER 1 277 " (cutoff:3.500A) Processing helix chain '1' and resid 305 through 315 removed outlier: 3.683A pdb=" N ILE 1 309 " --> pdb=" O VAL 1 305 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN 1 310 " --> pdb=" O ARG 1 306 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP 1 314 " --> pdb=" O ASN 1 310 " (cutoff:3.500A) Processing helix chain '1' and resid 384 through 394 removed outlier: 4.559A pdb=" N ARG 1 390 " --> pdb=" O THR 1 386 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA 1 393 " --> pdb=" O ILE 1 389 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY 1 394 " --> pdb=" O ARG 1 390 " (cutoff:3.500A) Processing helix chain '1' and resid 423 through 428 Processing helix chain '1' and resid 438 through 445 removed outlier: 7.296A pdb=" N VAL 1 442 " --> pdb=" O HIS 1 438 " (cutoff:3.500A) removed outlier: 8.889A pdb=" N THR 1 443 " --> pdb=" O PRO 1 439 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ASP 1 444 " --> pdb=" O GLN 1 440 " (cutoff:3.500A) Processing helix chain '1' and resid 450 through 456 removed outlier: 4.751A pdb=" N ILE 1 454 " --> pdb=" O GLN 1 450 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ASP 1 456 " --> pdb=" O GLU 1 452 " (cutoff:3.500A) Processing helix chain '1' and resid 463 through 478 removed outlier: 3.882A pdb=" N ALA 1 473 " --> pdb=" O ARG 1 469 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU 1 474 " --> pdb=" O VAL 1 470 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS 1 475 " --> pdb=" O ALA 1 471 " (cutoff:3.500A) Processing helix chain '1' and resid 493 through 512 removed outlier: 3.866A pdb=" N ARG 1 497 " --> pdb=" O ASP 1 493 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU 1 498 " --> pdb=" O SER 1 494 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N MET 1 499 " --> pdb=" O GLU 1 495 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA 1 500 " --> pdb=" O GLN 1 496 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA 1 501 " --> pdb=" O ARG 1 497 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG 1 502 " --> pdb=" O LEU 1 498 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU 1 509 " --> pdb=" O LYS 1 505 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS 1 510 " --> pdb=" O ARG 1 506 " (cutoff:3.500A) Processing helix chain '1' and resid 521 through 529 removed outlier: 3.545A pdb=" N ALA 1 525 " --> pdb=" O ASP 1 521 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR 1 527 " --> pdb=" O ILE 1 523 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU 1 528 " --> pdb=" O MET 1 524 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA 1 529 " --> pdb=" O ALA 1 525 " (cutoff:3.500A) Processing helix chain '1' and resid 551 through 563 removed outlier: 3.508A pdb=" N ASN 1 556 " --> pdb=" O LEU 1 552 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER 1 560 " --> pdb=" O ASN 1 556 " (cutoff:3.500A) Processing helix chain '1' and resid 582 through 592 removed outlier: 3.832A pdb=" N GLU 1 587 " --> pdb=" O ILE 1 583 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER 1 591 " --> pdb=" O GLU 1 587 " (cutoff:3.500A) Processing helix chain 'N' and resid 58 through 68 removed outlier: 4.339A pdb=" N ALA N 62 " --> pdb=" O LYS N 58 " (cutoff:3.500A) Processing helix chain 'N' and resid 89 through 101 removed outlier: 5.066A pdb=" N ILE N 93 " --> pdb=" O GLN N 89 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N CYS N 94 " --> pdb=" O ARG N 90 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL N 98 " --> pdb=" O CYS N 94 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N GLY N 101 " --> pdb=" O LEU N 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 27 removed outlier: 5.402A pdb=" N ASP D 27 " --> pdb=" O GLU D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 60 removed outlier: 4.045A pdb=" N ASN D 57 " --> pdb=" O LYS D 53 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS D 58 " --> pdb=" O ARG D 54 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TYR D 59 " --> pdb=" O TYR D 55 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N SER D 60 " --> pdb=" O THR D 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 53 through 60' Processing helix chain 'D' and resid 175 through 182 removed outlier: 3.850A pdb=" N LEU D 179 " --> pdb=" O ASP D 175 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS D 181 " --> pdb=" O PRO D 177 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET D 182 " --> pdb=" O GLN D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 209 removed outlier: 4.497A pdb=" N ASP D 207 " --> pdb=" O ASP D 203 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ARG D 208 " --> pdb=" O LYS D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 233 Proline residue: D 233 - end of helix Processing helix chain 'D' and resid 234 through 242 removed outlier: 4.202A pdb=" N LYS D 240 " --> pdb=" O ARG D 236 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N THR D 241 " --> pdb=" O LYS D 237 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN D 242 " --> pdb=" O LEU D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 258 removed outlier: 3.636A pdb=" N ALA D 253 " --> pdb=" O ASP D 249 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET D 256 " --> pdb=" O LEU D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 327 removed outlier: 3.521A pdb=" N TYR D 318 " --> pdb=" O MET D 314 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLN D 325 " --> pdb=" O HIS D 321 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N CYS D 327 " --> pdb=" O PHE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 428 removed outlier: 3.902A pdb=" N VAL D 420 " --> pdb=" O GLN D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 443 removed outlier: 3.577A pdb=" N TRP D 435 " --> pdb=" O LYS D 431 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR D 436 " --> pdb=" O LEU D 432 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU D 440 " --> pdb=" O THR D 436 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU D 441 " --> pdb=" O CYS D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 481 removed outlier: 3.648A pdb=" N SER D 478 " --> pdb=" O ASN D 474 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN D 479 " --> pdb=" O GLU D 475 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE D 480 " --> pdb=" O PHE D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 502 removed outlier: 3.664A pdb=" N ALA D 487 " --> pdb=" O SER D 483 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TRP D 488 " --> pdb=" O VAL D 484 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY D 489 " --> pdb=" O GLU D 485 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL D 494 " --> pdb=" O ILE D 490 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LYS D 500 " --> pdb=" O ASP D 496 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU D 501 " --> pdb=" O ILE D 497 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N GLU D 502 " --> pdb=" O CYS D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 413 removed outlier: 4.370A pdb=" N LEU D 413 " --> pdb=" O ASP D 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 408 through 413' Processing helix chain 'Y' and resid 14 through 23 removed outlier: 4.518A pdb=" N ALA Y 20 " --> pdb=" O ALA Y 16 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA Y 21 " --> pdb=" O ALA Y 17 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ALA Y 22 " --> pdb=" O ALA Y 18 " (cutoff:3.500A) Processing helix chain 'Y' and resid 52 through 66 removed outlier: 3.511A pdb=" N ALA Y 57 " --> pdb=" O ALA Y 53 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA Y 60 " --> pdb=" O ALA Y 56 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA Y 62 " --> pdb=" O ALA Y 58 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ALA Y 65 " --> pdb=" O ALA Y 61 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA Y 66 " --> pdb=" O ALA Y 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 172 removed outlier: 3.794A pdb=" N GLN G 169 " --> pdb=" O ASP G 165 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N TYR G 170 " --> pdb=" O LYS G 166 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU G 171 " --> pdb=" O ILE G 167 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LYS G 172 " --> pdb=" O THR G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 192 removed outlier: 3.627A pdb=" N ILE G 189 " --> pdb=" O ARG G 185 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N SER G 190 " --> pdb=" O ASP G 186 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LEU G 191 " --> pdb=" O VAL G 187 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N GLU G 192 " --> pdb=" O CYS G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 213 removed outlier: 3.834A pdb=" N LEU G 206 " --> pdb=" O SER G 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 172 removed outlier: 3.884A pdb=" N GLN J 169 " --> pdb=" O ASP J 165 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TYR J 170 " --> pdb=" O LYS J 166 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU J 171 " --> pdb=" O ILE J 167 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LYS J 172 " --> pdb=" O THR J 168 " (cutoff:3.500A) Processing helix chain 'J' and resid 175 through 192 removed outlier: 4.744A pdb=" N SER J 190 " --> pdb=" O ASP J 186 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU J 191 " --> pdb=" O VAL J 187 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N GLU J 192 " --> pdb=" O CYS J 188 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 216 removed outlier: 3.621A pdb=" N GLN J 216 " --> pdb=" O LYS J 212 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'a' and resid 24 through 28 removed outlier: 5.368A pdb=" N HIS a 24 " --> pdb=" O ILE a 49 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N TYR a 47 " --> pdb=" O GLY a 26 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR a 28 " --> pdb=" O GLY a 45 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N GLY a 45 " --> pdb=" O THR a 28 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'a' and resid 96 through 100 removed outlier: 3.651A pdb=" N LEU a 147 " --> pdb=" O VAL a 124 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'p' and resid 42 through 47 removed outlier: 6.254A pdb=" N ARG p 42 " --> pdb=" O ALA p 35 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL p 33 " --> pdb=" O ILE p 44 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LYS p 46 " --> pdb=" O TYR p 31 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N TYR p 31 " --> pdb=" O LYS p 46 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ARG p 65 " --> pdb=" O THR p 88 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'p' and resid 120 through 128 removed outlier: 3.943A pdb=" N ALA p 123 " --> pdb=" O CYS p 139 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LEU p 134 " --> pdb=" O LEU p 218 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS p 214 " --> pdb=" O PHE p 138 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'p' and resid 101 through 105 removed outlier: 7.818A pdb=" N HIS p 101 " --> pdb=" O MET p 217 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET p 217 " --> pdb=" O HIS p 101 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N ARG p 213 " --> pdb=" O LEU p 105 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'd' and resid 102 through 107 removed outlier: 3.719A pdb=" N LYS d 103 " --> pdb=" O GLY d 131 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N PHE d 127 " --> pdb=" O LEU d 107 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'd' and resid 183 through 187 removed outlier: 4.789A pdb=" N ALA d 198 " --> pdb=" O ASP d 221 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASP d 221 " --> pdb=" O ALA d 198 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'd' and resid 123 through 132 Processing sheet with id= 9, first strand: chain 'Q' and resid 20 through 24 removed outlier: 4.618A pdb=" N ARG Q 28 " --> pdb=" O CYS Q 23 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'Q' and resid 36 through 43 removed outlier: 3.584A pdb=" N ARG Q 42 " --> pdb=" O LEU Q 67 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'q' and resid 88 through 92 removed outlier: 4.936A pdb=" N ASP q 88 " --> pdb=" O LEU q 101 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'q' and resid 121 through 126 removed outlier: 3.512A pdb=" N LYS q 122 " --> pdb=" O ILE q 162 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASP q 158 " --> pdb=" O VAL q 126 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP q 171 " --> pdb=" O GLN q 161 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'q' and resid 128 through 131 removed outlier: 3.547A pdb=" N LYS q 128 " --> pdb=" O VAL q 140 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE q 130 " --> pdb=" O HIS q 138 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'q' and resid 197 through 200 removed outlier: 3.665A pdb=" N VAL q 207 " --> pdb=" O GLU q 199 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'r' and resid 12 through 17 removed outlier: 3.709A pdb=" N CYS r 12 " --> pdb=" O PHE r 7 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU r 109 " --> pdb=" O LYS r 2 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN r 4 " --> pdb=" O LEU r 109 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ASN r 110 " --> pdb=" O SER r 53 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL r 49 " --> pdb=" O VAL r 114 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL r 50 " --> pdb=" O VAL r 36 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE r 52 " --> pdb=" O THR r 34 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N THR r 34 " --> pdb=" O ILE r 52 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 's' and resid 47 through 53 removed outlier: 3.702A pdb=" N ALA s 47 " --> pdb=" O PHE s 63 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N HIS s 91 " --> pdb=" O LYS s 58 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 's' and resid 141 through 147 removed outlier: 3.617A pdb=" N GLY s 141 " --> pdb=" O HIS s 157 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N SER s 151 " --> pdb=" O LYS s 147 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ASP s 184 " --> pdb=" O ARG s 152 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 't' and resid 42 through 49 removed outlier: 6.399A pdb=" N ARG t 42 " --> pdb=" O LEU t 58 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ASN t 52 " --> pdb=" O VAL t 48 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 't' and resid 63 through 67 removed outlier: 4.661A pdb=" N ASN t 64 " --> pdb=" O ALA t 185 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASP t 186 " --> pdb=" O ALA t 176 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LEU t 172 " --> pdb=" O LEU t 190 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU t 171 " --> pdb=" O ILE t 104 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N CYS t 100 " --> pdb=" O ILE t 175 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE t 101 " --> pdb=" O VAL t 82 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP t 80 " --> pdb=" O LEU t 103 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'n' and resid 71 through 76 removed outlier: 5.730A pdb=" N ARG n 71 " --> pdb=" O GLU n 130 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR n 127 " --> pdb=" O LEU n 143 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'n' and resid 84 through 97 No H-bonds generated for sheet with id= 21 Processing sheet with id= 22, first strand: chain 'n' and resid 124 through 127 Processing sheet with id= 23, first strand: chain 'i' and resid 40 through 46 removed outlier: 5.697A pdb=" N ILE i 95 " --> pdb=" O GLY i 127 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'f' and resid 23 through 28 removed outlier: 4.951A pdb=" N ARG f 23 " --> pdb=" O LEU f 65 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N GLU f 49 " --> pdb=" O ASN f 64 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'j' and resid 46 through 50 removed outlier: 6.492A pdb=" N LEU j 101 " --> pdb=" O VAL j 123 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'j' and resid 52 through 59 removed outlier: 3.591A pdb=" N GLU j 53 " --> pdb=" O ARG j 71 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ALA j 65 " --> pdb=" O ALA j 59 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LYS j 79 " --> pdb=" O LEU j 74 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'z' and resid 5 through 10 Processing sheet with id= 28, first strand: chain 'z' and resid 54 through 58 removed outlier: 6.504A pdb=" N VAL z 54 " --> pdb=" O TYR z 76 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'z' and resid 20 through 28 Processing sheet with id= 30, first strand: chain 'R' and resid 43 through 47 removed outlier: 5.149A pdb=" N PHE R 32 " --> pdb=" O LYS R 82 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'g' and resid 9 through 15 removed outlier: 3.557A pdb=" N VAL g 12 " --> pdb=" O ALA g 23 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA g 23 " --> pdb=" O VAL g 12 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'b' and resid 36 through 42 removed outlier: 4.000A pdb=" N GLY b 36 " --> pdb=" O LEU b 51 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR b 42 " --> pdb=" O ARG b 45 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU b 85 " --> pdb=" O THR b 46 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE b 48 " --> pdb=" O GLU b 85 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL b 91 " --> pdb=" O ALA b 52 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'b' and resid 148 through 154 removed outlier: 3.661A pdb=" N MET b 150 " --> pdb=" O VAL b 138 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY b 133 " --> pdb=" O MET b 189 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'e' and resid 123 through 127 Processing sheet with id= 35, first strand: chain 'u' and resid 20 through 24 removed outlier: 3.859A pdb=" N ALA u 23 " --> pdb=" O PHE u 67 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'v' and resid 30 through 33 removed outlier: 7.204A pdb=" N GLY v 30 " --> pdb=" O LYS v 112 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N VAL v 110 " --> pdb=" O ALA v 32 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU v 49 " --> pdb=" O VAL v 111 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ASN v 75 " --> pdb=" O HIS v 48 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N CYS v 50 " --> pdb=" O ASN v 75 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU v 52 " --> pdb=" O ILE v 77 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL v 79 " --> pdb=" O LEU v 52 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'o' and resid 75 through 78 removed outlier: 3.598A pdb=" N GLY o 95 " --> pdb=" O VAL o 76 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'x' and resid 81 through 84 Processing sheet with id= 39, first strand: chain 'x' and resid 113 through 116 removed outlier: 3.629A pdb=" N GLU x 114 " --> pdb=" O LYS x 122 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLY x 120 " --> pdb=" O ASP x 116 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'h' and resid 19 through 27 Processing sheet with id= 41, first strand: chain 'S' and resid 31 through 34 removed outlier: 6.678A pdb=" N ARG S 31 " --> pdb=" O THR S 15 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASP S 54 " --> pdb=" O VAL S 14 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'U' and resid 138 through 142 removed outlier: 3.551A pdb=" N CYS U 141 " --> pdb=" O LEU U 146 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'V' and resid 5 through 10 removed outlier: 5.773A pdb=" N VAL V 309 " --> pdb=" O ARG V 8 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR V 10 " --> pdb=" O VAL V 307 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL V 307 " --> pdb=" O THR V 10 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LEU V 306 " --> pdb=" O TYR V 302 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL V 312 " --> pdb=" O GLN V 296 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N GLN V 296 " --> pdb=" O VAL V 312 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA V 290 " --> pdb=" O PHE V 299 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY V 301 " --> pdb=" O SER V 288 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER V 288 " --> pdb=" O GLY V 301 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'V' and resid 20 through 23 removed outlier: 5.421A pdb=" N ASP V 29 " --> pdb=" O LEU V 45 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N MET V 42 " --> pdb=" O GLN V 56 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'V' and resid 67 through 72 removed outlier: 6.992A pdb=" N PHE V 77 " --> pdb=" O SER V 72 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N GLN V 76 " --> pdb=" O LEU V 92 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER V 80 " --> pdb=" O ARG V 88 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG V 88 " --> pdb=" O SER V 80 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU V 89 " --> pdb=" O THR V 98 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR V 96 " --> pdb=" O ASP V 91 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'V' and resid 109 through 114 removed outlier: 3.814A pdb=" N VAL V 121 " --> pdb=" O ALA V 112 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N SER V 114 " --> pdb=" O GLN V 119 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N GLN V 119 " --> pdb=" O SER V 114 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS V 130 " --> pdb=" O SER V 122 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'V' and resid 152 through 156 removed outlier: 4.102A pdb=" N CYS V 153 " --> pdb=" O CYS V 168 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N SER V 167 " --> pdb=" O LYS V 175 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLY V 169 " --> pdb=" O LEU V 173 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N LEU V 173 " --> pdb=" O GLY V 169 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N HIS V 188 " --> pdb=" O VAL V 174 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'V' and resid 196 through 201 removed outlier: 3.610A pdb=" N ALA V 208 " --> pdb=" O THR V 199 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N LEU V 206 " --> pdb=" O SER V 201 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'V' and resid 238 through 241 removed outlier: 3.561A pdb=" N ALA V 238 " --> pdb=" O ALA V 251 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU V 248 " --> pdb=" O TRP V 259 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N TRP V 259 " --> pdb=" O LEU V 248 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER V 255 " --> pdb=" O THR V 252 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ILE V 258 " --> pdb=" O VAL V 267 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL V 267 " --> pdb=" O ILE V 258 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'V' and resid 39 through 42 Processing sheet with id= 51, first strand: chain 'V' and resid 86 through 89 removed outlier: 4.705A pdb=" N LEU V 87 " --> pdb=" O PHE V 101 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG V 99 " --> pdb=" O LEU V 89 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'I' and resid 1 through 6 removed outlier: 3.519A pdb=" N TYR I 313 " --> pdb=" O LYS I 2 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL I 309 " --> pdb=" O LEU I 6 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE I 314 " --> pdb=" O LYS I 298 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N LYS I 298 " --> pdb=" O PHE I 314 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N SER I 299 " --> pdb=" O HIS I 294 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER I 290 " --> pdb=" O GLY I 303 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'I' and resid 14 through 19 removed outlier: 3.882A pdb=" N GLN I 15 " --> pdb=" O VAL I 28 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU I 24 " --> pdb=" O ASN I 19 