Starting phenix.real_space_refine on Sat Mar 16 14:21:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8k_0370/03_2024/6n8k_0370_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8k_0370/03_2024/6n8k_0370.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8k_0370/03_2024/6n8k_0370.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8k_0370/03_2024/6n8k_0370.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8k_0370/03_2024/6n8k_0370_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8k_0370/03_2024/6n8k_0370_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3482 5.49 5 Mg 1 5.21 5 S 131 5.16 5 C 70113 2.51 5 N 24398 2.21 5 O 34696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "v ARG 162": "NH1" <-> "NH2" Residue "v ARG 303": "NH1" <-> "NH2" Residue "v PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ARG 330": "NH1" <-> "NH2" Residue "v ARG 342": "NH1" <-> "NH2" Residue "v ARG 356": "NH1" <-> "NH2" Residue "A ARG 9": "NH1" <-> "NH2" Residue "A ARG 37": "NH1" <-> "NH2" Residue "A TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 149": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "A ARG 200": "NH1" <-> "NH2" Residue "A ARG 227": "NH1" <-> "NH2" Residue "A ARG 241": "NH1" <-> "NH2" Residue "a TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 117": "NH1" <-> "NH2" Residue "a ARG 139": "NH1" <-> "NH2" Residue "B PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 300": "NH1" <-> "NH2" Residue "B ARG 339": "NH1" <-> "NH2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "b ARG 24": "NH1" <-> "NH2" Residue "b ARG 27": "NH1" <-> "NH2" Residue "b ARG 34": "NH1" <-> "NH2" Residue "b ARG 43": "NH1" <-> "NH2" Residue "b ARG 79": "NH1" <-> "NH2" Residue "b ARG 110": "NH1" <-> "NH2" Residue "b ARG 114": "NH1" <-> "NH2" Residue "b ARG 135": "NH1" <-> "NH2" Residue "b ARG 144": "NH1" <-> "NH2" Residue "b ARG 154": "NH1" <-> "NH2" Residue "b TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 332": "NH1" <-> "NH2" Residue "b TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 510": "NH1" <-> "NH2" Residue "b ARG 613": "NH1" <-> "NH2" Residue "b ARG 615": "NH1" <-> "NH2" Residue "b ARG 624": "NH1" <-> "NH2" Residue "b PHE 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 647": "NH1" <-> "NH2" Residue "C ARG 3": "NH1" <-> "NH2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 326": "NH1" <-> "NH2" Residue "c ARG 52": "NH1" <-> "NH2" Residue "c PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 70": "NH1" <-> "NH2" Residue "d ARG 79": "NH1" <-> "NH2" Residue "F ARG 30": "NH1" <-> "NH2" Residue "F ARG 100": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 48": "NH1" <-> "NH2" Residue "f ARG 60": "NH1" <-> "NH2" Residue "f PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 204": "NH1" <-> "NH2" Residue "g ARG 60": "NH1" <-> "NH2" Residue "I ARG 3": "NH1" <-> "NH2" Residue "I ARG 8": "NH1" <-> "NH2" Residue "I ARG 75": "NH1" <-> "NH2" Residue "I ARG 104": "NH1" <-> "NH2" Residue "H ARG 23": "NH1" <-> "NH2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 166": "NH1" <-> "NH2" Residue "H ARG 168": "NH1" <-> "NH2" Residue "H ARG 173": "NH1" <-> "NH2" Residue "h ARG 105": "NH1" <-> "NH2" Residue "j ARG 63": "NH1" <-> "NH2" Residue "k ARG 3": "NH1" <-> "NH2" Residue "k ARG 39": "NH1" <-> "NH2" Residue "L ARG 42": "NH1" <-> "NH2" Residue "L ARG 49": "NH1" <-> "NH2" Residue "L ARG 73": "NH1" <-> "NH2" Residue "L ARG 171": "NH1" <-> "NH2" Residue "M ARG 19": "NH1" <-> "NH2" Residue "M ARG 77": "NH1" <-> "NH2" Residue "M ARG 108": "NH1" <-> "NH2" Residue "p ARG 36": "NH1" <-> "NH2" Residue "N ARG 20": "NH1" <-> "NH2" Residue "u TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 23": "NH1" <-> "NH2" Residue "u ARG 33": "NH1" <-> "NH2" Residue "u ARG 43": "NH1" <-> "NH2" Residue "u ARG 44": "NH1" <-> "NH2" Residue "u ARG 56": "NH1" <-> "NH2" Residue "u ARG 75": "NH1" <-> "NH2" Residue "u ARG 80": "NH1" <-> "NH2" Residue "u ARG 83": "NH1" <-> "NH2" Residue "u ARG 105": "NH1" <-> "NH2" Residue "u ARG 111": "NH1" <-> "NH2" Residue "u ARG 113": "NH1" <-> "NH2" Residue "u ARG 122": "NH1" <-> "NH2" Residue "u ARG 135": "NH1" <-> "NH2" Residue "O PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 3": "NH1" <-> "NH2" Residue "P ARG 56": "NH1" <-> "NH2" Residue "P ARG 126": "NH1" <-> "NH2" Residue "P ARG 181": "NH1" <-> "NH2" Residue "Q ARG 12": "NH1" <-> "NH2" Residue "Q ARG 92": "NH1" <-> "NH2" Residue "R ARG 5": "NH1" <-> "NH2" Residue "R ARG 62": "NH1" <-> "NH2" Residue "R ARG 104": "NH1" <-> "NH2" Residue "R ARG 110": "NH1" <-> "NH2" Residue "S ARG 