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ASP I 23 " --> pdb=" O SER I 39 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL I 36 " --> pdb=" O LEU I 45 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU I 43 " --> pdb=" O TYR I 38 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'I' and resid 56 through 60 removed outlier: 7.318A pdb=" N LYS I 65 " --> pdb=" O CYS I 81 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG I 77 " --> pdb=" O THR I 69 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER I 71 " --> pdb=" O SER I 75 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N SER I 75 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'I' and resid 98 through 102 removed outlier: 4.435A pdb=" N THR I 98 " --> pdb=" O SER I 111 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY I 100 " --> pdb=" O MET I 109 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET I 109 " --> pdb=" O GLY I 100 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP I 102 " --> pdb=" O ILE I 107 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE I 107 " --> pdb=" O ASP I 102 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ASN I 106 " --> pdb=" O LEU I 127 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N PHE I 121 " --> pdb=" O THR I 112 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU I 137 " --> pdb=" O ASP I 126 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE I 133 " --> pdb=" O PRO I 130 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'I' and resid 151 through 155 removed outlier: 5.457A pdb=" N CYS I 160 " --> pdb=" O GLY I 155 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE I 161 " --> pdb=" O GLN I 172 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLN I 172 " --> pdb=" O ILE I 161 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA I 163 " --> pdb=" O LEU I 170 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LEU I 170 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N HIS I 165 " --> pdb=" O GLY I 168 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL I 182 " --> pdb=" O GLN I 172 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'I' and resid 193 through 197 removed outlier: 3.720A pdb=" N ASP I 193 " --> pdb=" O ALA I 206 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N MET I 202 " --> pdb=" O SER I 197 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N THR I 201 " --> pdb=" O SER I 217 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER I 217 " --> pdb=" O THR I 201 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS I 213 " --> pdb=" O THR I 205 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU I 214 " --> pdb=" O GLN I 223 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLU I 221 " --> pdb=" O ASP I 216 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'I' and resid 234 through 238 removed outlier: 3.881A pdb=" N SER I 234 " --> pdb=" O GLY I 247 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER I 238 " --> pdb=" O HIS I 243 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N HIS I 243 " --> pdb=" O SER I 238 " (cutoff:3.500A) removed outlier: 9.046A pdb=" N ASP I 242 " --> pdb=" O LEU I 272 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N PHE I 269 " --> pdb=" O PHE I 278 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU I 276 " --> pdb=" O HIS I 271 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'I' and resid 33 through 36 Processing sheet with id= 60, first strand: chain 'I' and resid 121 through 124 No H-bonds generated for sheet with id= 60 Processing sheet with id= 61, first strand: chain 'I' and resid 210 through 214 removed outlier: 5.611A pdb=" N ASN I 210 " --> pdb=" O THR I 228 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS I 224 " --> pdb=" O LEU I 214 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'I' and resid 266 through 269 removed outlier: 3.693A pdb=" N GLY I 279 " --> pdb=" O PHE I 269 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'B' and resid 187 through 190 removed outlier: 4.001A pdb=" N ARG B 262 " --> pdb=" O ASP B 190 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'B' and resid 219 through 222 removed outlier: 3.882A pdb=" N ASN B 219 " --> pdb=" O GLU B 236 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE B 221 " --> pdb=" O PHE B 234 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'B' and resid 305 through 308 removed outlier: 5.069A pdb=" N GLN B 305 " --> pdb=" O ARG B 705 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG B 705 " --> pdb=" O GLN B 305 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU B 703 " --> pdb=" O SER B 307 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'B' and resid 340 through 343 No H-bonds generated for sheet with id= 66 Processing sheet with id= 67, first strand: chain 'B' and resid 376 through 380 removed outlier: 6.411A pdb=" N PHE B 391 " --> pdb=" O GLN B 377 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ILE B 379 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL B 389 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ARG B 386 " --> pdb=" O ILE B 409 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE B 409 " --> pdb=" O ARG B 386 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'B' and resid 437 through 441 removed outlier: 3.557A pdb=" N TYR B 449 " --> pdb=" O PHE B 438 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N SER B 447 " --> pdb=" O ARG B 440 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'B' and resid 478 through 485 removed outlier: 4.508A pdb=" N ALA B 491 " --> pdb=" O LEU B 509 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU B 509 " --> pdb=" O ALA B 491 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 493 " --> pdb=" O ARG B 507 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'B' and resid 515 through 520 removed outlier: 5.395A pdb=" N TYR B 525 " --> pdb=" O GLN B 520 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N ASP B 524 " --> pdb=" O MET B 549 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU B 526 " --> pdb=" O PHE B 547 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 528 " --> pdb=" O GLU B 545 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU B 545 " --> pdb=" O VAL B 528 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL B 530 " --> pdb=" O ASN B 543 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ASN B 543 " --> pdb=" O VAL B 530 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR B 542 " --> pdb=" O MET B 561 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'B' and resid 567 through 570 removed outlier: 3.548A pdb=" N ALA B 567 " --> pdb=" O LEU B 580 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU B 580 " --> pdb=" O ALA B 567 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA B 578 " --> pdb=" O ALA B 569 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N SER B 575 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU B 583 " --> pdb=" O ARG B 586 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'B' and resid 612 through 616 removed outlier: 3.638A pdb=" N VAL B 624 " --> pdb=" O PHE B 615 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N GLN B 621 " --> pdb=" O THR B 640 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA B 634 " --> pdb=" O GLY B 627 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'B' and resid 655 through 660 removed outlier: 5.761A pdb=" N TYR B 665 " --> pdb=" O ASP B 660 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'A' and resid 482 through 486 Processing sheet with id= 75, first strand: chain 'C' and resid 418 through 421 removed outlier: 3.912A pdb=" N GLY C 421 " --> pdb=" O VAL C 440 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'C' and resid 833 through 836 No H-bonds generated for sheet with id= 76 Processing sheet with id= 77, first strand: chain 'F' and resid 127 through 131 removed outlier: 8.689A pdb=" N ARG F 90 " --> pdb=" O PRO F 234 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR F 236 " --> pdb=" O ARG F 90 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER F 218 " --> pdb=" O PRO F 197 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TRP F 172 " --> pdb=" O ILE F 198 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU F 200 " --> pdb=" O TRP F 172 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL F 202 " --> pdb=" O ALA F 174 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'H' and resid 74 through 78 removed outlier: 3.513A pdb=" N GLN H 38 " --> pdb=" O ASP H 74 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'H' and resid 80 through 84 removed outlier: 4.269A pdb=" N ASN H 80 " --> pdb=" O LEU H 68 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE H 82 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN H 64 " --> pdb=" O PHE H 84 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL H 63 " --> pdb=" O SER H 122 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR H 120 " --> pdb=" O GLY H 65 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY H 118 " --> pdb=" O LEU H 67 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL H 148 " --> pdb=" O VAL H 117 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU H 150 " --> pdb=" O TRP H 119 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLN H 121 " --> pdb=" O LEU H 150 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR H 123 " --> pdb=" O TYR H 152 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'M' and resid 322 through 326 removed outlier: 7.025A pdb=" N TYR M 322 " --> pdb=" O SER M 335 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain '1' and resid 6 through 11 removed outlier: 3.605A pdb=" N THR 1 6 " --> pdb=" O LEU 1 75 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain '1' and resid 38 through 41 removed outlier: 6.652A pdb=" N CYS 1 38 " --> pdb=" O SER 1 51 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TRP 1 49 " --> pdb=" O GLU 1 40 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain '1' and resid 92 through 95 removed outlier: 3.506A pdb=" N LYS 1 93 " --> pdb=" O ALA 1 295 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain '1' and resid 166 through 169 removed outlier: 3.584A pdb=" N MET 1 239 " --> pdb=" O ILE 1 167 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP 1 241 " --> pdb=" O LYS 1 169 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLY 1 110 " --> pdb=" O GLU 1 273 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain '1' and resid 352 through 356 removed outlier: 3.645A pdb=" N MET 1 353 " --> pdb=" O ILE 1 364 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS 1 355 " --> pdb=" O LEU 1 362 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N GLU 1 361 " --> pdb=" O LYS 1 541 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA 1 545 " --> pdb=" O ALA 1 363 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N VAL 1 534 " --> pdb=" O ASN 1 546 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N GLU 1 373 " --> pdb=" O LYS 1 513 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA 1 515 " --> pdb=" O GLU 1 373 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR 1 514 " --> pdb=" O ASP 1 481 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain '1' and resid 565 through 569 removed outlier: 5.510A pdb=" N THR 1 565 " --> pdb=" O ASN 1 578 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG 1 574 " --> pdb=" O ASP 1 569 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'N' and resid 70 through 73 removed outlier: 4.982A pdb=" N ASN N 70 " --> pdb=" O GLN N 86 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE N 83 " --> pdb=" O VAL N 47 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LYS N 42 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG N 38 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS N 109 " --> pdb=" O ILE N 31 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE N 33 " --> pdb=" O LYS N 109 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS N 111 " --> pdb=" O ILE N 33 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ILE N 35 " --> pdb=" O HIS N 111 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'D' and resid 190 through 193 removed outlier: 6.806A pdb=" N TYR D 360 " --> pdb=" O ILE D 193 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'D' and resid 379 through 383 removed outlier: 5.047A pdb=" N GLU D 387 " --> pdb=" O GLY D 383 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASN D 392 " --> pdb=" O TYR D 446 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS D 394 " --> pdb=" O LYS D 448 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N ARG D 462 " --> pdb=" O TYR D 455 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'D' and resid 519 through 522 removed outlier: 3.745A pdb=" N LYS D 505 " --> pdb=" O LEU D 522 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS D 510 " --> pdb=" O TRP D 265 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TRP D 265 " --> pdb=" O LYS D 510 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA D 247 " --> pdb=" O ILE D 372 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 'D' and resid 357 through 366 No H-bonds generated for sheet with id= 91 Processing sheet with id= 92, first strand: chain 'D' and resid 447 through 450 Processing sheet with id= 93, first strand: chain 'Y' and resid 47 through 51 removed outlier: 3.618A pdb=" N ALA Y 48 " --> pdb=" O ALA Y 4 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA Y 4 " --> pdb=" O ALA Y 48 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ALA Y 74 " --> pdb=" O ALA Y 7 " (cutoff:3.500A) 3037 hydrogen bonds defined for protein. 9033 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 940 hydrogen bonds 1546 hydrogen bond angles 0 basepair planarities 377 basepair parallelities 900 stacking parallelities Total time for adding SS restraints: 68.22 Time building geometry restraints manager: 38.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 47347 1.40 - 1.62: 72667 1.62 - 1.84: 622 1.84 - 2.06: 1 2.06 - 2.28: 24 Bond restraints: 120661 Sorted by residual: bond pdb=" C4 ATP 1 605 " pdb=" C5 ATP 1 605 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.88e+01 bond pdb=" C5 ATP 1 605 " pdb=" C6 ATP 1 605 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.32e+01 bond pdb=" C8 ATP 1 605 " pdb=" N7 ATP 1 605 " ideal model delta sigma weight residual 1.310 1.359 -0.049 1.00e-02 1.00e+04 2.36e+01 bond pdb=" C5 ATP 1 605 " pdb=" N7 ATP 1 605 " ideal model delta sigma weight residual 1.387 1.346 0.041 1.00e-02 1.00e+04 1.71e+01 bond pdb=" C4 ATP 1 605 " pdb=" N9 ATP 1 605 " ideal model delta sigma weight residual 1.374 1.334 0.040 1.00e-02 1.00e+04 1.56e+01 ... (remaining 120656 not shown) Histogram of bond angle deviations from ideal: 73.37 - 87.31: 24 87.31 - 101.24: 704 101.24 - 115.17: 86453 115.17 - 129.11: 82251 129.11 - 143.04: 1948 Bond angle restraints: 171380 Sorted by residual: angle pdb=" PB ATP 1 605 " pdb=" O3B ATP 1 605 " pdb=" PG ATP 1 605 " ideal model delta sigma weight residual 139.87 120.31 19.56 1.00e+00 1.00e+00 3.83e+02 angle pdb=" PA ATP 1 605 " pdb=" O3A ATP 1 605 " pdb=" PB ATP 1 605 " ideal model delta sigma weight residual 136.83 120.84 15.99 1.00e+00 1.00e+00 2.56e+02 angle pdb=" C5 ATP 1 605 " pdb=" C4 ATP 1 605 " pdb=" N3 ATP 1 605 " ideal model delta sigma weight residual 126.80 118.64 8.16 1.00e+00 1.00e+00 6.65e+01 angle pdb=" C PRO L 379 " pdb=" N MET L 380 " pdb=" CA MET L 380 " ideal model delta sigma weight residual 121.70 135.83 -14.13 1.80e+00 3.09e-01 6.17e+01 angle pdb=" C VAL V 174 " pdb=" N LYS V 175 " pdb=" CA LYS V 175 " ideal model delta sigma weight residual 122.41 138.48 -16.07 2.09e+00 2.29e-01 5.91e+01 ... (remaining 171375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 70106 35.96 - 71.92: 5015 71.92 - 107.88: 539 107.88 - 143.85: 12 143.85 - 179.81: 31 Dihedral angle restraints: 75703 sinusoidal: 46250 harmonic: 29453 Sorted by residual: 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 180.00 112.03 67.97 0 5.00e+00 4.00e-02 1.85e+02 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 180.00 123.28 56.72 0 5.00e+00 4.00e-02 1.29e+02 dihedral pdb=" CA ASP 1 189 " pdb=" C ASP 1 189 " pdb=" N ARG 1 190 " pdb=" CA ARG 1 190 " ideal model delta harmonic sigma weight residual 180.00 125.46 54.54 0 5.00e+00 4.00e-02 1.19e+02 ... (remaining 75700 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 19378 0.127 - 0.255: 1287 0.255 - 0.382: 57 0.382 - 0.510: 13 0.510 - 0.637: 1 Chirality restraints: 20736 Sorted by residual: chirality pdb=" CB ILE L 343 " pdb=" CA ILE L 343 " pdb=" CG1 ILE L 343 " pdb=" CG2 ILE L 343 " both_signs ideal model delta sigma weight residual False 2.64 2.01 0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" CB ILE v 35 " pdb=" CA ILE v 35 " pdb=" CG1 ILE v 35 " pdb=" CG2 ILE v 35 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 4.98e+00 chirality pdb=" CB VAL D 21 " pdb=" CA VAL D 21 " pdb=" CG1 VAL D 21 " pdb=" CG2 VAL D 21 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.42 2.00e-01 2.50e+01 4.39e+00 ... (remaining 20733 not shown) Planarity restraints: 15542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U 2 344 " 0.069 2.00e-02 2.50e+03 3.57e-02 2.87e+01 pdb=" N1 U 2 344 " -0.074 2.00e-02 2.50e+03 pdb=" C2 U 2 344 " -0.022 2.00e-02 2.50e+03 pdb=" O2 U 2 344 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U 2 344 " 0.004 2.00e-02 2.50e+03 pdb=" C4 U 2 344 " 0.017 2.00e-02 2.50e+03 pdb=" O4 U 2 344 " 0.017 2.00e-02 2.50e+03 pdb=" C5 U 2 344 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U 2 344 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS L 432 " -0.085 5.00e-02 4.00e+02 1.29e-01 2.66e+01 pdb=" N PRO L 433 " 0.223 5.00e-02 4.00e+02 pdb=" CA PRO L 433 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO L 433 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU H 73 " 0.021 2.00e-02 2.50e+03 4.41e-02 1.94e+01 pdb=" C GLU H 73 " -0.076 2.00e-02 2.50e+03 pdb=" O GLU H 73 " 0.029 2.00e-02 2.50e+03 pdb=" N ASP H 74 " 0.026 2.00e-02 2.50e+03 ... (remaining 15539 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.36: 112 2.36 - 3.00: 52677 3.00 - 3.63: 176316 3.63 - 4.27: 278086 4.27 - 4.90: 427418 Nonbonded interactions: 934609 Sorted by model distance: nonbonded pdb=" OG SER 1 218 " pdb=" O2B ATP 1 605 " model vdw 1.731 2.440 nonbonded pdb=" OD1 ASN 1 112 " pdb=" O1B ADP 1 603 " model vdw 1.961 3.040 nonbonded pdb=" OG SER 1 117 " pdb="MG MG 1 606 " model vdw 2.108 2.170 nonbonded pdb=" O CYS l 39 " pdb="ZN ZN l 201 " model vdw 2.131 2.230 nonbonded pdb=" OE1 GLN 1 414 " pdb="MG MG 1 604 " model vdw 2.166 2.170 ... (remaining 934604 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'G' selection = (chain 'J' and resid 144 through 213) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 16.820 Check model and map are aligned: 1.210 Set scattering table: 0.750 Process input model: 320.440 Find NCS groups from input model: 2.790 Set up NCS constraints: 0.360 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 347.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 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 0.156 120661 Z= 0.612 Angle : 1.335 22.891 171380 Z= 0.680 Chirality : 0.068 0.637 20736 Planarity : 0.009 0.129 15542 Dihedral : 21.450 179.807 56595 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 1.39 % Allowed : 9.66 % Favored : 88.95 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.10 % Twisted Proline : 0.54 % Twisted General : 0.78 % 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: -4.19 (0.06), residues: 9955 helix: -3.72 (0.05), residues: 3614 sheet: -1.27 (0.13), residues: 1332 loop : -2.43 (0.07), residues: 5009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP V 177 HIS 0.021 0.003 HIS M 111 PHE 0.067 0.004 PHE d 236 TYR 0.040 0.004 TYR b 167 ARG 0.018 0.001 ARG C 669 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19910 Ramachandran restraints generated. 9955 Oldfield, 0 Emsley, 9955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19910 Ramachandran restraints generated. 9955 Oldfield, 0 Emsley, 9955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1835 residues out of total 8865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 1724 time to evaluate : 7.357 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 14 ASP cc_start: 0.5974 (m-30) cc_final: 0.5717 (m-30) REVERT: a 97 THR cc_start: 0.9139 (OUTLIER) cc_final: 0.8889 (p) REVERT: p 120 MET cc_start: 0.7376 (ttt) cc_final: 0.7122 (ttm) REVERT: Q 51 ARG cc_start: 0.7058 (tpm170) cc_final: 0.6819 (tpm170) REVERT: Q 59 PHE cc_start: 0.6588 (m-80) cc_final: 0.6231 (m-80) REVERT: q 54 TYR cc_start: 0.7110 (m-10) cc_final: 0.6881 (m-80) REVERT: r 83 CYS cc_start: 0.7816 (m) cc_final: 0.7400 (t) REVERT: t 88 ASN cc_start: 0.6567 (t0) cc_final: 0.5921 (t0) REVERT: c 107 GLU cc_start: 0.7240 (tp30) cc_final: 0.7006 (tp30) REVERT: i 60 MET cc_start: 0.6355 (mtt) cc_final: 0.6087 (mtt) REVERT: i 81 VAL cc_start: 0.6430 (p) cc_final: 0.6134 (p) REVERT: i 129 ILE cc_start: 0.7799 (mt) cc_final: 0.7546 (mt) REVERT: R 8 LEU cc_start: 0.8096 (mt) cc_final: 0.7890 (mt) REVERT: R 31 TYR cc_start: 0.8190 (p90) cc_final: 0.7971 (p90) REVERT: R 53 VAL cc_start: 0.8666 (OUTLIER) cc_final: 0.8315 (m) REVERT: T 43 VAL cc_start: 0.7369 (m) cc_final: 0.7151 (p) REVERT: w 127 ASN cc_start: 0.8053 (p0) cc_final: 0.7600 (p0) REVERT: b 156 LEU cc_start: 0.8352 (pt) cc_final: 0.8037 (pt) REVERT: o 59 ARG cc_start: 0.6846 (mtp180) cc_final: 0.5901 (ttm170) REVERT: h 33 GLU cc_start: 0.5878 (tm-30) cc_final: 0.5641 (tm-30) REVERT: P 67 LEU cc_start: 0.6733 (tp) cc_final: 0.6326 (tp) REVERT: U 90 LYS cc_start: 0.4834 (tptm) cc_final: 0.4576 (tptt) REVERT: U 132 MET cc_start: 0.6492 (mtp) cc_final: 0.6090 (mtm) REVERT: B 496 MET cc_start: 0.3962 (mtt) cc_final: 0.3368 (mtp) REVERT: B 513 VAL cc_start: 0.3000 (OUTLIER) cc_final: 0.2506 (p) REVERT: B 544 PHE cc_start: 0.4714 (m-10) cc_final: 0.4407 (m-10) REVERT: B 546 ILE cc_start: 0.6051 (mt) cc_final: 0.5604 (tt) REVERT: C 631 ASN cc_start: 0.4237 (m-40) cc_final: 0.3802 (m110) REVERT: E 112 MET cc_start: 0.5135 (pmm) cc_final: 0.3907 (ptt) REVERT: E 173 LEU cc_start: 0.5844 (OUTLIER) cc_final: 0.5380 (tt) REVERT: F 278 ARG cc_start: 0.3891 (ttp-170) cc_final: 0.2516 (mmt-90) REVERT: F 317 LYS cc_start: 0.5784 (tttt) cc_final: 0.5191 (ptpp) REVERT: F 356 ASN cc_start: 0.4164 (p0) cc_final: 0.3699 (p0) REVERT: H 164 LEU cc_start: 0.0740 (mm) cc_final: 0.0299 (tp) REVERT: H 247 MET cc_start: 0.6452 (mtm) cc_final: 0.5111 (tpt) REVERT: H 269 LYS cc_start: 0.4971 (mttt) cc_final: 0.4188 (mmtt) REVERT: K 5 GLU cc_start: 0.2190 (tp30) cc_final: 0.1109 (tt0) REVERT: K 174 MET cc_start: -0.0385 (ptm) cc_final: -0.1301 (mtm) REVERT: L 304 MET cc_start: 0.1802 (pmm) cc_final: 0.0813 (mtt) REVERT: L 312 GLN cc_start: -0.0344 (pp30) cc_final: -0.0561 (pt0) REVERT: L 334 ARG cc_start: 0.4577 (mmt90) cc_final: 0.4335 (mmm-85) REVERT: L 402 GLN cc_start: 0.1633 (mm-40) cc_final: 0.0796 (tt0) REVERT: M 98 ARG cc_start: 0.0499 (tpp-160) cc_final: 0.0220 (ptt180) REVERT: M 163 THR cc_start: 0.3853 (t) cc_final: 0.3403 (m) REVERT: M 277 MET cc_start: 0.4009 (tpp) cc_final: 0.3761 (tpp) REVERT: M 283 MET cc_start: 0.4578 (ttm) cc_final: 0.4219 (ttm) REVERT: M 348 GLN cc_start: 0.3734 (tp40) cc_final: 0.2683 (tm-30) REVERT: 1 106 LEU cc_start: 0.7920 (tp) cc_final: 0.7542 (tp) REVERT: 1 485 ILE cc_start: 0.5295 (mt) cc_final: 0.5073 (mt) REVERT: D 54 ARG cc_start: 0.4987 (ttm170) cc_final: 0.4639 (ptm160) REVERT: D 191 GLN cc_start: 0.4722 (mp10) cc_final: 0.4428 (mp10) REVERT: D 326 GLN cc_start: 0.4640 (tp40) cc_final: 0.4341 (tp40) REVERT: D 332 LYS cc_start: 0.4605 (mmtp) cc_final: 0.4372 (mmtt) outliers start: 111 outliers final: 30 residues processed: 1818 average time/residue: 1.1039 time to fit residues: 3402.5755 Evaluate side-chains 966 residues out of total 8865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 932 time to evaluate : 7.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 97 THR Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 153 THR Chi-restraints excluded: chain Q residue 63 VAL Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain g residue 102 GLU Chi-restraints excluded: chain e residue 26 ASP Chi-restraints excluded: chain e residue 168 THR Chi-restraints excluded: chain u residue 2 LEU Chi-restraints excluded: chain v residue 103 VAL Chi-restraints excluded: chain x residue 35 ASP Chi-restraints excluded: chain V residue 113 PHE Chi-restraints excluded: chain V residue 166 VAL Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain C residue 444 ILE Chi-restraints excluded: chain C residue 709 MET Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 322 ASP Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain L residue 346 THR Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 503 THR Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain 1 residue 305 VAL Chi-restraints excluded: chain 1 residue 416 ILE Chi-restraints excluded: chain 1 residue 493 ASP Chi-restraints excluded: chain 1 residue 543 THR Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 491 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1162 random chunks: chunk 981 optimal weight: 4.9990 chunk 880 optimal weight: 9.9990 chunk 488 optimal weight: 10.0000 chunk 300 optimal weight: 7.9990 chunk 594 optimal weight: 7.9990 chunk 470 optimal weight: 3.9990 chunk 910 optimal weight: 10.0000 chunk 352 optimal weight: 8.9990 chunk 553 optimal weight: 30.0000 chunk 677 optimal weight: 50.0000 chunk 1055 optimal weight: 3.9990 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 ** p 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 92 GLN p 95 ASN p 157 GLN p 160 GLN ** p 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 17 HIS q 98 ASN q 138 HIS q 157 ASN q 201 HIS ** q 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 13 GLN ** r 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 126 HIS ** s 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 7 ASN t 35 ASN t 64 ASN t 146 GLN t 167 GLN c 132 GLN c 154 GLN n 13 GLN i 38 ASN i 79 GLN i 83 GLN f 15 ASN f 98 GLN j 23 HIS z 22 GLN R 19 HIS R 26 GLN R 83 GLN w 31 ASN ** w 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 142 GLN b 174 HIS b 179 GLN ** b 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 74 ASN e 82 ASN ** e 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 149 GLN u 7 ASN u 32 HIS ** u 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 77 GLN o 32 GLN k 85 ASN x 11 GLN x 12 GLN ** x 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 51 ASN x 128 GLN h 47 ASN h 81 GLN P 46 ASN ** l 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 ASN ** V 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 51 ASN V 178 ASN V 237 ASN B 477 ASN B 508 ASN B 518 HIS A 10 ASN A 16 ASN A 109 GLN A 138 GLN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 GLN A 549 GLN A 573 GLN ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 ASN C 478 GLN ** C 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 631 ASN C 674 HIS C 713 GLN C 717 GLN ** C 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 ASN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 845 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 858 GLN C 870 ASN E 49 ASN E 121 HIS ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 GLN ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 335 ASN E 377 ASN ** E 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 127 HIS F 182 HIS F 280 GLN F 332 ASN ** F 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 GLN H 114 HIS H 207 ASN H 212 ASN ** H 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 270 GLN H 322 GLN ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 36 GLN ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 ASN K 91 GLN K 144 HIS K 151 GLN L 195 GLN L 243 GLN ** L 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 514 GLN M 14 GLN M 79 GLN M 258 ASN ** M 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 175 GLN ** 1 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 556 ASN N 36 GLN ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 HIS ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 GLN ** D 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 479 GLN Total number of N/Q/H flips: 105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6479 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.121 120661 Z= 0.289 Angle : 0.743 14.458 171380 Z= 0.387 Chirality : 0.045 0.305 20736 Planarity : 0.006 0.123 15542 Dihedral : 22.059 179.827 37993 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.67 % Favored : 97.29 % Rotamer: Outliers : 3.88 % Allowed : 15.95 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.11 % Twisted Proline : 0.54 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.07), residues: 9955 helix: -1.95 (0.07), residues: 3860 sheet: -1.03 (0.13), residues: 1403 loop : -2.03 (0.08), residues: 4692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP V 177 HIS 0.014 0.002 HIS V 14 PHE 0.028 0.002 PHE d 236 TYR 0.027 0.002 TYR M 351 ARG 0.026 0.001 ARG B 505 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19910 Ramachandran restraints generated. 9955 Oldfield, 0 Emsley, 9955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19910 Ramachandran restraints generated. 9955 Oldfield, 0 Emsley, 9955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1340 residues out of total 8865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 309 poor density : 1031 time to evaluate : 6.870 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: a 33 GLN cc_start: 0.8375 (pt0) cc_final: 0.8046 (pt0) REVERT: r 83 CYS cc_start: 0.8099 (m) cc_final: 0.7626 (t) REVERT: t 88 ASN cc_start: 0.6770 (t0) cc_final: 0.6545 (t0) REVERT: c 157 ILE cc_start: 0.8311 (mm) cc_final: 0.8002 (mt) REVERT: w 94 GLU cc_start: 0.5757 (mp0) cc_final: 0.5556 (mp0) REVERT: w 127 ASN cc_start: 0.7906 (p0) cc_final: 0.7489 (p0) REVERT: v 60 MET cc_start: 0.5596 (tpp) cc_final: 0.5297 (tpp) REVERT: o 111 MET cc_start: 0.4845 (OUTLIER) cc_final: 0.4225 (mtt) REVERT: k 131 VAL cc_start: 0.5081 (t) cc_final: 0.4827 (t) REVERT: h 62 ARG cc_start: 0.6141 (mtp85) cc_final: 0.5931 (mtp85) REVERT: U 90 LYS cc_start: 0.5113 (tptm) cc_final: 0.4824 (tptt) REVERT: B 501 ARG cc_start: 0.3671 (mmt180) cc_final: 0.3130 (mtt180) REVERT: A 309 ASN cc_start: 0.3829 (OUTLIER) cc_final: 0.2732 (m-40) REVERT: A 318 MET cc_start: 0.5314 (ppp) cc_final: 0.3602 (ptp) REVERT: C 572 HIS cc_start: 0.6458 (OUTLIER) cc_final: 0.5092 (t-170) REVERT: C 589 MET cc_start: 0.4445 (tpp) cc_final: 0.4185 (tpp) REVERT: E 112 MET cc_start: 0.5309 (pmm) cc_final: 0.4899 (ptt) REVERT: E 173 LEU cc_start: 0.4849 (OUTLIER) cc_final: 0.4425 (tt) REVERT: E 297 GLU cc_start: 0.4451 (mm-30) cc_final: 0.4170 (mt-10) REVERT: E 393 MET cc_start: 0.4101 (mpp) cc_final: 0.3890 (mpp) REVERT: F 278 ARG cc_start: 0.3221 (ttp-170) cc_final: 0.2481 (mmt-90) REVERT: F 317 LYS cc_start: 0.5851 (tttt) cc_final: 0.5258 (pttm) REVERT: F 356 ASN cc_start: 0.4813 (p0) cc_final: 0.4426 (p0) REVERT: H 247 MET cc_start: 0.5997 (mtm) cc_final: 0.5129 (tpp) REVERT: H 314 MET cc_start: 0.4446 (tpt) cc_final: 0.4027 (tpt) REVERT: K 90 ASP cc_start: 0.3928 (OUTLIER) cc_final: 0.3361 (m-30) REVERT: L 199 GLN cc_start: 0.4177 (mm-40) cc_final: 0.3148 (tt0) REVERT: L 265 LEU cc_start: 0.1388 (OUTLIER) cc_final: 0.1052 (mt) REVERT: L 288 TYR cc_start: 0.2125 (t80) cc_final: 0.1732 (t80) REVERT: L 304 MET cc_start: 0.2188 (pmm) cc_final: 0.0949 (mtm) REVERT: L 312 GLN cc_start: 0.0381 (pp30) cc_final: -0.0013 (pt0) REVERT: L 336 PHE cc_start: 0.3642 (OUTLIER) cc_final: 0.3357 (m-80) REVERT: L 430 ASN cc_start: 0.0882 (OUTLIER) cc_final: 0.0380 (m110) REVERT: L 497 MET cc_start: 0.2636 (ppp) cc_final: 0.2152 (mmt) REVERT: M 14 GLN cc_start: 0.1886 (mt0) cc_final: 0.1115 (mm-40) REVERT: M 82 LEU cc_start: 0.0198 (OUTLIER) cc_final: -0.0287 (mp) REVERT: M 98 ARG cc_start: 0.0732 (tpp-160) cc_final: 0.0343 (ptt180) REVERT: M 113 MET cc_start: 0.0190 (ttp) cc_final: -0.0385 (ptm) REVERT: M 263 ILE cc_start: 0.2967 (OUTLIER) cc_final: 0.2487 (tp) REVERT: M 277 MET cc_start: 0.4347 (tpp) cc_final: 0.3625 (tpp) REVERT: M 348 GLN cc_start: 0.3583 (tp40) cc_final: 0.2796 (tm-30) REVERT: 1 555 MET cc_start: 0.3790 (mmm) cc_final: 0.3384 (mmm) REVERT: D 54 ARG cc_start: 0.4930 (ttm170) cc_final: 0.4571 (ptm160) REVERT: D 191 GLN cc_start: 0.4735 (mp10) cc_final: 0.4320 (mp10) REVERT: D 212 ARG cc_start: 0.2905 (mmt90) cc_final: 0.2244 (ptm-80) REVERT: D 326 GLN cc_start: 0.4798 (tp40) cc_final: 0.4406 (tp40) REVERT: D 332 LYS cc_start: 0.5035 (mmtp) cc_final: 0.4746 (mmtt) REVERT: D 499 MET cc_start: 0.1301 (mmt) cc_final: 0.0889 (mmm) outliers start: 309 outliers final: 171 residues processed: 1265 average time/residue: 0.9470 time to fit residues: 2096.4308 Evaluate side-chains 1016 residues out of total 8865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 835 time to evaluate : 7.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 87 VAL Chi-restraints excluded: chain a residue 134 LEU Chi-restraints excluded: chain p residue 43 ASN Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 95 ASN Chi-restraints excluded: chain p residue 104 ASP Chi-restraints excluded: chain p residue 153 THR Chi-restraints excluded: chain p residue 218 LEU Chi-restraints excluded: chain p residue 230 GLU Chi-restraints excluded: chain d residue 132 ASP Chi-restraints excluded: chain d residue 185 THR Chi-restraints excluded: chain d residue 212 LYS Chi-restraints excluded: chain d residue 220 ASP Chi-restraints excluded: chain d residue 244 ILE Chi-restraints excluded: chain d residue 259 THR Chi-restraints excluded: chain d residue 262 THR Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 63 VAL Chi-restraints excluded: chain Q residue 71 LEU Chi-restraints excluded: chain q residue 45 ILE Chi-restraints excluded: chain q residue 126 VAL Chi-restraints excluded: chain q residue 133 THR Chi-restraints excluded: chain q residue 212 ASP Chi-restraints excluded: chain q residue 247 THR Chi-restraints excluded: chain r residue 57 ASP Chi-restraints excluded: chain r residue 78 SER Chi-restraints excluded: chain r residue 89 THR Chi-restraints excluded: chain r residue 129 VAL Chi-restraints excluded: chain r residue 153 VAL Chi-restraints excluded: chain s residue 9 VAL Chi-restraints excluded: chain s residue 46 THR Chi-restraints excluded: chain s residue 66 VAL Chi-restraints excluded: chain s residue 71 SER Chi-restraints excluded: chain s residue 80 VAL Chi-restraints excluded: chain s residue 105 THR Chi-restraints excluded: chain s residue 160 LYS Chi-restraints excluded: chain t residue 14 THR Chi-restraints excluded: chain t residue 130 THR Chi-restraints excluded: chain c residue 15 THR 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 n residue 15 THR Chi-restraints excluded: chain m residue 52 VAL Chi-restraints excluded: chain m residue 87 ASP Chi-restraints excluded: chain i residue 54 CYS Chi-restraints excluded: chain i residue 100 THR Chi-restraints excluded: chain y residue 39 VAL Chi-restraints excluded: chain f residue 9 ASP Chi-restraints excluded: chain j residue 58 GLU Chi-restraints excluded: chain j residue 61 GLN Chi-restraints excluded: chain j residue 64 SER Chi-restraints excluded: chain j residue 96 GLU Chi-restraints excluded: chain j residue 102 VAL Chi-restraints excluded: chain j residue 130 LEU Chi-restraints excluded: chain j residue 138 LYS Chi-restraints excluded: chain z residue 17 LEU Chi-restraints excluded: chain z residue 55 ILE Chi-restraints excluded: chain z residue 102 THR Chi-restraints excluded: chain z residue 120 THR Chi-restraints excluded: chain R residue 13 GLU Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain w residue 16 ILE Chi-restraints excluded: chain g residue 20 THR Chi-restraints excluded: chain g residue 78 VAL Chi-restraints excluded: chain b residue 134 CYS Chi-restraints excluded: chain b residue 170 THR Chi-restraints excluded: chain b residue 193 ASP Chi-restraints excluded: chain b residue 209 SER Chi-restraints excluded: chain e residue 25 THR Chi-restraints excluded: chain e residue 26 ASP Chi-restraints excluded: chain e residue 116 ILE Chi-restraints excluded: chain e residue 126 THR Chi-restraints excluded: chain e residue 136 ARG Chi-restraints excluded: chain e residue 168 THR Chi-restraints excluded: chain u residue 2 LEU Chi-restraints excluded: chain v residue 51 VAL Chi-restraints excluded: chain v residue 62 VAL Chi-restraints excluded: chain v residue 103 VAL Chi-restraints excluded: chain o residue 37 TYR Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain o residue 57 LEU Chi-restraints excluded: chain o residue 66 GLU Chi-restraints excluded: chain o residue 111 MET Chi-restraints excluded: chain o residue 127 LYS Chi-restraints excluded: chain k residue 53 THR Chi-restraints excluded: chain k residue 60 THR Chi-restraints excluded: chain k residue 120 HIS Chi-restraints excluded: chain x residue 12 GLN Chi-restraints excluded: chain x residue 35 ASP Chi-restraints excluded: chain h residue 45 GLU Chi-restraints excluded: chain h residue 60 THR Chi-restraints excluded: chain h residue 90 ASP Chi-restraints excluded: chain h residue 110 VAL Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 60 GLU Chi-restraints excluded: chain V residue 59 LEU Chi-restraints excluded: chain V residue 113 PHE Chi-restraints excluded: chain V residue 166 VAL Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 572 HIS Chi-restraints excluded: chain C residue 619 CYS Chi-restraints excluded: chain C residue 695 ILE Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 817 THR Chi-restraints excluded: chain C residue 826 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 339 PHE Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 322 ASP Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 141 PHE Chi-restraints excluded: chain L residue 265 LEU Chi-restraints excluded: chain L residue 293 VAL Chi-restraints excluded: chain L residue 336 PHE Chi-restraints excluded: chain L residue 346 THR Chi-restraints excluded: chain L residue 349 MET Chi-restraints excluded: chain L residue 353 THR Chi-restraints excluded: chain L residue 378 TYR Chi-restraints excluded: chain L residue 430 ASN Chi-restraints excluded: chain L residue 464 LEU Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 503 THR Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain M residue 179 ASP Chi-restraints excluded: chain M residue 263 ILE Chi-restraints excluded: chain M residue 266 LEU Chi-restraints excluded: chain 1 residue 154 ASN Chi-restraints excluded: chain 1 residue 275 ASP Chi-restraints excluded: chain 1 residue 300 THR Chi-restraints excluded: chain 1 residue 305 VAL Chi-restraints excluded: chain 1 residue 357 MET Chi-restraints excluded: chain 1 residue 386 THR Chi-restraints excluded: chain 1 residue 392 LEU Chi-restraints excluded: chain 1 residue 416 ILE Chi-restraints excluded: chain 1 residue 437 THR Chi-restraints excluded: chain 1 residue 459 VAL Chi-restraints excluded: chain 1 residue 493 ASP Chi-restraints excluded: chain 1 residue 543 THR Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 491 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1162 random chunks: chunk 586 optimal weight: 5.9990 chunk 327 optimal weight: 10.0000 chunk 878 optimal weight: 20.0000 chunk 718 optimal weight: 8.9990 chunk 291 optimal weight: 20.0000 chunk 1057 optimal weight: 2.9990 chunk 1141 optimal weight: 50.0000 chunk 941 optimal weight: 20.0000 chunk 1048 optimal weight: 9.9990 chunk 360 optimal weight: 10.0000 chunk 848 optimal weight: 0.5980 overall best weight: 5.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 95 ASN p 208 HIS d 172 ASN d 235 ASN q 8 HIS q 67 GLN q 157 ASN ** q 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 59 GLN ** s 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 165 ASN t 7 ASN t 167 GLN c 113 GLN c 154 GLN n 106 HIS m 62 GLN f 113 HIS z 19 GLN z 94 HIS ** w 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 165 ASN ** b 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 72 HIS ** k 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 64 ASN S 29 GLN l 3 HIS ** V 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 196 ASN B 543 ASN A 40 HIS A 180 GLN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 HIS ** C 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 ASN ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 403 GLN F 207 GLN F 342 ASN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 GLN ** H 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 181 GLN ** L 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 402 GLN ** M 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 44 GLN 1 208 HIS ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 300 GLN ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 GLN ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6507 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 120661 Z= 0.273 Angle : 0.679 11.911 171380 Z= 0.353 Chirality : 0.043 0.330 20736 Planarity : 0.005 0.114 15542 Dihedral : 21.889 178.292 37980 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.32 % Favored : 95.66 % Rotamer: Outliers : 4.82 % Allowed : 18.35 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.11 % Twisted Proline : 0.27 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.08), residues: 9955 helix: -1.11 (0.08), residues: 3872 sheet: -0.77 (0.14), residues: 1399 loop : -1.86 (0.08), residues: 4684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP V 177 HIS 0.011 0.001 HIS C 736 PHE 0.042 0.002 PHE N 63 TYR 0.024 0.002 TYR c 35 ARG 0.015 0.001 ARG H 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19910 Ramachandran restraints generated. 9955 Oldfield, 0 Emsley, 9955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19910 Ramachandran restraints generated. 9955 Oldfield, 0 Emsley, 9955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1321 residues out of total 8865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 384 poor density : 937 time to evaluate : 7.389 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: a 33 GLN cc_start: 0.8300 (pt0) cc_final: 0.7947 (pt0) REVERT: d 162 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8174 (tp) REVERT: r 16 ILE cc_start: 0.8288 (pt) cc_final: 0.8014 (mt) REVERT: r 83 CYS cc_start: 0.8099 (m) cc_final: 0.7604 (t) REVERT: s 160 LYS cc_start: 0.6783 (OUTLIER) cc_final: 0.6524 (ttpt) REVERT: c 157 ILE cc_start: 0.8454 (mm) cc_final: 0.8140 (mt) REVERT: f 18 GLU cc_start: 0.7230 (tp30) cc_final: 0.6833 (tm-30) REVERT: j 95 GLU cc_start: 0.6392 (mm-30) cc_final: 0.6100 (mm-30) REVERT: w 127 ASN cc_start: 0.7739 (p0) cc_final: 0.7458 (p0) REVERT: g 86 GLN cc_start: 0.6846 (tm-30) cc_final: 0.6509 (tp40) REVERT: g 88 ILE cc_start: 0.6294 (mm) cc_final: 0.6038 (mm) REVERT: b 143 ARG cc_start: 0.4583 (OUTLIER) cc_final: 0.4253 (tpt170) REVERT: b 156 LEU cc_start: 0.8217 (pt) cc_final: 0.7958 (pt) REVERT: e 195 GLU cc_start: 0.5339 (tp30) cc_final: 0.5064 (tp30) REVERT: u 49 MET cc_start: 0.8194 (mmm) cc_final: 0.7962 (mmm) REVERT: v 60 MET cc_start: 0.5445 (tpp) cc_final: 0.5194 (tpp) REVERT: o 107 ILE cc_start: 0.5985 (mm) cc_final: 0.5544 (mm) REVERT: o 111 MET cc_start: 0.5106 (OUTLIER) cc_final: 0.4242 (mtt) REVERT: S 51 ARG cc_start: 0.6835 (ttp-170) cc_final: 0.6606 (ttp-170) REVERT: B 501 ARG cc_start: 0.3557 (mmt180) cc_final: 0.3139 (mtt180) REVERT: B 504 ILE cc_start: 0.3639 (OUTLIER) cc_final: 0.3397 (pt) REVERT: A 87 GLU cc_start: 0.4493 (OUTLIER) cc_final: 0.4107 (tp30) REVERT: A 306 MET cc_start: 0.4297 (ttp) cc_final: 0.2601 (mpp) REVERT: A 318 MET cc_start: 0.5199 (ppp) cc_final: 0.3703 (ptp) REVERT: C 572 HIS cc_start: 0.6274 (OUTLIER) cc_final: 0.5069 (t-170) REVERT: C 876 HIS cc_start: 0.1186 (OUTLIER) cc_final: 0.0960 (m-70) REVERT: E 112 MET cc_start: 0.5268 (pmm) cc_final: 0.4830 (ptt) REVERT: E 297 GLU cc_start: 0.4496 (mm-30) cc_final: 0.4260 (mt-10) REVERT: E 393 MET cc_start: 0.4115 (mpp) cc_final: 0.3783 (mpp) REVERT: E 407 LYS cc_start: 0.3735 (OUTLIER) cc_final: 0.2627 (mmmt) REVERT: F 278 ARG cc_start: 0.3432 (ttp-170) cc_final: 0.2947 (mmt-90) REVERT: F 317 LYS cc_start: 0.6047 (tttt) cc_final: 0.5297 (ptpp) REVERT: F 356 ASN cc_start: 0.4666 (p0) cc_final: 0.4437 (p0) REVERT: H 198 PHE cc_start: 0.1583 (m-10) cc_final: 0.1256 (m-10) REVERT: H 247 MET cc_start: 0.6181 (mtm) cc_final: 0.5141 (tpt) REVERT: H 253 MET cc_start: 0.2818 (ttp) cc_final: 0.2477 (ptm) REVERT: H 343 MET cc_start: 0.3500 (mtm) cc_final: 0.2945 (mtp) REVERT: K 82 PHE cc_start: 0.6404 (t80) cc_final: 0.5857 (t80) REVERT: K 90 ASP cc_start: 0.4074 (OUTLIER) cc_final: 0.3581 (m-30) REVERT: L 199 GLN cc_start: 0.4279 (mm-40) cc_final: 0.3857 (mt0) REVERT: L 240 ILE cc_start: -0.0347 (OUTLIER) cc_final: -0.0718 (mt) REVERT: L 265 LEU cc_start: 0.1530 (OUTLIER) cc_final: 0.1160 (mt) REVERT: L 268 MET cc_start: 0.2721 (mpp) cc_final: 0.2227 (mpp) REVERT: L 304 MET cc_start: 0.2614 (pmm) cc_final: 0.0959 (mtm) REVERT: L 336 PHE cc_start: 0.3343 (OUTLIER) cc_final: 0.2881 (m-80) REVERT: L 367 MET cc_start: 0.0467 (mmt) cc_final: -0.0079 (mmp) REVERT: L 483 GLU cc_start: 0.2599 (OUTLIER) cc_final: 0.2331 (mt-10) REVERT: L 527 MET cc_start: 0.2817 (ttm) cc_final: 0.2608 (tpp) REVERT: M 98 ARG cc_start: 0.0881 (tpp-160) cc_final: 0.0254 (ptt180) REVERT: M 113 MET cc_start: 0.0802 (ttp) cc_final: -0.0001 (ptm) REVERT: M 263 ILE cc_start: 0.3046 (OUTLIER) cc_final: 0.2327 (tp) REVERT: M 277 MET cc_start: 0.4712 (tpp) cc_final: 0.3971 (tpp) REVERT: M 348 GLN cc_start: 0.3638 (tp40) cc_final: 0.2911 (tm-30) REVERT: M 357 TRP cc_start: 0.6028 (m-10) cc_final: 0.5694 (m-10) REVERT: 1 99 ILE cc_start: 0.7867 (OUTLIER) cc_final: 0.7503 (mp) REVERT: D 54 ARG cc_start: 0.4914 (ttm170) cc_final: 0.4620 (ptm160) REVERT: D 191 GLN cc_start: 0.4493 (mp10) cc_final: 0.4137 (mp10) REVERT: D 326 GLN cc_start: 0.4757 (tp40) cc_final: 0.4401 (tp40) REVERT: D 332 LYS cc_start: 0.4853 (mmtp) cc_final: 0.4490 (mptt) outliers start: 384 outliers final: 249 residues processed: 1225 average time/residue: 0.9341 time to fit residues: 2008.9636 Evaluate side-chains 1074 residues out of total 8865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 809 time to evaluate : 6.