28": "NH1" <-> "NH2" Residue "S ARG 117": "NH1" <-> "NH2" Residue "S TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 108": "NH1" <-> "NH2" Residue "T ARG 139": "NH1" <-> "NH2" Residue "V ARG 32": "NH1" <-> "NH2" Residue "V ARG 70": "NH1" <-> "NH2" Residue "V ARG 88": "NH1" <-> "NH2" Residue "W ARG 31": "NH1" <-> "NH2" Residue "W ARG 57": "NH1" <-> "NH2" Residue "W ARG 126": "NH1" <-> "NH2" Residue "W ARG 166": "NH1" <-> "NH2" Residue "X ARG 33": "NH1" <-> "NH2" Residue "X TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 125": "NH1" <-> "NH2" Residue "X ARG 138": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Y ARG 121": "NH1" <-> "NH2" Residue "y TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 85": "NH1" <-> "NH2" Residue "y ARG 100": "NH1" <-> "NH2" Residue "Z PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 84": "NH1" <-> "NH2" Residue "Z ARG 135": "NH1" <-> "NH2" Residue "z ARG 6": "NH1" <-> "NH2" Residue "z ARG 19": "NH1" <-> "NH2" Residue "z ARG 29": "NH1" <-> "NH2" Residue "D ARG 15": "NH1" <-> "NH2" Residue "D ARG 22": "NH1" <-> "NH2" Residue "D ARG 140": "NH1" <-> "NH2" Residue "D ARG 158": "NH1" <-> "NH2" Residue "J TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 55": "NH1" <-> "NH2" Residue "J ARG 61": "NH1" <-> "NH2" Residue "q ARG 18": "NH1" <-> "NH2" Residue "q ARG 71": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 132821 Number of models: 1 Model: "" Number of chains: 49 Chain: "s" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1050 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 210} Link IDs: {'TRANS': 209} Unresolved non-hydrogen bonds: 420 Unresolved non-hydrogen angles: 630 Unresolved non-hydrogen dihedrals: 210 Planarities with less than four sites: {'UNK:plan-1': 210} Unresolved non-hydrogen planarities: 210 Chain: "v" Number of atoms: 1970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1970 Classifications: {'peptide': 252} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 243} Chain breaks: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 1863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1863 Classifications: {'peptide': 245} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 233} Chain: "a" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 742 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "B" Number of atoms: 3081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3081 Classifications: {'peptide': 386} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 371} Chain: "b" Number of atoms: 4895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4895 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 2749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2749 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 343} Chain: "c" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 743 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 95} Chain: "d" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 873 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "E" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1274 Classifications: {'peptide': 160} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 151} Chain breaks: 1 Chain: "e" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1020 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "F" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1784 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain: "f" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 850 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "G" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1798 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 12, 'TRANS': 217} Chain: "g" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 881 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "I" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1056 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 126} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 1493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1493 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 4, 'TRANS': 183} Chain: "h" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 969 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "i" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 743 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "j" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 670 Classifications: {'peptide': 85} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 82} Chain: "k" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 612 