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 134 LEU Chi-restraints excluded: chain p residue 43 ASN Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 96 CYS Chi-restraints excluded: chain p residue 104 ASP Chi-restraints excluded: chain p residue 153 THR Chi-restraints excluded: chain p residue 208 HIS Chi-restraints excluded: chain p residue 209 ASP Chi-restraints excluded: chain p residue 218 LEU Chi-restraints excluded: chain p residue 224 GLU Chi-restraints excluded: chain p residue 230 GLU Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 132 ASP Chi-restraints excluded: chain d residue 162 ILE Chi-restraints excluded: chain d residue 185 THR Chi-restraints excluded: chain d residue 212 LYS Chi-restraints excluded: chain d residue 220 ASP Chi-restraints excluded: chain d residue 244 ILE Chi-restraints excluded: chain d residue 259 THR Chi-restraints excluded: chain d residue 262 THR Chi-restraints excluded: chain d residue 270 THR Chi-restraints excluded: chain d residue 271 ASP Chi-restraints excluded: chain Q residue 55 GLU Chi-restraints excluded: chain Q residue 63 VAL Chi-restraints excluded: chain Q residue 71 LEU Chi-restraints excluded: chain Q residue 84 VAL Chi-restraints excluded: chain q residue 45 ILE Chi-restraints excluded: chain q residue 126 VAL Chi-restraints excluded: chain q residue 156 VAL Chi-restraints excluded: chain q residue 181 CYS Chi-restraints excluded: chain q residue 212 ASP Chi-restraints excluded: chain q residue 247 THR Chi-restraints excluded: chain r residue 57 ASP Chi-restraints excluded: chain r residue 78 SER Chi-restraints excluded: chain r residue 89 THR Chi-restraints excluded: chain r residue 112 VAL Chi-restraints excluded: chain r residue 129 VAL Chi-restraints excluded: chain r residue 153 VAL Chi-restraints excluded: chain r residue 163 ASN Chi-restraints excluded: chain s residue 9 VAL Chi-restraints excluded: chain s residue 46 THR Chi-restraints excluded: chain s residue 66 VAL Chi-restraints excluded: chain s residue 80 VAL Chi-restraints excluded: chain s residue 86 LYS Chi-restraints excluded: chain s residue 105 THR Chi-restraints excluded: chain s residue 132 ASP Chi-restraints excluded: chain s residue 148 LEU Chi-restraints excluded: chain s residue 160 LYS Chi-restraints excluded: chain t residue 14 THR Chi-restraints excluded: chain t residue 92 ARG Chi-restraints excluded: chain t residue 105 ASP Chi-restraints excluded: chain t residue 130 THR Chi-restraints excluded: chain c residue 61 LEU Chi-restraints excluded: chain c residue 95 ASP Chi-restraints excluded: chain c residue 104 ASP Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 149 VAL Chi-restraints excluded: chain n residue 6 THR Chi-restraints excluded: chain n residue 15 THR Chi-restraints excluded: chain n residue 91 ASP Chi-restraints excluded: chain n residue 143 LEU Chi-restraints excluded: chain m residue 37 ILE Chi-restraints excluded: chain m residue 87 ASP Chi-restraints excluded: chain i residue 27 VAL Chi-restraints excluded: chain i residue 52 THR Chi-restraints excluded: chain i residue 54 CYS Chi-restraints excluded: chain i residue 100 THR Chi-restraints excluded: chain i residue 119 LEU Chi-restraints excluded: chain i residue 131 ASP Chi-restraints excluded: chain y residue 35 ASN Chi-restraints excluded: chain y residue 39 VAL Chi-restraints excluded: chain f residue 25 VAL Chi-restraints excluded: chain f residue 41 MET Chi-restraints excluded: chain f residue 80 ASP Chi-restraints excluded: chain j residue 52 LEU Chi-restraints excluded: chain j residue 58 GLU Chi-restraints excluded: chain j residue 64 SER Chi-restraints excluded: chain j residue 102 VAL Chi-restraints excluded: chain j residue 130 LEU Chi-restraints excluded: chain j residue 138 LYS Chi-restraints excluded: chain z residue 14 THR Chi-restraints excluded: chain z residue 17 LEU Chi-restraints excluded: chain z residue 55 ILE Chi-restraints excluded: chain z residue 74 MET Chi-restraints excluded: chain z residue 102 THR Chi-restraints excluded: chain z residue 120 THR Chi-restraints excluded: chain R residue 13 GLU Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain w residue 57 LEU Chi-restraints excluded: chain w residue 69 ILE Chi-restraints excluded: chain w residue 118 GLN Chi-restraints excluded: chain g residue 20 THR Chi-restraints excluded: chain g residue 63 PHE Chi-restraints excluded: chain g residue 111 ILE Chi-restraints excluded: chain g residue 113 ILE Chi-restraints excluded: chain b residue 134 CYS Chi-restraints excluded: chain b residue 143 ARG Chi-restraints excluded: chain b residue 170 THR Chi-restraints excluded: chain b residue 193 ASP Chi-restraints excluded: chain b residue 209 SER Chi-restraints excluded: chain e residue 26 ASP Chi-restraints excluded: chain e residue 37 ASP Chi-restraints excluded: chain e residue 116 ILE Chi-restraints excluded: chain e residue 136 ARG Chi-restraints excluded: chain e residue 168 THR Chi-restraints excluded: chain u residue 2 LEU Chi-restraints excluded: chain u residue 74 GLU Chi-restraints excluded: chain v residue 62 VAL Chi-restraints excluded: chain v residue 103 VAL Chi-restraints excluded: chain o residue 37 TYR Chi-restraints excluded: chain o residue 66 GLU Chi-restraints excluded: chain o residue 111 MET Chi-restraints excluded: chain o residue 127 LYS Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 53 THR Chi-restraints excluded: chain k residue 60 THR Chi-restraints excluded: chain k residue 120 HIS Chi-restraints excluded: chain k residue 136 THR Chi-restraints excluded: chain x residue 35 ASP Chi-restraints excluded: chain x residue 50 GLU Chi-restraints excluded: chain x residue 66 LEU Chi-restraints excluded: chain h residue 45 GLU Chi-restraints excluded: chain h residue 76 THR Chi-restraints excluded: chain h residue 90 ASP Chi-restraints excluded: chain h residue 110 VAL Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain S residue 60 GLU Chi-restraints excluded: chain l residue 38 MET Chi-restraints excluded: chain l residue 53 ILE Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 102 VAL Chi-restraints excluded: chain V residue 113 PHE Chi-restraints excluded: chain V residue 115 SER Chi-restraints excluded: chain V residue 166 VAL Chi-restraints excluded: chain V residue 171 ASP Chi-restraints excluded: chain V residue 176 VAL Chi-restraints excluded: chain V residue 265 ILE Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain A residue 47 HIS Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 382 TYR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 504 ASP Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 403 ASP Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 444 ILE Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 572 HIS Chi-restraints excluded: chain C residue 591 MET Chi-restraints excluded: chain C residue 619 CYS Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 671 VAL Chi-restraints excluded: chain C residue 695 ILE Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain C residue 817 THR Chi-restraints excluded: chain C residue 826 ILE Chi-restraints excluded: chain C residue 876 HIS Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain E residue 407 LYS Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 322 ASP Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 128 LEU Chi-restraints excluded: chain K residue 141 PHE Chi-restraints excluded: chain L residue 181 GLN Chi-restraints excluded: chain L residue 240 ILE Chi-restraints excluded: chain L residue 265 LEU Chi-restraints excluded: chain L residue 293 VAL Chi-restraints excluded: chain L residue 296 ASN Chi-restraints excluded: chain L residue 336 PHE Chi-restraints excluded: chain L residue 339 ILE Chi-restraints excluded: chain L residue 346 THR Chi-restraints excluded: chain L residue 353 THR Chi-restraints excluded: chain L residue 378 TYR Chi-restraints excluded: chain L residue 388 LEU Chi-restraints excluded: chain L residue 452 GLN Chi-restraints excluded: chain L residue 483 GLU Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 503 THR Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 121 TYR Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain M residue 145 ASP Chi-restraints excluded: chain M residue 188 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 226 LEU Chi-restraints excluded: chain M residue 263 ILE Chi-restraints excluded: chain M residue 266 LEU Chi-restraints excluded: chain M residue 341 THR Chi-restraints excluded: chain M residue 361 LEU Chi-restraints excluded: chain 1 residue 13 HIS Chi-restraints excluded: chain 1 residue 44 GLN Chi-restraints excluded: chain 1 residue 63 LYS Chi-restraints excluded: chain 1 residue 99 ILE Chi-restraints excluded: chain 1 residue 154 ASN Chi-restraints excluded: chain 1 residue 196 THR Chi-restraints excluded: chain 1 residue 270 ILE Chi-restraints excluded: chain 1 residue 300 THR Chi-restraints excluded: chain 1 residue 305 VAL Chi-restraints excluded: chain 1 residue 357 MET Chi-restraints excluded: chain 1 residue 386 THR Chi-restraints excluded: chain 1 residue 416 ILE Chi-restraints excluded: chain 1 residue 437 THR Chi-restraints excluded: chain 1 residue 459 VAL Chi-restraints excluded: chain 1 residue 493 ASP Chi-restraints excluded: chain 1 residue 526 THR Chi-restraints excluded: chain 1 residue 543 THR Chi-restraints excluded: chain 1 residue 598 ASP Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 307 ASN Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 509 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1162 random chunks: chunk 1044 optimal weight: 10.0000 chunk 794 optimal weight: 7.9990 chunk 548 optimal weight: 30.0000 chunk 117 optimal weight: 7.9990 chunk 504 optimal weight: 9.9990 chunk 709 optimal weight: 10.0000 chunk 1060 optimal weight: 9.9990 chunk 1123 optimal weight: 0.4980 chunk 554 optimal weight: 5.9990 chunk 1005 optimal weight: 0.0040 chunk 302 optimal weight: 10.0000 overall best weight: 4.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** p 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 232 HIS d 136 HIS ** d 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 157 ASN ** q 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 7 ASN t 84 ASN t 167 GLN c 113 GLN m 62 GLN ** y 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 61 GLN z 19 GLN g 24 HIS b 165 ASN ** b 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 28 ASN S 29 GLN V 222 ASN B 502 GLN A 229 HIS ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 631 ASN C 724 GLN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN ** H 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 238 HIS ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 151 GLN K 218 GLN ** L 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 402 GLN L 454 GLN L 529 HIS ** M 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 272 GLN ** M 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 44 GLN 1 438 HIS ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 GLN ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6499 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 120661 Z= 0.222 Angle : 0.621 13.263 171380 Z= 0.323 Chirality : 0.041 0.289 20736 Planarity : 0.004 0.111 15542 Dihedral : 21.775 178.407 37977 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.49 % Favored : 95.49 % Rotamer: Outliers : 4.89 % Allowed : 20.34 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.11 % Twisted Proline : 0.27 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.08), residues: 9955 helix: -0.61 (0.08), residues: 3887 sheet: -0.66 (0.14), residues: 1391 loop : -1.73 (0.08), residues: 4677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP V 177 HIS 0.044 0.001 HIS p 208 PHE 0.023 0.002 PHE q 86 TYR 0.019 0.002 TYR d 82 ARG 0.007 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19910 Ramachandran restraints generated. 9955 Oldfield, 0 Emsley, 9955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19910 Ramachandran restraints generated. 9955 Oldfield, 0 Emsley, 9955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1300 residues out of total 8865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 390 poor density : 910 time to evaluate : 7.553 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: a 33 GLN cc_start: 0.8110 (pt0) cc_final: 0.7881 (pt0) REVERT: r 83 CYS cc_start: 0.8019 (m) cc_final: 0.7670 (t) REVERT: r 154 ARG cc_start: 0.6422 (OUTLIER) cc_final: 0.6219 (mtm180) REVERT: s 160 LYS cc_start: 0.6554 (OUTLIER) cc_final: 0.6333 (ttpt) REVERT: c 157 ILE cc_start: 0.8461 (mm) cc_final: 0.8249 (mt) REVERT: j 95 GLU cc_start: 0.6458 (mm-30) cc_final: 0.6254 (mm-30) REVERT: R 31 TYR cc_start: 0.8304 (p90) cc_final: 0.7985 (p90) REVERT: w 127 ASN cc_start: 0.7716 (p0) cc_final: 0.7400 (p0) REVERT: b 156 LEU cc_start: 0.8134 (pt) cc_final: 0.7831 (pt) REVERT: u 49 MET cc_start: 0.8235 (mmm) cc_final: 0.7993 (mmm) REVERT: v 60 MET cc_start: 0.5500 (tpp) cc_final: 0.5264 (tpp) REVERT: o 111 MET cc_start: 0.5312 (OUTLIER) cc_final: 0.4379 (mtt) REVERT: x 66 LEU cc_start: 0.6827 (OUTLIER) cc_final: 0.6613 (mt) REVERT: S 51 ARG cc_start: 0.6915 (ttp-170) cc_final: 0.6568 (ttp-170) REVERT: B 496 MET cc_start: 0.4048 (mtp) cc_final: 0.3822 (mtp) REVERT: B 501 ARG cc_start: 0.3274 (mmt180) cc_final: 0.2935 (mtt180) REVERT: A 87 GLU cc_start: 0.4395 (OUTLIER) cc_final: 0.4066 (tp30) REVERT: A 306 MET cc_start: 0.4356 (ttp) cc_final: 0.2824 (mpp) REVERT: A 318 MET cc_start: 0.5248 (ppp) cc_final: 0.3568 (ptp) REVERT: C 572 HIS cc_start: 0.6288 (OUTLIER) cc_final: 0.4900 (t-170) REVERT: E 104 MET cc_start: 0.1371 (mtt) cc_final: 0.0224 (ptt) REVERT: E 112 MET cc_start: 0.5228 (pmm) cc_final: 0.4918 (ptt) REVERT: E 393 MET cc_start: 0.3896 (mpp) cc_final: 0.3608 (mpp) REVERT: F 278 ARG cc_start: 0.3226 (ttp-170) cc_final: 0.2887 (mmt-90) REVERT: F 317 LYS cc_start: 0.5906 (tttt) cc_final: 0.4987 (ptpp) REVERT: H 168 ARG cc_start: 0.4807 (OUTLIER) cc_final: 0.4397 (tpt-90) REVERT: H 253 MET cc_start: 0.2734 (ttp) cc_final: 0.2297 (ptm) REVERT: H 338 LEU cc_start: 0.3966 (OUTLIER) cc_final: 0.3722 (tt) REVERT: K 82 PHE cc_start: 0.6389 (t80) cc_final: 0.5896 (t80) REVERT: K 90 ASP cc_start: 0.4059 (OUTLIER) cc_final: 0.3522 (m-30) REVERT: L 199 GLN cc_start: 0.4439 (mm-40) cc_final: 0.3270 (tt0) REVERT: L 265 LEU cc_start: 0.1714 (OUTLIER) cc_final: 0.1325 (mt) REVERT: L 268 MET cc_start: 0.3184 (OUTLIER) cc_final: 0.2754 (mpp) REVERT: L 304 MET cc_start: 0.2555 (pmm) cc_final: 0.0752 (ttm) REVERT: L 325 MET cc_start: 0.3716 (mmp) cc_final: 0.3076 (mmm) REVERT: L 336 PHE cc_start: 0.3352 (OUTLIER) cc_final: 0.2790 (m-80) REVERT: L 367 MET cc_start: 0.0506 (mmt) cc_final: -0.0006 (mmp) REVERT: L 430 ASN cc_start: 0.0871 (OUTLIER) cc_final: 0.0390 (m110) REVERT: L 483 GLU cc_start: 0.2741 (OUTLIER) cc_final: 0.2442 (mt-10) REVERT: L 497 MET cc_start: 0.2788 (ppp) cc_final: 0.2274 (mtt) REVERT: L 527 MET cc_start: 0.3485 (ttm) cc_final: 0.3268 (tpp) REVERT: L 547 ILE cc_start: -0.1573 (mm) cc_final: -0.2055 (mm) REVERT: M 98 ARG cc_start: 0.0807 (tpp-160) cc_final: 0.0018 (ptt180) REVERT: M 113 MET cc_start: 0.0848 (ttp) cc_final: -0.0152 (ptm) REVERT: M 277 MET cc_start: 0.4546 (tpp) cc_final: 0.3868 (tpp) REVERT: M 348 GLN cc_start: 0.3631 (tp40) cc_final: 0.3069 (tm-30) REVERT: 1 237 ILE cc_start: 0.5593 (OUTLIER) cc_final: 0.5339 (mt) REVERT: 1 436 TYR cc_start: 0.2600 (OUTLIER) cc_final: 0.2243 (m-10) REVERT: N 60 VAL cc_start: 0.5095 (OUTLIER) cc_final: 0.4774 (m) REVERT: D 54 ARG cc_start: 0.4929 (ttm170) cc_final: 0.4531 (ptm160) REVERT: D 191 GLN cc_start: 0.4555 (mp10) cc_final: 0.4085 (mp10) REVERT: D 326 GLN cc_start: 0.4657 (tp40) cc_final: 0.4371 (tp40) outliers start: 390 outliers final: 258 residues processed: 1201 average time/residue: 0.9330 time to fit residues: 1974.6776 Evaluate side-chains 1088 residues out of total 8865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 275 poor density : 813 time to evaluate : 7.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 87 VAL Chi-restraints excluded: chain a residue 130 ASP Chi-restraints excluded: chain a residue 134 LEU Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 96 CYS Chi-restraints excluded: chain p residue 98 THR Chi-restraints excluded: chain p residue 104 ASP Chi-restraints excluded: chain p residue 153 THR Chi-restraints excluded: chain p residue 218 LEU Chi-restraints excluded: chain p residue 224 GLU Chi-restraints excluded: chain p residue 230 GLU Chi-restraints excluded: chain d residue 132 ASP Chi-restraints excluded: chain d residue 185 THR Chi-restraints excluded: chain d residue 212 LYS Chi-restraints excluded: chain d residue 220 ASP Chi-restraints excluded: chain d residue 244 ILE Chi-restraints excluded: chain d residue 259 THR Chi-restraints excluded: chain d residue 262 THR Chi-restraints excluded: chain d residue 271 ASP Chi-restraints excluded: chain Q residue 2 THR Chi-restraints excluded: chain Q residue 46 GLU Chi-restraints excluded: chain Q residue 63 VAL Chi-restraints excluded: chain Q residue 67 LEU Chi-restraints excluded: chain Q residue 71 LEU Chi-restraints excluded: chain Q residue 84 VAL Chi-restraints excluded: chain q residue 45 ILE Chi-restraints excluded: chain q residue 117 GLU Chi-restraints excluded: chain q residue 126 VAL Chi-restraints excluded: chain q residue 156 VAL Chi-restraints excluded: chain q residue 181 CYS Chi-restraints excluded: chain q residue 212 ASP Chi-restraints excluded: chain q residue 247 THR Chi-restraints excluded: chain r residue 57 ASP Chi-restraints excluded: chain r residue 89 THR Chi-restraints excluded: chain r residue 112 VAL Chi-restraints excluded: chain r residue 114 VAL Chi-restraints excluded: chain r residue 153 VAL Chi-restraints excluded: chain r residue 154 ARG Chi-restraints excluded: chain s residue 9 VAL Chi-restraints excluded: chain s residue 46 THR Chi-restraints excluded: chain s residue 66 VAL Chi-restraints excluded: chain s residue 80 VAL Chi-restraints excluded: chain s residue 105 THR Chi-restraints excluded: chain s residue 148 LEU Chi-restraints excluded: chain s residue 160 LYS Chi-restraints excluded: chain t residue 14 THR Chi-restraints excluded: chain t residue 92 ARG Chi-restraints excluded: chain t residue 105 ASP Chi-restraints excluded: chain t residue 130 THR Chi-restraints excluded: chain t residue 166 PHE Chi-restraints excluded: chain c residue 18 ARG 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 n residue 15 THR Chi-restraints excluded: chain n residue 143 LEU Chi-restraints excluded: chain m residue 52 VAL Chi-restraints excluded: chain m residue 87 ASP Chi-restraints excluded: chain i residue 54 CYS Chi-restraints excluded: chain i residue 100 THR Chi-restraints excluded: chain i residue 119 LEU Chi-restraints excluded: chain i residue 131 ASP Chi-restraints excluded: chain y residue 35 ASN Chi-restraints excluded: chain y residue 39 VAL Chi-restraints excluded: chain f residue 9 ASP Chi-restraints excluded: chain f residue 41 MET Chi-restraints excluded: chain f residue 80 ASP Chi-restraints excluded: chain j residue 58 GLU Chi-restraints excluded: chain j residue 64 SER Chi-restraints excluded: chain j residue 96 GLU Chi-restraints excluded: chain j residue 102 VAL Chi-restraints excluded: chain j residue 105 PHE Chi-restraints excluded: chain j residue 123 VAL Chi-restraints excluded: chain j residue 128 VAL Chi-restraints excluded: chain j residue 138 LYS Chi-restraints excluded: chain z residue 14 THR Chi-restraints excluded: chain z residue 17 LEU Chi-restraints excluded: chain z residue 55 ILE Chi-restraints excluded: chain z residue 74 MET Chi-restraints excluded: chain z residue 102 THR Chi-restraints excluded: chain R residue 13 GLU Chi-restraints excluded: chain R residue 40 CYS Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain T residue 44 ASN Chi-restraints excluded: chain w residue 57 LEU Chi-restraints excluded: chain w residue 69 ILE Chi-restraints excluded: chain w residue 98 VAL Chi-restraints excluded: chain w residue 118 GLN Chi-restraints excluded: chain g residue 20 THR Chi-restraints excluded: chain g residue 63 PHE Chi-restraints excluded: chain g residue 84 ILE Chi-restraints excluded: chain g residue 113 ILE Chi-restraints excluded: chain b residue 134 CYS Chi-restraints excluded: chain b residue 170 THR Chi-restraints excluded: chain b residue 193 ASP Chi-restraints excluded: chain b residue 209 SER Chi-restraints excluded: chain e residue 26 ASP Chi-restraints excluded: chain e residue 78 MET Chi-restraints excluded: chain e residue 116 ILE Chi-restraints excluded: chain e residue 126 THR Chi-restraints excluded: chain e residue 136 ARG Chi-restraints excluded: chain e residue 140 ASP Chi-restraints excluded: chain e residue 168 THR Chi-restraints excluded: chain u residue 2 LEU Chi-restraints excluded: chain u residue 58 VAL Chi-restraints excluded: chain u residue 74 GLU Chi-restraints excluded: chain v residue 45 ARG Chi-restraints excluded: chain v residue 62 VAL Chi-restraints excluded: chain v residue 103 VAL Chi-restraints excluded: chain o residue 37 TYR Chi-restraints excluded: chain o residue 111 MET Chi-restraints excluded: chain o residue 127 LYS Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 44 VAL Chi-restraints excluded: chain k residue 53 THR Chi-restraints excluded: chain k residue 60 THR Chi-restraints excluded: chain k residue 136 THR Chi-restraints excluded: chain x residue 5 THR Chi-restraints excluded: chain x residue 35 ASP Chi-restraints excluded: chain x residue 50 GLU Chi-restraints excluded: chain x residue 66 LEU Chi-restraints excluded: chain x residue 124 THR Chi-restraints excluded: chain h residue 23 THR Chi-restraints excluded: chain h residue 36 CYS Chi-restraints excluded: chain h residue 45 GLU Chi-restraints excluded: chain h residue 90 ASP Chi-restraints excluded: chain h residue 110 VAL Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain l residue 53 ILE Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 104 HIS Chi-restraints excluded: chain V residue 113 PHE Chi-restraints excluded: chain V residue 166 VAL Chi-restraints excluded: chain V residue 171 ASP Chi-restraints excluded: chain V residue 186 THR Chi-restraints excluded: chain V residue 198 VAL Chi-restraints excluded: chain V residue 265 ILE Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 382 TYR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 403 ASP Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 444 ILE Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 572 HIS Chi-restraints excluded: chain C residue 591 MET Chi-restraints excluded: chain C residue 619 CYS Chi-restraints excluded: chain C residue 695 ILE Chi-restraints excluded: chain C residue 734 ARG Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain C residue 817 THR Chi-restraints excluded: chain C residue 826 ILE Chi-restraints excluded: chain C residue 876 HIS Chi-restraints excluded: chain E residue 20 PHE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain E residue 409 LYS Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 322 ASP Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 168 ARG Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 338 LEU Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 141 PHE Chi-restraints excluded: chain K residue 150 TYR Chi-restraints excluded: chain L residue 265 LEU Chi-restraints excluded: chain L residue 268 MET Chi-restraints excluded: chain L residue 293 VAL Chi-restraints excluded: chain L residue 336 PHE Chi-restraints excluded: chain L residue 339 ILE Chi-restraints excluded: chain L residue 346 THR Chi-restraints excluded: chain L residue 353 THR Chi-restraints excluded: chain L residue 378 TYR Chi-restraints excluded: chain L residue 388 LEU Chi-restraints excluded: chain L residue 412 LEU Chi-restraints excluded: chain L residue 430 ASN Chi-restraints excluded: chain L residue 452 GLN Chi-restraints excluded: chain L residue 470 MET Chi-restraints excluded: chain L residue 483 GLU Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 503 THR Chi-restraints excluded: chain L residue 522 TYR Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 121 TYR Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain M residue 145 ASP Chi-restraints excluded: chain M residue 188 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 226 LEU Chi-restraints excluded: chain M residue 266 LEU Chi-restraints excluded: chain M residue 297 MET Chi-restraints excluded: chain M residue 361 LEU Chi-restraints excluded: chain 1 residue 13 HIS Chi-restraints excluded: chain 1 residue 154 ASN Chi-restraints excluded: chain 1 residue 196 THR Chi-restraints excluded: chain 1 residue 237 ILE Chi-restraints excluded: chain 1 residue 270 ILE Chi-restraints excluded: chain 1 residue 271 VAL Chi-restraints excluded: chain 1 residue 300 THR Chi-restraints excluded: chain 1 residue 305 VAL Chi-restraints excluded: chain 1 residue 326 ASP Chi-restraints excluded: chain 1 residue 386 THR Chi-restraints excluded: chain 1 residue 392 LEU Chi-restraints excluded: chain 1 residue 416 ILE Chi-restraints excluded: chain 1 residue 436 TYR Chi-restraints excluded: chain 1 residue 437 THR Chi-restraints excluded: chain 1 residue 459 VAL Chi-restraints excluded: chain 1 residue 493 ASP Chi-restraints excluded: chain 1 residue 517 VAL Chi-restraints excluded: chain 1 residue 543 THR Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 69 CYS Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 465 ILE Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 509 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1162 random chunks: chunk 935 optimal weight: 3.9990 chunk 637 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 836 optimal weight: 20.0000 chunk 463 optimal weight: 0.5980 chunk 958 optimal weight: 30.0000 chunk 776 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 573 optimal weight: 0.8980 chunk 1008 optimal weight: 8.9990 chunk 283 optimal weight: 10.0000 overall best weight: 4.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 113 GLN ** p 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 208 HIS ** d 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 157 ASN ** q 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 7 ASN t 167 GLN c 113 GLN m 62 GLN ** y 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 24 HIS b 101 GLN b 165 ASN ** b 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 42 ASN ** u 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 61 GLN ** k 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 196 ASN V 311 GLN B 543 ASN A 229 HIS ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 ASN A 399 ASN ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 GLN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 336 GLN ** H 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 36 GLN ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 151 GLN K 218 GLN L 181 GLN L 363 GLN ** L 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 402 GLN ** M 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 233 GLN 1 593 ASN ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 120661 Z= 0.213 Angle : 0.609 13.817 171380 Z= 0.315 Chirality : 0.040 0.289 20736 Planarity : 0.004 0.106 15542 Dihedral : 21.690 178.384 37977 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.06 % Favored : 94.92 % Rotamer: Outliers : 5.37 % Allowed : 21.12 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.11 % Twisted Proline : 0.27 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.08), residues: 9955 helix: -0.32 (0.08), residues: 3915 sheet: -0.64 (0.14), residues: 1367 loop : -1.66 (0.09), residues: 4673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP V 177 HIS 0.010 0.001 HIS u 84 PHE 0.021 0.002 PHE q 86 TYR 0.022 0.001 TYR d 82 ARG 0.006 0.000 ARG B 532 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19910 Ramachandran restraints generated. 9955 Oldfield, 0 Emsley, 9955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19910 Ramachandran restraints generated. 9955 Oldfield, 0 Emsley, 9955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1304 residues out of total 8865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 428 poor density : 876 time to evaluate : 7.482 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: a 73 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7425 (p0) REVERT: d 79 GLU cc_start: 0.6862 (mm-30) cc_final: 0.6577 (mm-30) REVERT: Q 72 HIS cc_start: 0.7175 (OUTLIER) cc_final: 0.6881 (m90) REVERT: r 83 CYS cc_start: 0.7986 (m) cc_final: 0.7635 (t) REVERT: f 85 ASP cc_start: 0.6786 (OUTLIER) cc_final: 0.6447 (m-30) REVERT: R 75 GLU cc_start: 0.7054 (mm-30) cc_final: 0.6787 (mm-30) REVERT: w 127 ASN cc_start: 0.7630 (p0) cc_final: 0.7336 (p0) REVERT: b 143 ARG cc_start: 0.4712 (OUTLIER) cc_final: 0.4252 (tpt170) REVERT: b 156 LEU cc_start: 0.8011 (pt) cc_final: 0.7754 (pt) REVERT: v 60 MET cc_start: 0.5351 (tpp) cc_final: 0.5105 (tpp) REVERT: o 111 MET cc_start: 0.5320 (OUTLIER) cc_final: 0.4403 (mtt) REVERT: x 28 LEU cc_start: 0.4698 (OUTLIER) cc_final: 0.4017 (pt) REVERT: x 66 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6749 (mt) REVERT: x 126 GLN cc_start: 0.6147 (tm-30) cc_final: 0.5849 (tm-30) REVERT: A 87 GLU cc_start: 0.4400 (OUTLIER) cc_final: 0.4127 (tp30) REVERT: A 153 LEU cc_start: 0.7019 (tp) cc_final: 0.6792 (tp) REVERT: A 184 PHE cc_start: 0.5473 (OUTLIER) cc_final: 0.4177 (t80) REVERT: C 572 HIS cc_start: 0.6121 (OUTLIER) cc_final: 0.4981 (t-170) REVERT: E 50 MET cc_start: 0.4575 (tpp) cc_final: 0.3947 (tpp) REVERT: E 104 MET cc_start: 0.1198 (mtt) cc_final: 0.0165 (ptt) REVERT: E 112 MET cc_start: 0.5014 (pmm) cc_final: 0.4764 (ptt) REVERT: E 393 MET cc_start: 0.3871 (mpp) cc_final: 0.3433 (mpp) REVERT: F 207 GLN cc_start: 0.3403 (OUTLIER) cc_final: 0.2234 (tm130) REVERT: F 278 ARG cc_start: 0.2910 (ttp-170) cc_final: 0.2651 (mmt-90) REVERT: F 317 LYS cc_start: 0.6003 (tttt) cc_final: 0.5790 (tttt) REVERT: F 326 MET cc_start: 0.4618 (tpp) cc_final: 0.3355 (tpp) REVERT: H 168 ARG cc_start: 0.4498 (tpt170) cc_final: 0.3936 (tpt-90) REVERT: H 219 GLU cc_start: 0.3165 (OUTLIER) cc_final: 0.1417 (pp20) REVERT: H 253 MET cc_start: 0.2851 (ttp) cc_final: 0.2275 (ptm) REVERT: H 314 MET cc_start: 0.3713 (tpt) cc_final: 0.3291 (tpt) REVERT: K 82 PHE cc_start: 0.6439 (t80) cc_final: 0.6113 (t80) REVERT: K 90 ASP cc_start: 0.4129 (OUTLIER) cc_final: 0.3492 (m-30) REVERT: L 199 GLN cc_start: 0.4500 (mm-40) cc_final: 0.3360 (tt0) REVERT: L 240 ILE cc_start: -0.0320 (OUTLIER) cc_final: -0.0621 (mt) REVERT: L 268 MET cc_start: 0.3080 (OUTLIER) cc_final: 0.2602 (mpp) REVERT: L 304 MET cc_start: 0.2158 (pmm) cc_final: 0.0751 (ttm) REVERT: L 308 VAL cc_start: 0.2599 (OUTLIER) cc_final: 0.2384 (t) REVERT: L 318 TYR cc_start: 0.2596 (OUTLIER) cc_final: 0.0079 (m-10) REVERT: L 325 MET cc_start: 0.3797 (mmp) cc_final: 0.3055 (mmm) REVERT: L 350 PHE cc_start: 0.0234 (OUTLIER) cc_final: -0.0366 (m-80) REVERT: L 367 MET cc_start: 0.0490 (mmt) cc_final: 0.0069 (mmp) REVERT: L 483 GLU cc_start: 0.2761 (OUTLIER) cc_final: 0.2467 (mt-10) REVERT: L 497 MET cc_start: 0.2655 (ppp) cc_final: 0.2245 (mtt) REVERT: L 527 MET cc_start: 0.3639 (OUTLIER) cc_final: 0.3391 (tpp) REVERT: L 547 ILE cc_start: -0.1618 (mm) cc_final: -0.2184 (mm) REVERT: M 98 ARG cc_start: 0.1173 (tpp-160) cc_final: 0.0328 (ptt180) REVERT: M 113 MET cc_start: 0.0652 (ttp) cc_final: -0.0195 (ptm) REVERT: M 263 ILE cc_start: 0.3077 (OUTLIER) cc_final: 0.2292 (tp) REVERT: M 277 MET cc_start: 0.4626 (tpp) cc_final: 0.3745 (tpp) REVERT: M 348 GLN cc_start: 0.3738 (tp40) cc_final: 0.3140 (tm-30) REVERT: 1 436 TYR cc_start: 0.2718 (OUTLIER) cc_final: 0.2240 (m-10) REVERT: 1 468 GLN cc_start: 0.7063 (OUTLIER) cc_final: 0.6195 (tp-100) REVERT: 1 539 PRO cc_start: 0.7028 (Cg_endo) cc_final: 0.6666 (Cg_exo) REVERT: N 60 VAL cc_start: 0.5163 (OUTLIER) cc_final: 0.4853 (m) REVERT: N 109 LYS cc_start: 0.4123 (mttp) cc_final: 0.3726 (mttm) REVERT: D 54 ARG cc_start: 0.4940 (ttm170) cc_final: 0.4482 (ptm160) REVERT: D 191 GLN cc_start: 0.4391 (mp10) cc_final: 0.3909 (mp10) REVERT: D 252 LEU cc_start: 0.3956 (tt) cc_final: 0.3571 (tp) REVERT: D 326 GLN cc_start: 0.4640 (tp40) cc_final: 0.4370 (tp40) REVERT: D 414 ASP cc_start: 0.3922 (m-30) cc_final: 0.3261 (m-30) outliers start: 428 outliers final: 299 residues processed: 1204 average time/residue: 0.9436 time to fit residues: 2007.5780 Evaluate side-chains 1125 residues out of total 8865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 323 poor density : 802 time to evaluate : 7.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 73 ASP Chi-restraints excluded: chain a residue 87 VAL Chi-restraints excluded: chain a residue 134 LEU Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 96 CYS Chi-restraints excluded: chain p residue 98 THR Chi-restraints excluded: chain p residue 104 ASP Chi-restraints excluded: chain p residue 153 THR Chi-restraints excluded: chain p residue 208 HIS Chi-restraints excluded: chain p residue 209 ASP Chi-restraints excluded: chain p residue 218 LEU Chi-restraints excluded: chain p residue 224 GLU Chi-restraints excluded: chain p residue 230 GLU Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 132 ASP Chi-restraints excluded: chain d residue 185 THR Chi-restraints excluded: chain d residue 212 LYS Chi-restraints excluded: chain d residue 220 ASP Chi-restraints excluded: chain d residue 259 THR Chi-restraints excluded: chain d residue 262 THR Chi-restraints excluded: chain d residue 271 ASP Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 46 GLU Chi-restraints excluded: chain Q residue 53 ILE Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 63 VAL Chi-restraints excluded: chain Q residue 72 HIS Chi-restraints excluded: chain Q residue 84 VAL Chi-restraints excluded: chain Q residue 94 ASP Chi-restraints excluded: chain q residue 45 ILE Chi-restraints excluded: chain q residue 126 VAL Chi-restraints excluded: chain q residue 133 THR Chi-restraints excluded: chain q residue 156 VAL Chi-restraints excluded: chain q residue 181 CYS Chi-restraints excluded: chain q residue 212 ASP Chi-restraints excluded: chain q residue 247 THR Chi-restraints excluded: chain r residue 57 ASP Chi-restraints excluded: chain r residue 89 THR Chi-restraints excluded: chain r residue 112 VAL Chi-restraints excluded: chain r residue 114 VAL Chi-restraints excluded: chain r residue 125 THR Chi-restraints excluded: chain r residue 153 VAL Chi-restraints excluded: chain s residue 9 VAL Chi-restraints excluded: chain s residue 46 THR Chi-restraints excluded: chain s residue 66 VAL Chi-restraints excluded: chain s residue 80 VAL Chi-restraints excluded: chain s residue 86 LYS Chi-restraints excluded: chain s residue 105 THR Chi-restraints excluded: chain s residue 132 ASP Chi-restraints excluded: chain s residue 148 LEU Chi-restraints excluded: chain t residue 14 THR Chi-restraints excluded: chain t residue 91 VAL Chi-restraints excluded: chain t residue 92 ARG Chi-restraints excluded: chain t residue 105 ASP Chi-restraints excluded: chain t residue 130 THR Chi-restraints excluded: chain t residue 166 PHE Chi-restraints excluded: chain c residue 18 ARG Chi-restraints excluded: chain c residue 61 LEU Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 149 VAL Chi-restraints excluded: chain n residue 6 THR Chi-restraints excluded: chain n residue 15 THR Chi-restraints excluded: chain n residue 66 VAL Chi-restraints excluded: chain n residue 120 VAL Chi-restraints excluded: chain n residue 143 LEU Chi-restraints excluded: chain n residue 146 THR Chi-restraints excluded: chain m residue 37 ILE Chi-restraints excluded: chain m residue 52 VAL Chi-restraints excluded: chain m residue 87 ASP Chi-restraints excluded: chain i residue 40 THR Chi-restraints excluded: chain i residue 52 THR Chi-restraints excluded: chain i residue 54 CYS Chi-restraints excluded: chain i residue 100 THR Chi-restraints excluded: chain i residue 119 LEU Chi-restraints excluded: chain i residue 131 ASP Chi-restraints excluded: chain y residue 35 ASN Chi-restraints excluded: chain f residue 9 ASP Chi-restraints excluded: chain f residue 25 VAL Chi-restraints excluded: chain f residue 41 MET Chi-restraints excluded: chain f residue 80 ASP Chi-restraints excluded: chain f residue 85 ASP Chi-restraints excluded: chain j residue 19 ASP Chi-restraints excluded: chain j residue 52 LEU Chi-restraints excluded: chain j residue 58 GLU Chi-restraints excluded: chain j residue 64 SER Chi-restraints excluded: chain j residue 96 GLU Chi-restraints excluded: chain j residue 102 VAL Chi-restraints excluded: chain j residue 123 VAL Chi-restraints excluded: chain j residue 128 VAL Chi-restraints excluded: chain j residue 138 LYS Chi-restraints excluded: chain z residue 14 THR Chi-restraints excluded: chain z residue 17 LEU Chi-restraints excluded: chain z residue 55 ILE Chi-restraints excluded: chain z residue 74 MET Chi-restraints excluded: chain z residue 102 THR Chi-restraints excluded: chain z residue 120 THR Chi-restraints excluded: chain R residue 13 GLU Chi-restraints excluded: chain R residue 40 CYS Chi-restraints excluded: chain R residue 43 ILE Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain T residue 22 GLN Chi-restraints excluded: chain w residue 98 VAL Chi-restraints excluded: chain w residue 118 GLN Chi-restraints excluded: chain g residue 20 THR Chi-restraints excluded: chain g residue 46 THR Chi-restraints excluded: chain g residue 63 PHE Chi-restraints excluded: chain g residue 113 ILE Chi-restraints excluded: chain b residue 134 CYS Chi-restraints excluded: chain b residue 143 ARG Chi-restraints excluded: chain b residue 170 THR Chi-restraints excluded: chain b residue 193 ASP Chi-restraints excluded: chain b residue 209 SER Chi-restraints excluded: chain b residue 218 LEU Chi-restraints excluded: chain e residue 26 ASP Chi-restraints excluded: chain e residue 28 VAL Chi-restraints excluded: chain e residue 78 MET Chi-restraints excluded: chain e residue 116 ILE Chi-restraints excluded: chain e residue 126 THR Chi-restraints excluded: chain e residue 136 ARG Chi-restraints excluded: chain e residue 168 THR Chi-restraints excluded: chain u residue 2 LEU Chi-restraints excluded: chain u residue 15 LEU Chi-restraints excluded: chain u residue 58 VAL Chi-restraints excluded: chain u residue 74 GLU Chi-restraints excluded: chain u residue 85 LEU Chi-restraints excluded: chain v residue 45 ARG Chi-restraints excluded: chain v residue 62 VAL Chi-restraints excluded: chain v residue 103 VAL Chi-restraints excluded: chain o residue 37 TYR Chi-restraints excluded: chain o residue 66 GLU Chi-restraints excluded: chain o residue 111 MET Chi-restraints excluded: chain o residue 127 LYS Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 44 VAL Chi-restraints excluded: chain k residue 53 THR Chi-restraints excluded: chain k residue 60 THR Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain k residue 136 THR Chi-restraints excluded: chain x residue 5 THR Chi-restraints excluded: chain x residue 28 LEU Chi-restraints excluded: chain x residue 35 ASP Chi-restraints excluded: chain x residue 45 LEU Chi-restraints excluded: chain x residue 50 GLU Chi-restraints excluded: chain x residue 66 LEU Chi-restraints excluded: chain x residue 124 THR Chi-restraints excluded: chain h residue 23 THR Chi-restraints excluded: chain h residue 36 CYS Chi-restraints excluded: chain h residue 45 GLU Chi-restraints excluded: chain h residue 76 THR Chi-restraints excluded: chain h residue 90 ASP Chi-restraints excluded: chain h residue 91 LEU Chi-restraints excluded: chain h residue 110 VAL Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain S residue 14 VAL Chi-restraints excluded: chain S residue 35 MET Chi-restraints excluded: chain S residue 60 GLU Chi-restraints excluded: chain l residue 4 GLN Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 102 VAL Chi-restraints excluded: chain V residue 104 HIS Chi-restraints excluded: chain V residue 113 PHE Chi-restraints excluded: chain V residue 115 SER Chi-restraints excluded: chain V residue 166 VAL Chi-restraints excluded: chain V residue 171 ASP Chi-restraints excluded: chain V residue 176 VAL Chi-restraints excluded: chain V residue 237 ASN Chi-restraints excluded: chain V residue 265 ILE Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 47 HIS Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 382 TYR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 504 ASP Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 527 SER Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 572 HIS Chi-restraints excluded: chain C residue 591 MET Chi-restraints excluded: chain C residue 619 CYS Chi-restraints excluded: chain C residue 695 ILE Chi-restraints excluded: chain C residue 734 ARG Chi-restraints excluded: chain C residue 736 HIS Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain C residue 826 ILE Chi-restraints excluded: chain C residue 876 HIS Chi-restraints excluded: chain E residue 20 PHE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain E residue 409 LYS Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain F residue 322 ASP Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 219 GLU Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 141 PHE Chi-restraints excluded: chain L residue 240 ILE Chi-restraints excluded: chain L residue 268 MET Chi-restraints excluded: chain L residue 293 VAL Chi-restraints excluded: chain L residue 296 ASN Chi-restraints excluded: chain L residue 308 VAL Chi-restraints excluded: chain L residue 318 TYR Chi-restraints excluded: chain L residue 336 PHE Chi-restraints excluded: chain L residue 339 ILE Chi-restraints excluded: chain L residue 346 THR Chi-restraints excluded: chain L residue 350 PHE Chi-restraints excluded: chain L residue 353 THR Chi-restraints excluded: chain L residue 388 LEU Chi-restraints excluded: chain L residue 412 LEU Chi-restraints excluded: chain L residue 414 SER Chi-restraints excluded: chain L residue 452 GLN Chi-restraints excluded: chain L residue 470 MET Chi-restraints excluded: chain L residue 483 GLU Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 503 THR Chi-restraints excluded: chain L residue 527 MET Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 121 TYR Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain M residue 140 ILE Chi-restraints excluded: chain M residue 145 ASP Chi-restraints excluded: chain M residue 188 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 226 LEU Chi-restraints excluded: chain M residue 263 ILE Chi-restraints excluded: chain M residue 266 LEU Chi-restraints excluded: chain M residue 269 LEU Chi-restraints excluded: chain M residue 297 MET Chi-restraints excluded: chain M residue 341 THR Chi-restraints excluded: chain M residue 361 LEU Chi-restraints excluded: chain 1 residue 13 HIS Chi-restraints excluded: chain 1 residue 154 ASN Chi-restraints excluded: chain 1 residue 196 THR Chi-restraints excluded: chain 1 residue 270 ILE Chi-restraints excluded: chain 1 residue 271 VAL Chi-restraints excluded: chain 1 residue 275 ASP Chi-restraints excluded: chain 1 residue 300 THR Chi-restraints excluded: chain 1 residue 305 VAL Chi-restraints excluded: chain 1 residue 326 ASP Chi-restraints excluded: chain 1 residue 357 MET Chi-restraints excluded: chain 1 residue 386 THR Chi-restraints excluded: chain 1 residue 408 ASN Chi-restraints excluded: chain 1 residue 416 ILE Chi-restraints excluded: chain 1 residue 436 TYR Chi-restraints excluded: chain 1 residue 437 THR Chi-restraints excluded: chain 1 residue 459 VAL Chi-restraints excluded: chain 1 residue 468 GLN Chi-restraints excluded: chain 1 residue 493 ASP Chi-restraints excluded: chain 1 residue 517 VAL Chi-restraints excluded: chain 1 residue 543 THR Chi-restraints excluded: chain 1 residue 598 ASP Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 69 CYS Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 307 ASN Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 519 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1162 random chunks: chunk 377 optimal weight: 10.0000 chunk 1011 optimal weight: 0.0370 chunk 222 optimal weight: 0.1980 chunk 659 optimal weight: 0.0270 chunk 277 optimal weight: 10.0000 chunk 1124 optimal weight: 1.9990 chunk 933 optimal weight: 6.9990 chunk 520 optimal weight: 30.0000 chunk 93 optimal weight: 20.0000 chunk 371 optimal weight: 10.0000 chunk 590 optimal weight: 9.9990 overall best weight: 1.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: p 53 GLN p 208 HIS d 267 GLN q 157 ASN ** q 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 7 ASN c 113 GLN m 62 GLN ** i 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 35 ASN w 31 ASN g 24 HIS b 165 ASN b 226 GLN e 51 HIS ** u 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 133 ASN ** V 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 73 GLN ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 ASN ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 321 ASN ** E 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 36 GLN ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 151 GLN L 181 GLN ** L 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 ASN ** D 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6453 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 120661 Z= 0.145 Angle : 0.559 14.119 171380 Z= 0.290 Chirality : 0.038 0.273 20736 Planarity : 0.004 0.104 15542 Dihedral : 21.570 179.845 37977 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.20 % Favored : 95.78 % Rotamer: Outliers : 4.28 % Allowed : 22.44 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.11 % Twisted Proline : 0.27 % 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: -1.18 (0.08), residues: 9955 helix: 0.04 (0.08), residues: 3917 sheet: -0.53 (0.14), residues: 1389 loop : -1.56 (0.09), residues: 4649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP V 177 HIS 0.032 0.001 HIS p 208 PHE 0.025 0.001 PHE H 138 TYR 0.031 0.001 TYR N 30 ARG 0.007 0.000 ARG B 532 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19910 Ramachandran restraints generated. 9955 Oldfield, 0 Emsley, 9955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19910 Ramachandran restraints generated. 9955 Oldfield, 0 Emsley, 9955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1262 residues out of total 8865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 341 poor density : 921 time to evaluate : 7.612 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: a 73 ASP cc_start: 0.7758 (OUTLIER) cc_final: 0.7337 (p0) REVERT: p 198 GLU cc_start: 0.6858 (tt0) cc_final: 0.6546 (tt0) REVERT: r 83 CYS cc_start: 0.8035 (m) cc_final: 0.7694 (t) REVERT: j 87 ASN cc_start: 0.6325 (m-40) cc_final: 0.5876 (m-40) REVERT: R 31 TYR cc_start: 0.8099 (p90) cc_final: 0.7772 (p90) REVERT: w 58 MET cc_start: 0.7436 (mmt) cc_final: 0.7075 (mmt) REVERT: w 127 ASN cc_start: 0.7529 (p0) cc_final: 0.7230 (p0) REVERT: b 143 ARG cc_start: 0.4800 (OUTLIER) cc_final: 0.4303 (tpt170) REVERT: o 111 MET cc_start: 0.5375 (OUTLIER) cc_final: 0.4595 (mtt) REVERT: x 28 LEU cc_start: 0.4631 (OUTLIER) cc_final: 0.4092 (pt) REVERT: B 504 ILE cc_start: 0.3684 (OUTLIER) cc_final: 0.3245 (mp) REVERT: B 521 LYS cc_start: 0.3509 (mmtt) cc_final: 0.2221 (tptt) REVERT: A 87 GLU cc_start: 0.4488 (OUTLIER) cc_final: 0.4185 (tp30) REVERT: A 306 MET cc_start: 0.3354 (ttm) cc_final: 0.2535 (mpp) REVERT: A 309 ASN cc_start: 0.3549 (OUTLIER) cc_final: 0.2352 (m-40) REVERT: A 374 MET cc_start: 0.3962 (pmm) cc_final: 0.3716 (pmm) REVERT: E 44 LEU cc_start: 0.4929 (OUTLIER) cc_final: 0.4305 (pp) REVERT: E 104 MET cc_start: 0.1215 (mtt) cc_final: 0.0241 (ptt) REVERT: E 112 MET cc_start: 0.4895 (pmm) cc_final: 0.4669 (ptt) REVERT: E 359 LYS cc_start: 0.5451 (OUTLIER) cc_final: 0.4871 (mttm) REVERT: E 388 LEU cc_start: 0.4469 (tt) cc_final: 0.4267 (mt) REVERT: E 393 MET cc_start: 0.3780 (mpp) cc_final: 0.3446 (mpp) REVERT: E 420 MET cc_start: 0.5648 (ppp) cc_final: 0.5001 (ppp) REVERT: F 207 GLN cc_start: 0.3515 (OUTLIER) cc_final: 0.2358 (tm130) REVERT: H 219 GLU cc_start: 0.3371 (OUTLIER) cc_final: 0.1639 (pp20) REVERT: H 253 MET cc_start: 0.2787 (ttp) cc_final: 0.2302 (ptm) REVERT: H 314 MET cc_start: 0.3409 (tpt) cc_final: 0.3057 (tpt) REVERT: K 90 ASP cc_start: 0.4134 (OUTLIER) cc_final: 0.3414 (m-30) REVERT: L 199 GLN cc_start: 0.4717 (mm-40) cc_final: 0.3516 (tt0) REVERT: L 240 ILE cc_start: 0.0168 (OUTLIER) cc_final: -0.0082 (mt) REVERT: L 304 MET cc_start: 0.2763 (pmm) cc_final: 0.0914 (ttm) REVERT: L 367 MET cc_start: 0.0408 (mmt) cc_final: -0.0027 (mmp) REVERT: L 483 GLU cc_start: 0.2878 (OUTLIER) cc_final: 0.2534 (mt-10) REVERT: L 497 MET cc_start: 0.3043 (ppp) cc_final: 0.2326 (mtt) REVERT: L 547 ILE cc_start: -0.1789 (mm) cc_final: -0.2325 (mm) REVERT: M 14 GLN cc_start: 0.1495 (mt0) cc_final: 0.0024 (mm-40) REVERT: M 98 ARG cc_start: 0.1171 (tpp-160) cc_final: 0.0362 (ptt180) REVERT: M 113 MET cc_start: 0.0759 (ttp) cc_final: 0.0037 (ptm) REVERT: M 248 LYS cc_start: 0.6200 (mtmm) cc_final: 0.4459 (ptmm) REVERT: M 277 MET cc_start: 0.4604 (tpp) cc_final: 0.3700 (tpp) REVERT: M 348 GLN cc_start: 0.3686 (tp40) cc_final: 0.3039 (tm-30) REVERT: 1 436 TYR cc_start: 0.2960 (OUTLIER) cc_final: 0.2516 (m-10) REVERT: 1 468 GLN cc_start: 0.6949 (OUTLIER) cc_final: 0.6149 (tp-100) REVERT: N 37 GLN cc_start: 0.7116 (OUTLIER) cc_final: 0.6490 (mm110) REVERT: D 54 ARG cc_start: 0.4873 (ttm170) cc_final: 0.4432 (ptm160) REVERT: D 191 GLN cc_start: 0.4346 (mp10) cc_final: 0.3904 (mp10) REVERT: D 252 LEU cc_start: 0.4022 (OUTLIER) cc_final: 0.3602 (tp) REVERT: D 300 GLN cc_start: 0.5627 (OUTLIER) cc_final: 0.4455 (mm110) outliers start: 341 outliers final: 230 residues processed: 1186 average time/residue: 0.9490 time to fit residues: 1982.1001 Evaluate side-chains 1073 residues out of total 8865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 824 time to evaluate : 6.