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "L" Number of atoms: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1491 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 178} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "l" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "M" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1059 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 4, 'TRANS': 132} Chain: "p" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 694 Classifications: {'peptide': 91} Link IDs: {'TRANS': 90} Chain: "N" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1720 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 7, 'TRANS': 195} Chain: "u" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1256 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 5, 'TRANS': 143} Chain: "O" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1555 Classifications: {'peptide': 197} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 188} Chain: "P" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1409 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain breaks: 1 Chain: "Q" Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1191 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 8, 'TRANS': 145} Chain: "R" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1241 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 2, 'TRANS': 151} Chain: "S" Number of atoms: 1425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1425 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 7, 'TRANS': 162} Chain: "T" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 476 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 5, 'TRANS': 55} Chain: "U" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 826 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 3, 'TRANS': 100} Chain: "V" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1003 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "W" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "X" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 959 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "Y" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 993 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "y" Number of atoms: 1826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1826 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 233} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "Z" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1092 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "z" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 444 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "D" Number of atoms: 1983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1983 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 240} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 46 Chain: "J" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1304 Classifications: {'peptide': 164} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 159} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "q" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 783 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "o" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 433 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "1" Number of atoms: 68471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3201, 68471 Classifications: {'RNA': 3201} Modifications used: {'rna2p_pur': 339, 'rna2p_pyr': 239, 'rna3p_pur': 1436, 'rna3p_pyr': 1187} Link IDs: {'rna2p': 578, 'rna3p': 2622} Chain breaks: 3 Chain: "2" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2579 Classifications: {'RNA': 121} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 57, 'rna3p_pyr': 51} Link IDs: {'rna2p': 12, 'rna3p': 108} Chain: "3" Number of atoms: 3333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 3333 Classifications: {'RNA': 157} Modifications used: {'rna2p_pur': 16, 'rna2p_pyr': 13, 'rna3p_pur': 62, 'rna3p_pyr': 66} Link IDs: {'rna2p': 29, 'rna3p': 127} Chain: "b" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 197 residue: pdb=" N VAL O 3 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 3 " occ=0.50 residue: pdb=" N GLU O 4 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU O 4 " occ=0.50 residue: pdb=" N PRO O 5 " occ=0.50 ... (5 atoms not shown) pdb=" CD PRO O 5 " occ=0.50 residue: pdb=" N VAL O 6 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 6 " occ=0.50 residue: pdb=" N VAL O 7 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 7 " occ=0.50 residue: pdb=" N VAL O 8 