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 73 ASP Chi-restraints excluded: chain a residue 87 VAL Chi-restraints excluded: chain a residue 130 ASP Chi-restraints excluded: chain a residue 134 LEU Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 98 THR Chi-restraints excluded: chain p residue 104 ASP Chi-restraints excluded: chain p residue 153 THR Chi-restraints excluded: chain p residue 208 HIS Chi-restraints excluded: chain p residue 218 LEU Chi-restraints excluded: chain p residue 224 GLU Chi-restraints excluded: chain p residue 230 GLU Chi-restraints excluded: chain d residue 132 ASP Chi-restraints excluded: chain d residue 184 VAL Chi-restraints excluded: chain d residue 212 LYS Chi-restraints excluded: chain d residue 220 ASP Chi-restraints excluded: chain d residue 259 THR Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 63 VAL Chi-restraints excluded: chain Q residue 84 VAL Chi-restraints excluded: chain q residue 45 ILE Chi-restraints excluded: chain q residue 126 VAL Chi-restraints excluded: chain q residue 133 THR Chi-restraints excluded: chain q residue 156 VAL Chi-restraints excluded: chain q residue 212 ASP Chi-restraints excluded: chain r residue 89 THR Chi-restraints excluded: chain r residue 112 VAL Chi-restraints excluded: chain r residue 125 THR Chi-restraints excluded: chain r residue 153 VAL Chi-restraints excluded: chain s residue 9 VAL Chi-restraints excluded: chain s residue 80 VAL Chi-restraints excluded: chain s residue 105 THR Chi-restraints excluded: chain s residue 132 ASP Chi-restraints excluded: chain s residue 148 LEU Chi-restraints excluded: chain t residue 14 THR Chi-restraints excluded: chain t residue 92 ARG Chi-restraints excluded: chain t residue 130 THR Chi-restraints excluded: chain t residue 166 PHE Chi-restraints excluded: chain c residue 18 ARG Chi-restraints excluded: chain c residue 61 LEU Chi-restraints excluded: chain c residue 95 ASP Chi-restraints excluded: chain c residue 104 ASP Chi-restraints excluded: chain c residue 149 VAL Chi-restraints excluded: chain c residue 160 SER Chi-restraints excluded: chain n residue 91 ASP Chi-restraints excluded: chain m residue 52 VAL Chi-restraints excluded: chain m residue 87 ASP Chi-restraints excluded: chain i residue 54 CYS Chi-restraints excluded: chain i residue 100 THR Chi-restraints excluded: chain y residue 35 ASN Chi-restraints excluded: chain f residue 25 VAL Chi-restraints excluded: chain f residue 41 MET Chi-restraints excluded: chain f residue 80 ASP Chi-restraints excluded: chain j residue 52 LEU Chi-restraints excluded: chain j residue 58 GLU Chi-restraints excluded: chain j residue 64 SER Chi-restraints excluded: chain j residue 96 GLU Chi-restraints excluded: chain j residue 105 PHE Chi-restraints excluded: chain j residue 123 VAL Chi-restraints excluded: chain j residue 128 VAL Chi-restraints excluded: chain j residue 138 LYS Chi-restraints excluded: chain z residue 17 LEU Chi-restraints excluded: chain z residue 35 VAL Chi-restraints excluded: chain z residue 55 ILE Chi-restraints excluded: chain z residue 74 MET Chi-restraints excluded: chain z residue 120 THR Chi-restraints excluded: chain R residue 40 CYS Chi-restraints excluded: chain T residue 22 GLN Chi-restraints excluded: chain T residue 44 ASN Chi-restraints excluded: chain w residue 118 GLN Chi-restraints excluded: chain g residue 20 THR Chi-restraints excluded: chain g residue 46 THR Chi-restraints excluded: chain g residue 63 PHE Chi-restraints excluded: chain g residue 113 ILE Chi-restraints excluded: chain b residue 12 VAL Chi-restraints excluded: chain b residue 134 CYS Chi-restraints excluded: chain b residue 143 ARG Chi-restraints excluded: chain b residue 193 ASP Chi-restraints excluded: chain b residue 209 SER Chi-restraints excluded: chain e residue 26 ASP Chi-restraints excluded: chain e residue 28 VAL Chi-restraints excluded: chain e residue 78 MET Chi-restraints excluded: chain e residue 116 ILE Chi-restraints excluded: chain e residue 168 THR Chi-restraints excluded: chain u residue 2 LEU Chi-restraints excluded: chain u residue 58 VAL Chi-restraints excluded: chain u residue 74 GLU Chi-restraints excluded: chain u residue 85 LEU Chi-restraints excluded: chain v residue 62 VAL Chi-restraints excluded: chain v residue 103 VAL Chi-restraints excluded: chain o residue 37 TYR Chi-restraints excluded: chain o residue 86 LEU Chi-restraints excluded: chain o residue 111 MET Chi-restraints excluded: chain o residue 127 LYS Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 60 THR Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain k residue 136 THR Chi-restraints excluded: chain x residue 28 LEU Chi-restraints excluded: chain x residue 35 ASP Chi-restraints excluded: chain x residue 45 LEU Chi-restraints excluded: chain x residue 50 GLU Chi-restraints excluded: chain h residue 36 CYS Chi-restraints excluded: chain h residue 90 ASP Chi-restraints excluded: chain S residue 35 MET Chi-restraints excluded: chain S residue 61 SER Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain l residue 53 ILE Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 102 VAL Chi-restraints excluded: chain V residue 104 HIS Chi-restraints excluded: chain V residue 113 PHE Chi-restraints excluded: chain V residue 115 SER Chi-restraints excluded: chain V residue 135 LEU Chi-restraints excluded: chain V residue 166 VAL Chi-restraints excluded: chain V residue 171 ASP Chi-restraints excluded: chain V residue 186 THR Chi-restraints excluded: chain V residue 198 VAL Chi-restraints excluded: chain V residue 265 ILE Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 47 HIS Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 382 TYR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 504 ASP Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 591 MET Chi-restraints excluded: chain C residue 695 ILE Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain C residue 876 HIS Chi-restraints excluded: chain E residue 20 PHE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain E residue 339 PHE Chi-restraints excluded: chain E residue 359 LYS Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 322 ASP Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 219 GLU Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 141 PHE Chi-restraints excluded: chain L residue 181 GLN Chi-restraints excluded: chain L residue 240 ILE Chi-restraints excluded: chain L residue 274 LEU Chi-restraints excluded: chain L residue 293 VAL Chi-restraints excluded: chain L residue 346 THR Chi-restraints excluded: chain L residue 353 THR Chi-restraints excluded: chain L residue 383 ASP Chi-restraints excluded: chain L residue 412 LEU Chi-restraints excluded: chain L residue 414 SER Chi-restraints excluded: chain L residue 452 GLN Chi-restraints excluded: chain L residue 460 ILE Chi-restraints excluded: chain L residue 466 LEU Chi-restraints excluded: chain L residue 470 MET Chi-restraints excluded: chain L residue 483 GLU Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 503 THR Chi-restraints excluded: chain L residue 522 TYR Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 121 TYR Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain M residue 188 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 266 LEU Chi-restraints excluded: chain M residue 361 LEU Chi-restraints excluded: chain 1 residue 13 HIS Chi-restraints excluded: chain 1 residue 154 ASN Chi-restraints excluded: chain 1 residue 196 THR Chi-restraints excluded: chain 1 residue 270 ILE Chi-restraints excluded: chain 1 residue 271 VAL Chi-restraints excluded: chain 1 residue 275 ASP Chi-restraints excluded: chain 1 residue 300 THR Chi-restraints excluded: chain 1 residue 305 VAL Chi-restraints excluded: chain 1 residue 357 MET Chi-restraints excluded: chain 1 residue 408 ASN Chi-restraints excluded: chain 1 residue 416 ILE Chi-restraints excluded: chain 1 residue 436 TYR Chi-restraints excluded: chain 1 residue 437 THR Chi-restraints excluded: chain 1 residue 459 VAL Chi-restraints excluded: chain 1 residue 468 GLN Chi-restraints excluded: chain 1 residue 493 ASP Chi-restraints excluded: chain 1 residue 517 VAL Chi-restraints excluded: chain 1 residue 543 THR Chi-restraints excluded: chain 1 residue 598 ASP Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain N residue 69 CYS Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 300 GLN Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 519 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1162 random chunks: chunk 1083 optimal weight: 0.2980 chunk 126 optimal weight: 0.7980 chunk 640 optimal weight: 20.0000 chunk 821 optimal weight: 9.9990 chunk 636 optimal weight: 50.0000 chunk 946 optimal weight: 30.0000 chunk 627 optimal weight: 20.0000 chunk 1119 optimal weight: 0.6980 chunk 700 optimal weight: 20.0000 chunk 682 optimal weight: 50.0000 chunk 517 optimal weight: 6.9990 overall best weight: 3.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: p 208 HIS q 157 ASN ** q 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 7 ASN c 75 ASN c 113 GLN m 62 GLN ** i 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 83 ASN ** u 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 12 GLN ** x 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 28 ASN ** V 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 196 ASN A 425 GLN ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 845 HIS ** C 870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 36 GLN ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 181 GLN ** L 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 529 HIS ** M 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 326 GLN ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6483 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 120661 Z= 0.194 Angle : 0.583 13.844 171380 Z= 0.301 Chirality : 0.039 0.306 20736 Planarity : 0.004 0.102 15542 Dihedral : 21.517 178.940 37977 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.19 % Favored : 94.79 % Rotamer: Outliers : 4.70 % Allowed : 22.61 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.11 % Twisted Proline : 0.27 % 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: -1.10 (0.08), residues: 9955 helix: 0.15 (0.08), residues: 3917 sheet: -0.53 (0.14), residues: 1407 loop : -1.54 (0.09), residues: 4631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP e 152 HIS 0.017 0.001 HIS p 208 PHE 0.021 0.001 PHE H 138 TYR 0.039 0.001 TYR N 30 ARG 0.009 0.000 ARG N 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19910 Ramachandran restraints generated. 9955 Oldfield, 0 Emsley, 9955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19910 Ramachandran restraints generated. 9955 Oldfield, 0 Emsley, 9955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1212 residues out of total 8865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 375 poor density : 837 time to evaluate : 7.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 73 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.7384 (p0) REVERT: p 198 GLU cc_start: 0.6988 (tt0) cc_final: 0.6644 (tt0) REVERT: d 79 GLU cc_start: 0.6971 (mm-30) cc_final: 0.6723 (tp30) REVERT: d 123 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7741 (mtm180) REVERT: Q 72 HIS cc_start: 0.7214 (OUTLIER) cc_final: 0.6848 (m90) REVERT: r 83 CYS cc_start: 0.8104 (m) cc_final: 0.7708 (t) REVERT: R 31 TYR cc_start: 0.8143 (p90) cc_final: 0.7888 (p90) REVERT: w 58 MET cc_start: 0.7515 (mmt) cc_final: 0.7234 (mmt) REVERT: w 127 ASN cc_start: 0.7574 (p0) cc_final: 0.7264 (p0) REVERT: g 86 GLN cc_start: 0.6841 (tm-30) cc_final: 0.6459 (tp40) REVERT: b 143 ARG cc_start: 0.4667 (OUTLIER) cc_final: 0.4251 (tpt170) REVERT: e 204 ARG cc_start: 0.6839 (mtm110) cc_final: 0.6519 (mtm110) REVERT: v 114 TYR cc_start: 0.4418 (m-80) cc_final: 0.4170 (m-10) REVERT: o 111 MET cc_start: 0.5348 (OUTLIER) cc_final: 0.4430 (mtt) REVERT: x 28 LEU cc_start: 0.4299 (OUTLIER) cc_final: 0.3779 (pt) REVERT: B 521 LYS cc_start: 0.3456 (mmtt) cc_final: 0.2101 (tptp) REVERT: A 87 GLU cc_start: 0.4442 (OUTLIER) cc_final: 0.4136 (tp30) REVERT: A 184 PHE cc_start: 0.5488 (OUTLIER) cc_final: 0.4119 (t80) REVERT: A 306 MET cc_start: 0.3331 (ttm) cc_final: 0.2641 (mpp) REVERT: A 309 ASN cc_start: 0.3716 (OUTLIER) cc_final: 0.2629 (m-40) REVERT: A 374 MET cc_start: 0.4086 (pmm) cc_final: 0.3769 (pmm) REVERT: C 438 LEU cc_start: 0.5153 (OUTLIER) cc_final: 0.4925 (mp) REVERT: C 572 HIS cc_start: 0.6192 (OUTLIER) cc_final: 0.4833 (t-170) REVERT: C 734 ARG cc_start: 0.5268 (OUTLIER) cc_final: 0.4960 (ptt-90) REVERT: E 44 LEU cc_start: 0.4958 (OUTLIER) cc_final: 0.4360 (pp) REVERT: E 50 MET cc_start: 0.4252 (tpp) cc_final: 0.3868 (tpp) REVERT: E 104 MET cc_start: 0.1268 (mtt) cc_final: 0.0388 (ptt) REVERT: E 112 MET cc_start: 0.4976 (OUTLIER) cc_final: 0.4649 (ptt) REVERT: E 388 LEU cc_start: 0.4442 (tt) cc_final: 0.4209 (mt) REVERT: E 393 MET cc_start: 0.3508 (mpp) cc_final: 0.3133 (mpp) REVERT: F 207 GLN cc_start: 0.3315 (OUTLIER) cc_final: 0.2246 (tm130) REVERT: F 239 TYR cc_start: 0.3343 (OUTLIER) cc_final: 0.1424 (m-80) REVERT: F 326 MET cc_start: 0.4985 (tpp) cc_final: 0.4782 (tpp) REVERT: H 47 LEU cc_start: 0.1389 (OUTLIER) cc_final: 0.1084 (pp) REVERT: H 82 PHE cc_start: 0.0755 (OUTLIER) cc_final: -0.0458 (p90) REVERT: H 217 GLU cc_start: -0.0470 (OUTLIER) cc_final: -0.0957 (tt0) REVERT: H 219 GLU cc_start: 0.3454 (OUTLIER) cc_final: 0.1587 (pp20) REVERT: H 253 MET cc_start: 0.2792 (ttp) cc_final: 0.2249 (ptm) REVERT: H 314 MET cc_start: 0.3369 (tpt) cc_final: 0.3047 (tpt) REVERT: K 90 ASP cc_start: 0.4233 (OUTLIER) cc_final: 0.3427 (m-30) REVERT: L 199 GLN cc_start: 0.4804 (mm-40) cc_final: 0.3549 (tt0) REVERT: L 240 ILE cc_start: -0.0049 (OUTLIER) cc_final: -0.0317 (mt) REVERT: L 304 MET cc_start: 0.2741 (pmm) cc_final: 0.1188 (ttm) REVERT: L 350 PHE cc_start: 0.0514 (OUTLIER) cc_final: -0.0253 (m-80) REVERT: L 367 MET cc_start: 0.0727 (mmt) cc_final: 0.0269 (mmp) REVERT: L 483 GLU cc_start: 0.2753 (OUTLIER) cc_final: 0.2409 (mt-10) REVERT: L 497 MET cc_start: 0.2919 (ppp) cc_final: 0.2182 (mtt) REVERT: L 547 ILE cc_start: -0.1484 (mm) cc_final: -0.2051 (mm) REVERT: M 14 GLN cc_start: 0.1411 (mt0) cc_final: 0.0487 (mm-40) REVERT: M 98 ARG cc_start: 0.1228 (tpp-160) cc_final: 0.0349 (ptt180) REVERT: M 113 MET cc_start: 0.0644 (ttp) cc_final: -0.0009 (ptm) REVERT: M 248 LYS cc_start: 0.6185 (mtmm) cc_final: 0.4438 (ptmm) REVERT: M 277 MET cc_start: 0.4585 (tpp) cc_final: 0.3882 (tpp) REVERT: M 348 GLN cc_start: 0.3804 (tp40) cc_final: 0.3260 (tm-30) REVERT: 1 436 TYR cc_start: 0.3135 (OUTLIER) cc_final: 0.2609 (m-10) REVERT: 1 468 GLN cc_start: 0.6988 (OUTLIER) cc_final: 0.6139 (tp-100) REVERT: D 45 TRP cc_start: 0.6322 (OUTLIER) cc_final: 0.4977 (m-90) REVERT: D 54 ARG cc_start: 0.4902 (ttm170) cc_final: 0.4454 (ptm160) REVERT: D 191 GLN cc_start: 0.4395 (mp10) cc_final: 0.3917 (mp10) REVERT: D 252 LEU cc_start: 0.4020 (OUTLIER) cc_final: 0.3694 (tp) REVERT: D 300 GLN cc_start: 0.5724 (OUTLIER) cc_final: 0.4468 (mm110) outliers start: 375 outliers final: 280 residues processed: 1124 average time/residue: 0.9162 time to fit residues: 1823.4161 Evaluate side-chains 1109 residues out of total 8865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 309 poor density : 800 time to evaluate : 7.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 73 ASP Chi-restraints excluded: chain a residue 76 VAL Chi-restraints excluded: chain a residue 87 VAL Chi-restraints excluded: chain a residue 111 GLN Chi-restraints excluded: chain a residue 130 ASP Chi-restraints excluded: chain a residue 134 LEU Chi-restraints excluded: chain a residue 185 MET Chi-restraints excluded: chain p residue 29 ASP Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 98 THR Chi-restraints excluded: chain p residue 104 ASP Chi-restraints excluded: chain p residue 153 THR Chi-restraints excluded: chain p residue 218 LEU Chi-restraints excluded: chain p residue 224 GLU Chi-restraints excluded: chain p residue 230 GLU Chi-restraints excluded: chain d residue 123 ARG Chi-restraints excluded: chain d residue 132 ASP Chi-restraints excluded: chain d residue 184 VAL Chi-restraints excluded: chain d residue 185 THR Chi-restraints excluded: chain d residue 212 LYS Chi-restraints excluded: chain d residue 220 ASP Chi-restraints excluded: chain d residue 259 THR Chi-restraints excluded: chain d residue 271 ASP Chi-restraints excluded: chain Q residue 2 THR Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 52 ASP Chi-restraints excluded: chain Q residue 53 ILE Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 63 VAL Chi-restraints excluded: chain Q residue 72 HIS Chi-restraints excluded: chain Q residue 84 VAL Chi-restraints excluded: chain Q residue 94 ASP Chi-restraints excluded: chain q residue 45 ILE Chi-restraints excluded: chain q residue 126 VAL Chi-restraints excluded: chain q residue 133 THR Chi-restraints excluded: chain q residue 156 VAL Chi-restraints excluded: chain q residue 181 CYS Chi-restraints excluded: chain q residue 206 ASP Chi-restraints excluded: chain q residue 212 ASP Chi-restraints excluded: chain r residue 89 THR Chi-restraints excluded: chain r residue 112 VAL Chi-restraints excluded: chain r residue 114 VAL Chi-restraints excluded: chain r residue 125 THR Chi-restraints excluded: chain r residue 153 VAL Chi-restraints excluded: chain s residue 9 VAL Chi-restraints excluded: chain s residue 66 VAL Chi-restraints excluded: chain s residue 80 VAL Chi-restraints excluded: chain s residue 105 THR Chi-restraints excluded: chain s residue 132 ASP Chi-restraints excluded: chain s residue 148 LEU Chi-restraints excluded: chain t residue 14 THR Chi-restraints excluded: chain t residue 91 VAL Chi-restraints excluded: chain t residue 92 ARG Chi-restraints excluded: chain t residue 130 THR Chi-restraints excluded: chain t residue 166 PHE Chi-restraints excluded: chain c residue 18 ARG Chi-restraints excluded: chain c residue 61 LEU Chi-restraints excluded: chain c residue 104 ASP Chi-restraints excluded: chain c residue 149 VAL Chi-restraints excluded: chain c residue 160 SER Chi-restraints excluded: chain n residue 6 THR Chi-restraints excluded: chain n residue 15 THR Chi-restraints excluded: chain n residue 66 VAL Chi-restraints excluded: chain n residue 146 THR Chi-restraints excluded: chain m residue 52 VAL Chi-restraints excluded: chain m residue 87 ASP Chi-restraints excluded: chain i residue 27 VAL Chi-restraints excluded: chain i residue 54 CYS Chi-restraints excluded: chain i residue 100 THR Chi-restraints excluded: chain y residue 35 ASN Chi-restraints excluded: chain f residue 9 ASP Chi-restraints excluded: chain f residue 25 VAL Chi-restraints excluded: chain f residue 41 MET Chi-restraints excluded: chain f residue 80 ASP Chi-restraints excluded: chain j residue 45 SER Chi-restraints excluded: chain j residue 52 LEU Chi-restraints excluded: chain j residue 58 GLU Chi-restraints excluded: chain j residue 64 SER Chi-restraints excluded: chain j residue 96 GLU Chi-restraints excluded: chain j residue 105 PHE Chi-restraints excluded: chain j residue 123 VAL Chi-restraints excluded: chain j residue 128 VAL Chi-restraints excluded: chain j residue 138 LYS Chi-restraints excluded: chain z residue 14 THR Chi-restraints excluded: chain z residue 17 LEU Chi-restraints excluded: chain z residue 55 ILE Chi-restraints excluded: chain z residue 74 MET Chi-restraints excluded: chain z residue 102 THR Chi-restraints excluded: chain z residue 120 THR Chi-restraints excluded: chain R residue 40 CYS Chi-restraints excluded: chain R residue 43 ILE Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain T residue 22 GLN Chi-restraints excluded: chain g residue 20 THR Chi-restraints excluded: chain g residue 46 THR Chi-restraints excluded: chain g residue 63 PHE Chi-restraints excluded: chain g residue 113 ILE Chi-restraints excluded: chain b residue 12 VAL Chi-restraints excluded: chain b residue 134 CYS Chi-restraints excluded: chain b residue 143 ARG Chi-restraints excluded: chain b residue 193 ASP Chi-restraints excluded: chain b residue 209 SER Chi-restraints excluded: chain b residue 218 LEU Chi-restraints excluded: chain e residue 26 ASP Chi-restraints excluded: chain e residue 28 VAL Chi-restraints excluded: chain e residue 78 MET Chi-restraints excluded: chain e residue 93 VAL Chi-restraints excluded: chain e residue 116 ILE Chi-restraints excluded: chain e residue 126 THR Chi-restraints excluded: chain e residue 168 THR Chi-restraints excluded: chain u residue 2 LEU Chi-restraints excluded: chain u residue 58 VAL Chi-restraints excluded: chain u residue 74 GLU Chi-restraints excluded: chain u residue 85 LEU Chi-restraints excluded: chain v residue 62 VAL Chi-restraints excluded: chain v residue 103 VAL Chi-restraints excluded: chain o residue 37 TYR Chi-restraints excluded: chain o residue 66 GLU Chi-restraints excluded: chain o residue 86 LEU Chi-restraints excluded: chain o residue 111 MET Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 53 THR Chi-restraints excluded: chain k residue 60 THR Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain k residue 136 THR Chi-restraints excluded: chain x residue 5 THR Chi-restraints excluded: chain x residue 12 GLN Chi-restraints excluded: chain x residue 28 LEU Chi-restraints excluded: chain x residue 35 ASP Chi-restraints excluded: chain x residue 45 LEU Chi-restraints excluded: chain x residue 50 GLU Chi-restraints excluded: chain x residue 124 THR Chi-restraints excluded: chain x residue 132 ASP Chi-restraints excluded: chain h residue 23 THR Chi-restraints excluded: chain h residue 36 CYS Chi-restraints excluded: chain h residue 90 ASP Chi-restraints excluded: chain h residue 110 VAL Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain S residue 14 VAL Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 35 MET Chi-restraints excluded: chain S residue 61 SER Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain l residue 53 ILE Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 102 VAL Chi-restraints excluded: chain V residue 104 HIS Chi-restraints excluded: chain V residue 113 PHE Chi-restraints excluded: chain V residue 115 SER Chi-restraints excluded: chain V residue 166 VAL Chi-restraints excluded: chain V residue 171 ASP Chi-restraints excluded: chain V residue 176 VAL Chi-restraints excluded: chain V residue 186 THR Chi-restraints excluded: chain V residue 237 ASN Chi-restraints excluded: chain V residue 265 ILE Chi-restraints excluded: chain B residue 477 ASN Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 47 HIS Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 382 TYR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 504 ASP Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 572 HIS Chi-restraints excluded: chain C residue 591 MET Chi-restraints excluded: chain C residue 671 VAL Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 695 ILE Chi-restraints excluded: chain C residue 734 ARG Chi-restraints excluded: chain C residue 736 HIS Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain C residue 876 HIS Chi-restraints excluded: chain E residue 20 PHE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 324 PHE Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain E residue 339 PHE Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 239 TYR Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain F residue 322 ASP Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 82 PHE Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 219 GLU Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 82 PHE Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 141 PHE Chi-restraints excluded: chain L residue 240 ILE Chi-restraints excluded: chain L residue 274 LEU Chi-restraints excluded: chain L residue 293 VAL Chi-restraints excluded: chain L residue 296 ASN Chi-restraints excluded: chain L residue 336 PHE Chi-restraints excluded: chain L residue 339 ILE Chi-restraints excluded: chain L residue 346 THR Chi-restraints excluded: chain L residue 350 PHE Chi-restraints excluded: chain L residue 383 ASP Chi-restraints excluded: chain L residue 412 LEU Chi-restraints excluded: chain L residue 414 SER Chi-restraints excluded: chain L residue 452 GLN Chi-restraints excluded: chain L residue 460 ILE Chi-restraints excluded: chain L residue 466 LEU Chi-restraints excluded: chain L residue 483 GLU Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 503 THR Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 91 VAL Chi-restraints excluded: chain M residue 121 TYR Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain M residue 179 ASP Chi-restraints excluded: chain M residue 188 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 266 LEU Chi-restraints excluded: chain M residue 361 LEU Chi-restraints excluded: chain 1 residue 13 HIS Chi-restraints excluded: chain 1 residue 154 ASN Chi-restraints excluded: chain 1 residue 196 THR Chi-restraints excluded: chain 1 residue 270 ILE Chi-restraints excluded: chain 1 residue 271 VAL Chi-restraints excluded: chain 1 residue 275 ASP Chi-restraints excluded: chain 1 residue 300 THR Chi-restraints excluded: chain 1 residue 305 VAL Chi-restraints excluded: chain 1 residue 326 ASP Chi-restraints excluded: chain 1 residue 357 MET Chi-restraints excluded: chain 1 residue 392 LEU Chi-restraints excluded: chain 1 residue 408 ASN Chi-restraints excluded: chain 1 residue 416 ILE Chi-restraints excluded: chain 1 residue 436 TYR Chi-restraints excluded: chain 1 residue 437 THR Chi-restraints excluded: chain 1 residue 459 VAL Chi-restraints excluded: chain 1 residue 468 GLN Chi-restraints excluded: chain 1 residue 493 ASP Chi-restraints excluded: chain 1 residue 517 VAL Chi-restraints excluded: chain 1 residue 543 THR Chi-restraints excluded: chain 1 residue 598 ASP Chi-restraints excluded: chain N residue 54 TYR Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain N residue 69 CYS Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 45 TRP Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 300 GLN Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 519 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1162 random chunks: chunk 692 optimal weight: 0.0270 chunk 447 optimal weight: 5.9990 chunk 668 optimal weight: 0.0770 chunk 337 optimal weight: 40.0000 chunk 220 optimal weight: 0.0670 chunk 216 optimal weight: 9.9990 chunk 712 optimal weight: 5.9990 chunk 763 optimal weight: 3.9990 chunk 553 optimal weight: 20.0000 chunk 104 optimal weight: 0.0040 chunk 880 optimal weight: 4.9990 overall best weight: 0.8348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** q 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 7 ASN c 113 GLN m 58 HIS m 62 GLN g 24 HIS b 165 ASN e 83 ASN u 44 HIS ** k 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 29 GLN ** V 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 191 HIS B 543 ASN ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 870 ASN ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 181 GLN ** L 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 529 HIS ** M 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 251 GLN ** 1 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 326 GLN ** D 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6405 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 120661 Z= 0.128 Angle : 0.550 13.714 171380 Z= 0.281 Chirality : 0.037 0.257 20736 Planarity : 0.004 0.092 15542 Dihedral : 21.405 178.562 37977 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.96 % Favored : 96.02 % Rotamer: Outliers : 3.10 % Allowed : 24.38 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.11 % Twisted Proline : 0.27 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.08), residues: 9955 helix: 0.45 (0.08), residues: 3926 sheet: -0.41 (0.14), residues: 1410 loop : -1.43 (0.09), residues: 4619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP e 152 HIS 0.010 0.001 HIS k 42 PHE 0.016 0.001 PHE H 138 TYR 0.020 0.001 TYR H 260 ARG 0.006 0.000 ARG W 12 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19910 Ramachandran restraints generated. 9955 Oldfield, 0 Emsley, 9955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19910 Ramachandran restraints generated. 9955 Oldfield, 0 Emsley, 9955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1178 residues out of total 8865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 931 time to evaluate : 7.798 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: a 34 MET cc_start: 0.7778 (mmm) cc_final: 0.7179 (mmt) REVERT: a 73 ASP cc_start: 0.7744 (OUTLIER) cc_final: 0.7309 (p0) REVERT: p 198 GLU cc_start: 0.7076 (tt0) cc_final: 0.6767 (tt0) REVERT: d 79 GLU cc_start: 0.6962 (mm-30) cc_final: 0.6626 (tp30) REVERT: d 123 ARG cc_start: 0.8224 (mtp180) cc_final: 0.7766 (mtm180) REVERT: Q 46 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6741 (mp0) REVERT: j 87 ASN cc_start: 0.6089 (m-40) cc_final: 0.5696 (m-40) REVERT: R 31 TYR cc_start: 0.7921 (p90) cc_final: 0.7698 (p90) REVERT: w 58 MET cc_start: 0.7391 (mmt) cc_final: 0.6511 (mmt) REVERT: w 127 ASN cc_start: 0.7538 (p0) cc_final: 0.7244 (p0) REVERT: b 41 VAL cc_start: 0.6194 (t) cc_final: 0.5877 (m) REVERT: o 111 MET cc_start: 0.5329 (OUTLIER) cc_final: 0.4903 (mtt) REVERT: B 511 ASN cc_start: 0.5272 (m110) cc_final: 0.5058 (m-40) REVERT: B 521 LYS cc_start: 0.3369 (mmtt) cc_final: 0.1984 (tptp) REVERT: B 561 MET cc_start: 0.2795 (mmm) cc_final: 0.2035 (ptt) REVERT: A 87 GLU cc_start: 0.4500 (OUTLIER) cc_final: 0.4216 (tp30) REVERT: A 184 PHE cc_start: 0.5407 (OUTLIER) cc_final: 0.3775 (t80) REVERT: A 306 MET cc_start: 0.3347 (ttm) cc_final: 0.2950 (mpp) REVERT: A 309 ASN cc_start: 0.4206 (OUTLIER) cc_final: 0.3498 (m-40) REVERT: C 61 THR cc_start: 0.7165 (m) cc_final: 0.6870 (p) REVERT: C 438 LEU cc_start: 0.5243 (OUTLIER) cc_final: 0.5039 (mp) REVERT: E 104 MET cc_start: 0.1148 (mtt) cc_final: 0.0447 (ptt) REVERT: E 179 MET cc_start: 0.6443 (mpp) cc_final: 0.6196 (mpp) REVERT: E 359 LYS cc_start: 0.5362 (OUTLIER) cc_final: 0.4577 (mttm) REVERT: E 393 MET cc_start: 0.3296 (mpp) cc_final: 0.2925 (mpp) REVERT: F 149 ASP cc_start: 0.4957 (OUTLIER) cc_final: 0.4332 (t0) REVERT: F 220 LEU cc_start: 0.0298 (OUTLIER) cc_final: 0.0017 (mm) REVERT: F 336 MET cc_start: 0.4054 (tmm) cc_final: 0.3789 (tmm) REVERT: H 47 LEU cc_start: 0.1577 (OUTLIER) cc_final: 0.1275 (pp) REVERT: H 82 PHE cc_start: 0.0464 (OUTLIER) cc_final: -0.0727 (p90) REVERT: H 217 GLU cc_start: -0.0056 (OUTLIER) cc_final: -0.0538 (mm-30) REVERT: H 314 MET cc_start: 0.3309 (tpt) cc_final: 0.2941 (tpt) REVERT: K 90 ASP cc_start: 0.4252 (OUTLIER) cc_final: 0.3518 (m-30) REVERT: L 199 GLN cc_start: 0.4666 (mm-40) cc_final: 0.4426 (mt0) REVERT: L 240 ILE cc_start: 0.0159 (OUTLIER) cc_final: -0.0118 (mt) REVERT: L 268 MET cc_start: 0.3181 (OUTLIER) cc_final: 0.2660 (mtm) REVERT: L 304 MET cc_start: 0.2695 (pmm) cc_final: 0.1221 (ttm) REVERT: L 312 GLN cc_start: 0.0449 (pp30) cc_final: 0.0097 (pt0) REVERT: L 367 MET cc_start: 0.0485 (mmt) cc_final: 0.0020 (mmp) REVERT: L 483 GLU cc_start: 0.2898 (OUTLIER) cc_final: 0.2684 (mt-10) REVERT: L 497 MET cc_start: 0.2678 (ppp) cc_final: 0.2096 (mtt) REVERT: L 542 PHE cc_start: 0.5028 (t80) cc_final: 0.4791 (m-80) REVERT: L 547 ILE cc_start: -0.1315 (mm) cc_final: -0.1796 (mm) REVERT: M 14 GLN cc_start: 0.1244 (mt0) cc_final: -0.0153 (mm-40) REVERT: M 98 ARG cc_start: 0.0951 (tpp-160) cc_final: 0.0172 (ptt180) REVERT: M 113 MET cc_start: 0.0496 (ttp) cc_final: -0.0002 (ptm) REVERT: M 162 HIS cc_start: -0.0875 (m170) cc_final: -0.1270 (m-70) REVERT: M 248 LYS cc_start: 0.6135 (mtmm) cc_final: 0.4400 (ptmm) REVERT: M 277 MET cc_start: 0.4052 (tpp) cc_final: 0.3330 (tpp) REVERT: M 309 GLU cc_start: 0.3594 (mm-30) cc_final: 0.2322 (mt-10) REVERT: M 348 GLN cc_start: 0.3570 (tp40) cc_final: 0.2995 (tm-30) REVERT: 1 436 TYR cc_start: 0.2903 (OUTLIER) cc_final: 0.2370 (m-10) REVERT: 1 468 GLN cc_start: 0.6836 (OUTLIER) cc_final: 0.6073 (tp-100) REVERT: D 45 TRP cc_start: 0.6337 (OUTLIER) cc_final: 0.5103 (m-90) REVERT: D 54 ARG cc_start: 0.4839 (ttm170) cc_final: 0.4405 (ptm160) REVERT: D 180 MET cc_start: 0.2813 (mtm) cc_final: 0.2517 (mmp) REVERT: D 191 GLN cc_start: 0.4292 (mp10) cc_final: 0.3844 (mp10) REVERT: D 252 LEU cc_start: 0.4160 (OUTLIER) cc_final: 0.3773 (tp) outliers start: 247 outliers final: 170 residues processed: 1121 average time/residue: 0.9822 time to fit residues: 1954.2812 Evaluate side-chains 1032 residues out of total 8865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 841 time to evaluate : 7.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 73 ASP Chi-restraints excluded: chain a residue 76 VAL Chi-restraints excluded: chain a residue 134 LEU Chi-restraints excluded: chain p residue 29 ASP Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 104 ASP Chi-restraints excluded: chain p residue 153 THR Chi-restraints excluded: chain p residue 208 HIS Chi-restraints excluded: chain p residue 224 GLU Chi-restraints excluded: chain p residue 230 GLU Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 46 GLU Chi-restraints excluded: chain Q residue 63 VAL Chi-restraints excluded: chain q residue 126 VAL Chi-restraints excluded: chain q residue 133 THR Chi-restraints excluded: chain q residue 156 VAL Chi-restraints excluded: chain q residue 181 CYS Chi-restraints excluded: chain q residue 212 ASP Chi-restraints excluded: chain r residue 112 VAL Chi-restraints excluded: chain r residue 114 VAL Chi-restraints excluded: chain r residue 125 THR Chi-restraints excluded: chain r residue 153 VAL Chi-restraints excluded: chain s residue 80 VAL Chi-restraints excluded: chain s residue 105 THR Chi-restraints excluded: chain s residue 132 ASP Chi-restraints excluded: chain t residue 91 VAL Chi-restraints excluded: chain t residue 92 ARG Chi-restraints excluded: chain t residue 130 THR Chi-restraints excluded: chain t residue 136 ILE Chi-restraints excluded: chain t residue 166 PHE Chi-restraints excluded: chain c residue 61 LEU Chi-restraints excluded: chain c residue 104 ASP Chi-restraints excluded: chain c residue 149 VAL Chi-restraints excluded: chain c residue 156 HIS Chi-restraints excluded: chain c residue 160 SER Chi-restraints excluded: chain n residue 66 VAL Chi-restraints excluded: chain i residue 40 THR Chi-restraints excluded: chain i residue 100 THR Chi-restraints excluded: chain y residue 69 ILE Chi-restraints excluded: chain f residue 14 ILE Chi-restraints excluded: chain f residue 25 VAL Chi-restraints excluded: chain f residue 41 MET Chi-restraints excluded: chain j residue 19 ASP Chi-restraints excluded: chain j residue 52 LEU Chi-restraints excluded: chain j residue 58 GLU Chi-restraints excluded: chain j residue 64 SER Chi-restraints excluded: chain j residue 105 PHE Chi-restraints excluded: chain j residue 128 VAL Chi-restraints excluded: chain z residue 17 LEU Chi-restraints excluded: chain z residue 35 VAL Chi-restraints excluded: chain z residue 102 THR Chi-restraints excluded: chain z residue 120 THR Chi-restraints excluded: chain R residue 40 CYS Chi-restraints excluded: chain T residue 44 ASN Chi-restraints excluded: chain g residue 46 THR Chi-restraints excluded: chain g residue 63 PHE Chi-restraints excluded: chain b residue 12 VAL Chi-restraints excluded: chain b residue 181 VAL Chi-restraints excluded: chain e residue 26 ASP Chi-restraints excluded: chain e residue 78 MET Chi-restraints excluded: chain e residue 93 VAL Chi-restraints excluded: chain e residue 116 ILE Chi-restraints excluded: chain e residue 168 THR Chi-restraints excluded: chain u residue 2 LEU Chi-restraints excluded: chain u residue 58 VAL Chi-restraints excluded: chain u residue 74 GLU Chi-restraints excluded: chain u residue 85 LEU Chi-restraints excluded: chain v residue 103 VAL Chi-restraints excluded: chain o residue 37 TYR Chi-restraints excluded: chain o residue 111 MET Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain k residue 81 ASP Chi-restraints excluded: chain k residue 136 THR Chi-restraints excluded: chain x residue 35 ASP Chi-restraints excluded: chain x residue 45 LEU Chi-restraints excluded: chain x residue 50 GLU Chi-restraints excluded: chain x residue 132 ASP Chi-restraints excluded: chain h residue 36 CYS Chi-restraints excluded: chain h residue 61 LEU Chi-restraints excluded: chain h residue 90 ASP Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain S residue 35 MET Chi-restraints excluded: chain S residue 61 SER Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain l residue 53 ILE Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 104 HIS Chi-restraints excluded: chain V residue 113 PHE Chi-restraints excluded: chain V residue 115 SER Chi-restraints excluded: chain V residue 135 LEU Chi-restraints excluded: chain V residue 166 VAL Chi-restraints excluded: chain V residue 186 THR Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain A residue 47 HIS Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 382 TYR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 591 MET Chi-restraints excluded: chain C residue 736 HIS Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 324 PHE Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain E residue 339 PHE Chi-restraints excluded: chain E residue 359 LYS Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 322 ASP Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 82 PHE Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 141 PHE Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 174 MET Chi-restraints excluded: chain L residue 181 GLN Chi-restraints excluded: chain L residue 240 ILE Chi-restraints excluded: chain L residue 268 MET Chi-restraints excluded: chain L residue 274 LEU Chi-restraints excluded: chain L residue 293 VAL Chi-restraints excluded: chain L residue 336 PHE Chi-restraints excluded: chain L residue 346 THR Chi-restraints excluded: chain L residue 383 ASP Chi-restraints excluded: chain L residue 412 LEU Chi-restraints excluded: chain L residue 414 SER Chi-restraints excluded: chain L residue 452 GLN Chi-restraints excluded: chain L residue 460 ILE Chi-restraints excluded: chain L residue 483 GLU Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 503 THR Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain M residue 266 LEU Chi-restraints excluded: chain 1 residue 13 HIS Chi-restraints excluded: chain 1 residue 154 ASN Chi-restraints excluded: chain 1 residue 196 THR Chi-restraints excluded: chain 1 residue 271 VAL Chi-restraints excluded: chain 1 residue 275 ASP Chi-restraints excluded: chain 1 residue 305 VAL Chi-restraints excluded: chain 1 residue 357 MET Chi-restraints excluded: chain 1 residue 416 ILE Chi-restraints excluded: chain 1 residue 436 TYR Chi-restraints excluded: chain 1 residue 459 VAL Chi-restraints excluded: chain 1 residue 468 GLN Chi-restraints excluded: chain 1 residue 493 ASP Chi-restraints excluded: chain 1 residue 517 VAL Chi-restraints excluded: chain 1 residue 598 ASP Chi-restraints excluded: chain N residue 54 TYR Chi-restraints excluded: chain D residue 45 TRP Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 519 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1162 random chunks: chunk 1018 optimal weight: 4.9990 chunk 1072 optimal weight: 20.0000 chunk 978 optimal weight: 6.9990 chunk 1043 optimal weight: 3.9990 chunk 628 optimal weight: 6.9990 chunk 454 optimal weight: 10.0000 chunk 819 optimal weight: 10.0000 chunk 320 optimal weight: 10.0000 chunk 943 optimal weight: 0.9980 chunk 987 optimal weight: 2.9990 chunk 1040 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** q 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 7 ASN t 155 ASN t 167 GLN c 113 GLN n 65 ASN m 62 GLN j 61 GLN ** b 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 83 ASN ** k 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 12 GLN ** x 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 126 GLN ** V 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 GLN ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 GLN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 321 ASN ** E 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 181 GLN ** L 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 65 ASN ** M 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6471 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 120661 Z= 0.203 Angle : 0.590 13.865 171380 Z= 0.301 Chirality : 0.039 0.259 20736 Planarity : 0.004 0.095 15542 Dihedral : 21.375 178.821 37974 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.30 % Favored : 94.68 % Rotamer: Outliers : 3.52 % Allowed : 24.51 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.11 % Twisted Proline : 0.27 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.08), residues: 9955 helix: 0.46 (0.08), residues: 3928 sheet: -0.39 (0.14), residues: 1412 loop : -1.46 (0.09), residues: 4615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP V 177 HIS 0.009 0.001 HIS C 736 PHE 0.023 0.001 PHE M 282 TYR 0.037 0.002 TYR H 196 ARG 0.010 0.000 ARG v 45 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19910 Ramachandran restraints generated. 9955 Oldfield, 0 Emsley, 9955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19910 Ramachandran restraints generated. 9955 Oldfield, 0 Emsley, 9955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1121 residues out of total 8865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 840 time to evaluate : 7.684 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: a 34 MET cc_start: 0.7862 (mmm) cc_final: 0.6971 (mmt) REVERT: a 73 ASP cc_start: 0.7753 (OUTLIER) cc_final: 0.7345 (p0) REVERT: p 198 GLU cc_start: 0.7103 (tt0) cc_final: 0.6739 (tt0) REVERT: d 79 GLU cc_start: 0.6948 (mm-30) cc_final: 0.6593 (mm-30) REVERT: R 31 TYR cc_start: 0.8009 (p90) cc_final: 0.7794 (p90) REVERT: w 58 MET cc_start: 0.6886 (mmt) cc_final: 0.6500 (mmt) REVERT: w 127 ASN cc_start: 0.7620 (p0) cc_final: 0.7300 (p0) REVERT: g 86 GLN cc_start: 0.6833 (tm-30) cc_final: 0.6463 (tp40) REVERT: b 41 VAL cc_start: 0.5735 (t) cc_final: 0.5452 (m) REVERT: b 143 ARG cc_start: 0.4648 (OUTLIER) cc_final: 0.3759 (tpt-90) REVERT: e 204 ARG cc_start: 0.6946 (mtm110) cc_final: 0.6445 (mtm-85) REVERT: o 86 LEU cc_start: 0.6279 (OUTLIER) cc_final: 0.5853 (mm) REVERT: o 111 MET cc_start: 0.5435 (OUTLIER) cc_final: 0.4722 (mtt) REVERT: B 497 GLN cc_start: 0.3496 (tp-100) cc_final: 0.3190 (tp40) REVERT: B 511 ASN cc_start: 0.5165 (m110) cc_final: 0.4941 (m-40) REVERT: B 521 LYS cc_start: 0.3393 (mmtt) cc_final: 0.1929 (tptp) REVERT: B 561 MET cc_start: 0.2827 (mmm) cc_final: 0.2081 (ptt) REVERT: A 87 GLU cc_start: 0.4546 (OUTLIER) cc_final: 0.4226 (tp30) REVERT: A 184 PHE cc_start: 0.5465 (OUTLIER) cc_final: 0.4069 (t80) REVERT: A 306 MET cc_start: 0.3309 (ttm) cc_final: 0.2807 (mpp) REVERT: A 309 ASN cc_start: 0.3413 (OUTLIER) cc_final: 0.2595 (m-40) REVERT: C 438 LEU cc_start: 0.5352 (OUTLIER) cc_final: 0.5044 (mp) REVERT: E 50 MET cc_start: 0.4256 (tpp) cc_final: 0.4025 (tpp) REVERT: E 104 MET cc_start: 0.1308 (mtt) cc_final: 0.0474 (ptt) REVERT: E 359 LYS cc_start: 0.5398 (OUTLIER) cc_final: 0.4656 (mttm) REVERT: E 393 MET cc_start: 0.3372 (mpp) cc_final: 0.3024 (mpp) REVERT: F 220 LEU cc_start: 0.0338 (OUTLIER) cc_final: -0.0001 (mm) REVERT: H 47 LEU cc_start: 0.1304 (OUTLIER) cc_final: 0.0922 (pp) REVERT: H 82 PHE cc_start: 0.0684 (OUTLIER) cc_final: -0.0485 (p90) REVERT: H 197 MET cc_start: -0.0177 (mmm) cc_final: -0.0821 (ttp) REVERT: H 217 GLU cc_start: -0.0090 (OUTLIER) cc_final: -0.0640 (tt0) REVERT: H 314 MET cc_start: 0.3140 (tpt) cc_final: 0.2912 (tpt) REVERT: K 7 MET cc_start: -0.2347 (tpt) cc_final: -0.2665 (mmm) REVERT: K 90 ASP cc_start: 0.4255 (OUTLIER) cc_final: 0.3415 (m-30) REVERT: L 181 GLN cc_start: 0.0916 (OUTLIER) cc_final: -0.0571 (mt0) REVERT: L 240 ILE cc_start: -0.0047 (OUTLIER) cc_final: -0.0321 (mt) REVERT: L 268 MET cc_start: 0.3190 (OUTLIER) cc_final: 0.2122 (mtm) REVERT: L 304 MET cc_start: 0.2897 (pmm) cc_final: 0.1452 (ttm) REVERT: L 312 GLN cc_start: 0.0695 (pp30) cc_final: 0.0370 (pt0) REVERT: L 367 MET cc_start: 0.0597 (mmt) cc_final: 0.0072 (mmp) REVERT: L 483 GLU cc_start: 0.2502 (OUTLIER) cc_final: 0.2227 (mt-10) REVERT: L 497 MET cc_start: 0.2669 (ppp) cc_final: 0.2099 (mtt) REVERT: L 547 ILE cc_start: -0.1500 (mm) cc_final: -0.2077 (mm) REVERT: M 14 GLN cc_start: 0.1278 (mt0) cc_final: 0.0334 (mm-40) REVERT: M 98 ARG cc_start: 0.1340 (tpp-160) cc_final: 0.0388 (ptt180) REVERT: M 113 MET cc_start: 0.0645 (ttp) cc_final: 0.0140 (ptm) REVERT: M 162 HIS cc_start: -0.0984 (m170) cc_final: -0.1350 (m-70) REVERT: M 248 LYS cc_start: 0.6002 (mtmm) cc_final: 0.4398 (ptmm) REVERT: M 277 MET cc_start: 0.4800 (tpp) cc_final: 0.3962 (tpp) REVERT: M 309 GLU cc_start: 0.3658 (mm-30) cc_final: 0.2401 (mt-10) REVERT: M 348 GLN cc_start: 0.4171 (tp40) cc_final: 0.3482 (tm-30) REVERT: 1 359 GLU cc_start: 0.5595 (pm20) cc_final: 0.4922 (tp30) REVERT: 1 436 TYR cc_start: 0.3144 (OUTLIER) cc_final: 0.2529 (m-10) REVERT: 1 468 GLN cc_start: 0.6971 (OUTLIER) cc_final: 0.6155 (tp-100) REVERT: D 45 TRP cc_start: 0.6424 (OUTLIER) cc_final: 0.5142 (m-90) REVERT: D 54 ARG cc_start: 0.4855 (ttm170) cc_final: 0.4385 (ptm160) REVERT: D 191 GLN cc_start: 0.4383 (mp10) cc_final: 0.3898 (mp10) REVERT: D 252 LEU cc_start: 0.4169 (OUTLIER) cc_final: 0.3807 (tp) REVERT: D 300 GLN cc_start: 0.5715 (OUTLIER) cc_final: 0.4416 (mm110) outliers start: 281 outliers final: 217 residues processed: 1059 average time/residue: 0.9207 time to fit residues: 1726.8373 Evaluate side-chains 1052 residues out of total 8865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 812 time to evaluate : 7.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 73 ASP Chi-restraints excluded: chain a residue 76 VAL Chi-restraints excluded: chain a residue 112 ILE Chi-restraints excluded: chain a residue 134 LEU Chi-restraints excluded: chain p residue 29 ASP Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 104 ASP Chi-restraints excluded: chain p residue 113 MET Chi-restraints excluded: chain p residue 153 THR Chi-restraints excluded: chain p residue 224 GLU Chi-restraints excluded: chain p residue 230 GLU Chi-restraints excluded: chain d residue 184 VAL Chi-restraints excluded: chain d residue 271 ASP Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 52 ASP Chi-restraints excluded: chain Q residue 53 ILE Chi-restraints excluded: chain Q residue 63 VAL Chi-restraints excluded: chain Q residue 84 VAL Chi-restraints excluded: chain Q residue 94 ASP Chi-restraints excluded: chain q residue 45 ILE Chi-restraints excluded: chain q residue 126 VAL Chi-restraints excluded: chain q residue 133 THR Chi-restraints excluded: chain q residue 156 VAL Chi-restraints excluded: chain q residue 165 GLU Chi-restraints excluded: chain q residue 181 CYS Chi-restraints excluded: chain q residue 206 ASP Chi-restraints excluded: chain q residue 212 ASP Chi-restraints excluded: chain r residue 112 VAL Chi-restraints excluded: chain r residue 114 VAL Chi-restraints excluded: chain r residue 125 THR Chi-restraints excluded: chain r residue 153 VAL Chi-restraints excluded: chain s residue 80 VAL Chi-restraints excluded: chain s residue 105 THR Chi-restraints excluded: chain s residue 132 ASP Chi-restraints excluded: chain s residue 148 LEU Chi-restraints excluded: chain t residue 91 VAL Chi-restraints excluded: chain t residue 92 ARG Chi-restraints excluded: chain t residue 130 THR Chi-restraints excluded: chain t residue 155 ASN Chi-restraints excluded: chain t residue 166 PHE Chi-restraints excluded: chain c residue 18 ARG Chi-restraints excluded: chain c residue 61 LEU Chi-restraints excluded: chain c residue 104 ASP Chi-restraints excluded: chain c residue 149 VAL Chi-restraints excluded: chain c residue 156 HIS Chi-restraints excluded: chain c residue 160 SER Chi-restraints excluded: chain n residue 66 VAL Chi-restraints excluded: chain m residue 87 ASP Chi-restraints excluded: chain i residue 40 THR Chi-restraints excluded: chain y residue 35 ASN Chi-restraints excluded: chain f residue 9 ASP Chi-restraints excluded: chain f residue 25 VAL Chi-restraints excluded: chain f residue 41 MET Chi-restraints excluded: chain j residue 52 LEU Chi-restraints excluded: chain j residue 58 GLU Chi-restraints excluded: chain j residue 64 SER Chi-restraints excluded: chain j residue 105 PHE Chi-restraints excluded: chain j residue 128 VAL Chi-restraints excluded: chain j residue 138 LYS Chi-restraints excluded: chain z residue 17 LEU Chi-restraints excluded: chain z residue 74 MET Chi-restraints excluded: chain z residue 102 THR Chi-restraints excluded: chain z residue 120 THR Chi-restraints excluded: chain R residue 40 CYS Chi-restraints excluded: chain R residue 43 ILE Chi-restraints excluded: chain w residue 130 THR Chi-restraints excluded: chain g residue 46 THR Chi-restraints excluded: chain g residue 113 ILE Chi-restraints excluded: chain b residue 12 VAL Chi-restraints excluded: chain b residue 143 ARG Chi-restraints excluded: chain b residue 181 VAL Chi-restraints excluded: chain b residue 193 ASP Chi-restraints excluded: chain b residue 218 LEU Chi-restraints excluded: chain e residue 26 ASP Chi-restraints excluded: chain e residue 28 VAL Chi-restraints excluded: chain e residue 78 MET Chi-restraints excluded: chain e residue 93 VAL Chi-restraints excluded: chain e residue 116 ILE Chi-restraints excluded: chain e residue 168 THR Chi-restraints excluded: chain u residue 2 LEU Chi-restraints excluded: chain u residue 58 VAL Chi-restraints excluded: chain u residue 74 GLU Chi-restraints excluded: chain u residue 85 LEU Chi-restraints excluded: chain v residue 103 VAL Chi-restraints excluded: chain o residue 37 TYR Chi-restraints excluded: chain o residue 66 GLU Chi-restraints excluded: chain o residue 86 LEU Chi-restraints excluded: chain o residue 111 MET Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain k residue 81 ASP Chi-restraints excluded: chain k residue 136 THR Chi-restraints excluded: chain x residue 12 GLN Chi-restraints excluded: chain x residue 35 ASP Chi-restraints excluded: chain x residue 45 LEU Chi-restraints excluded: chain x residue 50 GLU Chi-restraints excluded: chain h residue 23 THR Chi-restraints excluded: chain h residue 36 CYS Chi-restraints excluded: chain h residue 61 LEU Chi-restraints excluded: chain h residue 90 ASP Chi-restraints excluded: chain h residue 110 VAL Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain S residue 14 VAL Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 35 MET Chi-restraints excluded: chain S residue 61 SER Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain l residue 53 ILE Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 104 HIS Chi-restraints excluded: chain V residue 113 PHE Chi-restraints excluded: chain V residue 115 SER Chi-restraints excluded: chain V residue 135 LEU Chi-restraints excluded: chain V residue 166 VAL Chi-restraints excluded: chain V residue 176 VAL Chi-restraints excluded: chain V residue 186 THR Chi-restraints excluded: chain V residue 237 ASN Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain A residue 47 HIS Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 382 TYR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 504 ASP Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 591 MET Chi-restraints excluded: chain C residue 619 CYS Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 671 VAL Chi-restraints excluded: chain C residue 736 HIS Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 324 PHE Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain E residue 339 PHE Chi-restraints excluded: chain E residue 359 LYS Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 322 ASP Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 82 PHE Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 141 PHE Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 161 MET Chi-restraints excluded: chain K residue 174 MET Chi-restraints excluded: chain L residue 181 GLN Chi-restraints excluded: chain L residue 240 ILE Chi-restraints excluded: chain L residue 268 MET Chi-restraints excluded: chain L residue 274 LEU Chi-restraints excluded: chain L residue 293 VAL Chi-restraints excluded: chain L residue 296 ASN Chi-restraints excluded: chain L residue 336 PHE Chi-restraints excluded: chain L residue 339 ILE Chi-restraints excluded: chain L residue 346 THR Chi-restraints excluded: chain L residue 412 LEU Chi-restraints excluded: chain L residue 414 SER Chi-restraints excluded: chain L residue 452 GLN Chi-restraints excluded: chain L residue 460 ILE Chi-restraints excluded: chain L residue 483 GLU Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 503 THR Chi-restraints excluded: chain L residue 510 ASP Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 91 VAL Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain M residue 145 ASP Chi-restraints excluded: chain M residue 179 ASP Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 266 LEU Chi-restraints excluded: chain M residue 341 THR Chi-restraints excluded: chain 1 residue 13 HIS Chi-restraints excluded: chain 1 residue 73 VAL Chi-restraints excluded: chain 1 residue 80 GLU Chi-restraints excluded: chain 1 residue 154 ASN Chi-restraints excluded: chain 1 residue 271 VAL Chi-restraints excluded: chain 1 residue 275 ASP Chi-restraints excluded: chain 1 residue 305 VAL Chi-restraints excluded: chain 1 residue 357 MET Chi-restraints excluded: chain 1 residue 392 LEU Chi-restraints excluded: chain 1 residue 408 ASN Chi-restraints excluded: chain 1 residue 416 ILE Chi-restraints excluded: chain 1 residue 436 TYR Chi-restraints excluded: chain 1 residue 459 VAL Chi-restraints excluded: chain 1 residue 468 GLN Chi-restraints excluded: chain 1 residue 493 ASP Chi-restraints excluded: chain 1 residue 517 VAL Chi-restraints excluded: chain 1 residue 598 ASP Chi-restraints excluded: chain N residue 54 TYR Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain N residue 69 CYS Chi-restraints excluded: chain D residue 45 TRP Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 300 GLN Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 519 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1162 random chunks: chunk 685 optimal weight: 6.9990 chunk 1103 optimal weight: 30.0000 chunk 673 optimal weight: 3.9990 chunk 523 optimal weight: 10.0000 chunk 767 optimal weight: 0.8980 chunk 1157 optimal weight: 50.0000 chunk 1065 optimal weight: 3.9990 chunk 921 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 712 optimal weight: 0.2980 chunk 565 optimal weight: 0.1980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** q 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 7 ASN t 155 ASN t 167 GLN c 113 GLN ** n 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 62 GLN b 165 ASN ** b 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 83 ASN ** k 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 311 GLN ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 181 GLN ** L 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 216 ASN ** M 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 326 GLN ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6467 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.379 120661 Z= 0.241 Angle : 0.645 59.199 171380 Z= 0.341 Chirality : 0.039 0.866 20736 Planarity : 0.004 0.138 15542 Dihedral : 21.377 178.937 37974 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.23 % Favored : 94.75 % Rotamer: Outliers : 3.34 % Allowed : 24.68 % Favored : 71.98 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.11 % Twisted Proline : 0.27 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.08), residues: 9955 helix: 0.47 (0.08), residues: 3927 sheet: -0.39 (0.14), residues: 1412 loop : -1.45 (0.09), residues: 4616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP V 177 HIS 0.010 0.001 HIS C 876 PHE 0.032 0.001 PHE A 465 TYR 0.079 0.002 TYR H 167 ARG 0.024 0.000 ARG D 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19910 Ramachandran restraints generated. 9955 Oldfield, 0 Emsley, 9955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19910 Ramachandran restraints generated. 9955 Oldfield, 0 Emsley, 9955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1078 residues out of total 8865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 812 time to evaluate : 7.696 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: a 34 MET cc_start: 0.7858 (mmm) cc_final: 0.6984 (mmt) REVERT: a 73 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7342 (p0) REVERT: p 198 GLU cc_start: 0.7101 (tt0) cc_final: 0.6732 (tt0) REVERT: d 79 GLU cc_start: 0.6937 (mm-30) cc_final: 0.6597 (mm-30) REVERT: R 31 TYR cc_start: 0.8016 (p90) cc_final: 0.7810 (p90) REVERT: w 58 MET cc_start: 0.6874 (mmt) cc_final: 0.6494 (mmt) REVERT: w 127 ASN cc_start: 0.7620 (p0) cc_final: 0.7298 (p0) REVERT: g 86 GLN cc_start: 0.6820 (tm-30) cc_final: 0.6447 (tp40) REVERT: g 146 ARG cc_start: 0.4051 (OUTLIER) cc_final: 0.3170 (ptp-170) REVERT: b 41 VAL cc_start: 0.5834 (t) cc_final: 0.5548 (m) REVERT: b 143 ARG cc_start: 0.4639 (OUTLIER) cc_final: 0.3902 (tpt-90) REVERT: o 111 MET cc_start: 0.5465 (OUTLIER) cc_final: 0.4717 (mtt) REVERT: B 497 GLN cc_start: 0.3486 (tp-100) cc_final: 0.3192 (tp40) REVERT: B 511 ASN cc_start: 0.5170 (m110) cc_final: 0.4944 (m-40) REVERT: B 521 LYS cc_start: 0.3384 (mmtt) cc_final: 0.1928 (tptp) REVERT: B 561 MET cc_start: 0.2821 (mmm) cc_final: 0.2078 (ptt) REVERT: A 87 GLU cc_start: 0.4517 (OUTLIER) cc_final: 0.4219 (tp30) REVERT: A 184 PHE cc_start: 0.5443 (OUTLIER) cc_final: 0.4063 (t80) REVERT: A 306 MET cc_start: 0.3305 (ttm) cc_final: 0.2809 (mpp) REVERT: A 309 ASN cc_start: 0.3702 (OUTLIER) cc_final: 0.2845 (m-40) REVERT: C 438 LEU cc_start: 0.5354 (OUTLIER) cc_final: 0.5036 (mp) REVERT: E 50 MET cc_start: 0.4249 (tpp) cc_final: 0.4009 (tpp) REVERT: E 104 MET cc_start: 0.1282 (mtt) cc_final: 0.0496 (ptt) REVERT: E 359 LYS cc_start: 0.5385 (OUTLIER) cc_final: 0.4651 (mttm) REVERT: E 393 MET cc_start: 0.3395 (mpp) cc_final: 0.3022 (mpp) REVERT: F 220 LEU cc_start: 0.0323 (OUTLIER) cc_final: -0.0002 (mm) REVERT: H 47 LEU cc_start: 0.1348 (OUTLIER) cc_final: 0.0992 (pp) REVERT: H 82 PHE cc_start: 0.0715 (OUTLIER) cc_final: -0.0494 (p90) REVERT: H 197 MET cc_start: -0.0131 (mmm) cc_final: -0.0848 (ttp) REVERT: H 217 GLU cc_start: -0.0071 (OUTLIER) cc_final: -0.0652 (tt0) REVERT: H 253 MET cc_start: 0.2595 (ttp) cc_final: 0.2158 (ptm) REVERT: H 314 MET cc_start: 0.3159 (tpt) cc_final: 0.2876 (tpt) REVERT: K 15 LEU cc_start: 0.3229 (OUTLIER) cc_final: 0.2916 (mt) REVERT: K 90 ASP cc_start: 0.4244 (OUTLIER) cc_final: 0.3405 (m-30) REVERT: L 199 GLN cc_start: 0.4762 (mm-40) cc_final: 0.4504 (mt0) REVERT: L 240 ILE cc_start: -0.0039 (OUTLIER) cc_final: -0.0325 (mt) REVERT: L 268 MET cc_start: 0.3183 (OUTLIER) cc_final: 0.2119 (mtm) REVERT: L 304 MET cc_start: 0.2900 (pmm) cc_final: 0.1447 (ttm) REVERT: L 312 GLN cc_start: 0.0701 (pp30) cc_final: 0.0350 (pt0) REVERT: L 367 MET cc_start: 0.0601 (mmt) cc_final: 0.0064 (mmp) REVERT: L 483 GLU cc_start: 0.2494 (OUTLIER) cc_final: 0.2225 (mt-10) REVERT: L 497 MET cc_start: 0.2671 (ppp) cc_final: 0.2103 (mtt) REVERT: L 547 ILE cc_start: -0.1511 (mm) cc_final: -0.2082 (mm) REVERT: M 14 GLN cc_start: 0.1271 (mt0) cc_final: 0.0337 (mm-40) REVERT: M 98 ARG cc_start: 0.1343 (tpp-160) cc_final: 0.0385 (ptt180) REVERT: M 113 MET cc_start: 0.0637 (ttp) cc_final: 0.0137 (ptm) REVERT: M 162 HIS cc_start: -0.0904 (m170) cc_final: -0.1352 (m-70) REVERT: M 248 LYS cc_start: 0.5991 (mtmm) cc_final: 0.4406 (ptmm) REVERT: M 277 MET cc_start: 0.4752 (tpp) cc_final: 0.3757 (tpp) REVERT: M 309 GLU cc_start: 0.3658 (mm-30) cc_final: 0.2392 (mt-10) REVERT: M 348 GLN cc_start: 0.4162 (tp40) cc_final: 0.3478 (tm-30) REVERT: 1 359 GLU cc_start: 0.5583 (pm20) cc_final: 0.4921 (tp30) REVERT: 1 436 TYR cc_start: 0.3139 (OUTLIER) cc_final: 0.2526 (m-10) REVERT: 1 468 GLN cc_start: 0.6968 (OUTLIER) cc_final: 0.6151 (tp-100) REVERT: D 45 TRP cc_start: 0.6414 (OUTLIER) cc_final: 0.5137 (m-90) REVERT: D 54 ARG cc_start: 0.4862 (ttm170) cc_final: 0.4394 (ptm160) REVERT: D 189 GLU cc_start: 0.4188 (OUTLIER) cc_final: 0.3705 (tm-30) REVERT: D 191 GLN cc_start: 0.4374 (mp10) cc_final: 0.3872 (mp10) REVERT: D 252 LEU cc_start: 0.4153 (OUTLIER) cc_final: 0.3775 (tp) REVERT: D 300 GLN cc_start: 0.5719 (OUTLIER) cc_final: 0.4424 (mm110) outliers start: 266 outliers final: 229 residues processed: 1019 average time/residue: 0.9328 time to fit residues: 1680.7246 Evaluate side-chains 1063 residues out of total 8865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 810 time to evaluate : 7.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 73 ASP Chi-restraints excluded: chain a residue 76 VAL Chi-restraints excluded: chain a residue 112 ILE Chi-restraints excluded: chain a residue 134 LEU Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain p residue 104 ASP Chi-restraints excluded: chain p residue 113 MET Chi-restraints excluded: chain p residue 153 THR Chi-restraints excluded: chain p residue 224 GLU Chi-restraints excluded: chain p residue 230 GLU Chi-restraints excluded: chain d residue 78 LEU Chi-restraints excluded: chain d residue 184 VAL Chi-restraints excluded: chain d residue 271 ASP Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 52 ASP Chi-restraints excluded: chain Q residue 53 ILE Chi-restraints excluded: chain Q residue 63 VAL Chi-restraints excluded: chain Q residue 84 VAL Chi-restraints excluded: chain q residue 45 ILE Chi-restraints excluded: chain q residue 126 VAL Chi-restraints excluded: chain q residue 133 THR Chi-restraints excluded: chain q residue 156 VAL Chi-restraints excluded: chain q residue 165 GLU Chi-restraints excluded: chain q residue 181 CYS Chi-restraints excluded: chain q residue 212 ASP Chi-restraints excluded: chain r residue 112 VAL Chi-restraints excluded: chain r residue 114 VAL Chi-restraints excluded: chain r residue 125 THR Chi-restraints excluded: chain r residue 153 VAL Chi-restraints excluded: chain s residue 80 VAL Chi-restraints excluded: chain s residue 86 LYS Chi-restraints excluded: chain s residue 105 THR Chi-restraints excluded: chain s residue 132 ASP Chi-restraints excluded: chain s residue 148 LEU Chi-restraints excluded: chain t residue 91 VAL Chi-restraints excluded: chain t residue 92 ARG Chi-restraints excluded: chain t residue 130 THR Chi-restraints excluded: chain t residue 166 PHE Chi-restraints excluded: chain c residue 18 ARG Chi-restraints excluded: chain c residue 61 LEU Chi-restraints excluded: chain c residue 95 ASP Chi-restraints excluded: chain c residue 104 ASP Chi-restraints excluded: chain c residue 149 VAL Chi-restraints excluded: chain c residue 156 HIS Chi-restraints excluded: chain c residue 160 SER Chi-restraints excluded: chain n residue 40 ILE Chi-restraints excluded: chain n residue 66 VAL Chi-restraints excluded: chain m residue 87 ASP Chi-restraints excluded: chain i residue 40 THR Chi-restraints excluded: chain y residue 35 ASN Chi-restraints excluded: chain f residue 9 ASP Chi-restraints excluded: chain f residue 25 VAL Chi-restraints excluded: chain f residue 41 MET Chi-restraints excluded: chain f residue 80 ASP Chi-restraints excluded: chain j residue 45 SER Chi-restraints excluded: chain j residue 52 LEU Chi-restraints excluded: chain j residue 58 GLU Chi-restraints excluded: chain j residue 64 SER Chi-restraints excluded: chain j residue 105 PHE Chi-restraints excluded: chain j residue 128 VAL Chi-restraints excluded: chain j residue 138 LYS Chi-restraints excluded: chain z residue 14 THR Chi-restraints excluded: chain z residue 17 LEU Chi-restraints excluded: chain z residue 74 MET Chi-restraints excluded: chain z residue 102 THR Chi-restraints excluded: chain z residue 120 THR Chi-restraints excluded: chain R residue 40 CYS Chi-restraints excluded: chain R residue 43 ILE Chi-restraints excluded: chain w residue 130 THR Chi-restraints excluded: chain g residue 46 THR Chi-restraints excluded: chain g residue 63 PHE Chi-restraints excluded: chain g residue 113 ILE Chi-restraints excluded: chain g residue 146 ARG Chi-restraints excluded: chain b residue 12 VAL Chi-restraints excluded: chain b residue 143 ARG Chi-restraints excluded: chain b residue 181 VAL Chi-restraints excluded: chain b residue 193 ASP Chi-restraints excluded: chain e residue 26 ASP Chi-restraints excluded: chain e residue 28 VAL Chi-restraints excluded: chain e residue 78 MET Chi-restraints excluded: chain e residue 93 VAL Chi-restraints excluded: chain e residue 116 ILE Chi-restraints excluded: chain e residue 140 ASP Chi-restraints excluded: chain e residue 168 THR Chi-restraints excluded: chain u residue 2 LEU Chi-restraints excluded: chain u residue 58 VAL Chi-restraints excluded: chain u residue 74 GLU Chi-restraints excluded: chain u residue 85 LEU Chi-restraints excluded: chain v residue 103 VAL Chi-restraints excluded: chain o residue 37 TYR Chi-restraints excluded: chain o residue 66 GLU Chi-restraints excluded: chain o residue 111 MET Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain k residue 81 ASP Chi-restraints excluded: chain k residue 136 THR Chi-restraints excluded: chain x residue 5 THR Chi-restraints excluded: chain x residue 35 ASP Chi-restraints excluded: chain x residue 45 LEU Chi-restraints excluded: chain x residue 50 GLU Chi-restraints excluded: chain x residue 124 THR Chi-restraints excluded: chain h residue 36 CYS Chi-restraints excluded: chain h residue 61 LEU Chi-restraints excluded: chain h residue 90 ASP Chi-restraints excluded: chain h residue 110 VAL Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain S residue 14 VAL Chi-restraints excluded: chain S residue 35 MET Chi-restraints excluded: chain S residue 61 SER Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain l residue 53 ILE Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 104 HIS Chi-restraints excluded: chain V residue 113 PHE Chi-restraints excluded: chain V residue 115 SER Chi-restraints excluded: chain V residue 135 LEU Chi-restraints excluded: chain V residue 166 VAL Chi-restraints excluded: chain V residue 176 VAL Chi-restraints excluded: chain V residue 186 THR Chi-restraints excluded: chain V residue 237 ASN Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain A residue 47 HIS Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 382 TYR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 591 MET Chi-restraints excluded: chain C residue 619 CYS Chi-restraints excluded: chain C residue 736 HIS Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain C residue 809 ASP Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 324 PHE Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain E residue 339 PHE Chi-restraints excluded: chain E residue 359 LYS Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain F residue 322 ASP Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 82 PHE Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 167 TYR Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 82 PHE Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 141 PHE Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 161 MET Chi-restraints excluded: chain K residue 174 MET Chi-restraints excluded: chain L residue 240 ILE Chi-restraints excluded: chain L residue 260 TYR Chi-restraints excluded: chain L residue 268 MET Chi-restraints excluded: chain L residue 274 LEU Chi-restraints excluded: chain L residue 293 VAL Chi-restraints excluded: chain L residue 296 ASN Chi-restraints excluded: chain L residue 336 PHE Chi-restraints excluded: chain L residue 339 ILE Chi-restraints excluded: chain L residue 346 THR Chi-restraints excluded: chain L residue 412 LEU Chi-restraints excluded: chain L residue 414 SER Chi-restraints excluded: chain L residue 452 GLN Chi-restraints excluded: chain L residue 460 ILE Chi-restraints excluded: chain L residue 483 GLU Chi-restraints excluded: chain L residue 501 VAL Chi-restraints excluded: chain L residue 503 THR Chi-restraints excluded: chain L residue 510 ASP Chi-restraints excluded: chain M residue 68 VAL Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 91 VAL Chi-restraints excluded: chain M residue 121 TYR Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain M residue 145 ASP Chi-restraints excluded: chain M residue 179 ASP Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 266 LEU Chi-restraints excluded: chain M residue 341 THR Chi-restraints excluded: chain 1 residue 13 HIS Chi-restraints excluded: chain 1 residue 73 VAL Chi-restraints excluded: chain 1 residue 80 GLU Chi-restraints excluded: chain 1 residue 154 ASN Chi-restraints excluded: chain 1 residue 271 VAL Chi-restraints excluded: chain 1 residue 275 ASP Chi-restraints excluded: chain 1 residue 305 VAL Chi-restraints excluded: chain 1 residue 357 MET Chi-restraints excluded: chain 1 residue 392 LEU Chi-restraints excluded: chain 1 residue 408 ASN Chi-restraints excluded: chain 1 residue 416 ILE Chi-restraints excluded: chain 1 residue 436 TYR Chi-restraints excluded: chain 1 residue 459 VAL Chi-restraints excluded: chain 1 residue 468 GLN Chi-restraints excluded: chain 1 residue 493 ASP Chi-restraints excluded: chain 1 residue 517 VAL Chi-restraints excluded: chain 1 residue 598 ASP Chi-restraints excluded: chain N residue 54 TYR Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain N residue 69 CYS Chi-restraints excluded: chain D residue 45 TRP Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 300 GLN Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 348 MET Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 519 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1162 random chunks: chunk 732 optimal weight: 6.9990 chunk 981 optimal weight: 8.9990 chunk 282 optimal weight: 10.0000 chunk 849 optimal weight: 20.0000 chunk 136 optimal weight: 10.0000 chunk 256 optimal weight: 7.9990 chunk 923 optimal weight: 6.9990 chunk 386 optimal weight: 40.0000 chunk 948 optimal weight: 7.9990 chunk 116 optimal weight: 20.0000 chunk 170 optimal weight: 5.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** q 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 7 ASN ** t 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 113 GLN ** n 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 62 GLN b 165 ASN ** b 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 83 ASN ** k 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.101546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.079025 restraints weight = 483309.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.079037 restraints weight = 248649.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.078983 restraints weight = 214914.172| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.379 120661 Z= 0.241 Angle : 0.645 59.199 171380 Z= 0.341 Chirality : 0.039 0.866 20736 Planarity : 0.004 0.138 15542 Dihedral : 21.377 178.937 37974 Min Nonbonded Distance : 1.403 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.23 % Favored : 94.75 % Rotamer: Outliers : 3.21 % Allowed : 24.73 % Favored : 72.06 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.90 % Cis-general : 0.11 % Twisted Proline : 0.27 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.08), residues: 9955 helix: 0.47 (0.08), residues: 3927 sheet: -0.39 (0.14), residues: 1412 loop : -1.45 (0.09), residues: 4616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP V 177 HIS 0.010 0.001 HIS C 876 PHE 0.032 0.001 PHE A 465 TYR 0.079 0.002 TYR H 167 ARG 0.024 0.000 ARG D 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28325.15 seconds wall clock time: 495 minutes 29.02 seconds (29729.02 seconds total)