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 8 " occ=0.50 residue: pdb=" N ILE O 9 " occ=0.50 ... (6 atoms not shown) pdb=" CD1 ILE O 9 " occ=0.50 residue: pdb=" N ASP O 10 " occ=0.50 ... (6 atoms not shown) pdb=" OD2 ASP O 10 " occ=0.50 residue: pdb=" N GLY O 11 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY O 11 " occ=0.50 residue: pdb=" N LYS O 12 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS O 12 " occ=0.50 residue: pdb=" N GLY O 13 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY O 13 " occ=0.50 residue: pdb=" N HIS O 14 " occ=0.50 ... (8 atoms not shown) pdb=" NE2 HIS O 14 " occ=0.50 ... (remaining 185 not shown) Time building chain proxies: 49.72, per 1000 atoms: 0.37 Number of scatterers: 132821 At special positions: 0 Unit cell: (236.5, 214.5, 261.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 131 16.00 P 3482 15.00 Mg 1 11.99 O 34696 8.00 N 24398 7.00 C 70113 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS g 44 " - pdb=" SG CYS g 47 " distance=2.04 Simple disulfide: pdb=" SG CYS g 44 " - pdb=" SG CYS g 81 " distance=2.03 Simple disulfide: pdb=" SG CYS g 47 " - pdb=" SG CYS g 81 " distance=2.01 Simple disulfide: pdb=" SG CYS g 47 " - pdb=" SG CYS g 84 " distance=2.03 Simple disulfide: pdb=" SG CYS j 22 " - pdb=" SG CYS j 37 " distance=2.02 Simple disulfide: pdb=" SG CYS p 39 " - pdb=" SG CYS p 57 " distance=2.04 Simple disulfide: pdb=" SG CYS p 42 " - pdb=" SG CYS p 59 " distance=2.02 Simple disulfide: pdb=" SG CYS u 6 " - pdb=" SG CYS u 9 " distance=2.03 Simple disulfide: pdb=" SG CYS u 6 " - pdb=" SG CYS u 32 " distance=2.06 Simple disulfide: pdb=" SG CYS u 9 " - pdb=" SG CYS u 32 " distance=2.04 Simple disulfide: pdb=" SG CYS u 9 " - pdb=" SG CYS u 36 " distance=2.01 Simple disulfide: pdb=" SG CYS u 32 " - pdb=" SG CYS u 36 " distance=2.52 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: 48.26 Conformation dependent library (CDL) restraints added in 9.1 seconds 14246 Ramachandran restraints generated. 7123 Oldfield, 0 Emsley, 7123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13972 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: 254 helices and 62 sheets defined 43.9% alpha, 12.5% beta 766 base pairs and 1764 stacking pairs defined. Time for finding SS restraints: 68.93 Creating SS restraints... Processing helix chain 'v' and resid 168 through 182 removed outlier: 3.747A pdb=" N LEU v 172 " --> pdb=" O LYS v 168 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN v 176 " --> pdb=" O LEU v 172 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU v 179 " --> pdb=" O GLU v 175 " (cutoff:3.500A) Processing helix chain 'v' and resid 203 through 218 removed outlier: 3.843A pdb=" N ALA v 207 " --> pdb=" O GLN v 203 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE v 211 " --> pdb=" O ALA v 207 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA v 216 " --> pdb=" O ASP v 212 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL v 217 " --> pdb=" O PHE v 213 " (cutoff:3.500A) Processing helix chain 'v' and resid 260 through 268 removed outlier: 3.608A pdb=" N SER v 266 " --> pdb=" O LYS v 262 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET v 267 " --> pdb=" O LEU v 263 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLY v 268 " --> pdb=" O ALA v 264 " (cutoff:3.500A) Processing helix chain 'v' and resid 297 through 305 removed outlier: 4.440A pdb=" N ARG v 303 " --> pdb=" O SER v 299 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA v 304 " --> pdb=" O VAL v 300 " (cutoff:3.500A) Proline residue: v 305 - end of helix Processing helix chain 'v' and resid 342 through 349 removed outlier: 4.352A pdb=" N GLY v 347 " --> pdb=" O THR v 343 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N VAL v 348 " --> pdb=" O SER v 344 " (cutoff:3.500A) Processing helix chain 'v' and resid 381 through 388 removed outlier: 4.002A pdb=" N LEU v 387 " --> pdb=" O LEU v 383 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ASN v 388 " --> pdb=" O PHE v 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 13 removed outlier: 3.606A pdb=" N LYS A 10 " --> pdb=" O ARG A 6 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLY A 11 " --> pdb=" O ASN A 7 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ALA A 12 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLY A 13 " --> pdb=" O ARG A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 39 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.755A pdb=" N VAL A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Proline residue: A 108 - end of helix No H-bonds generated for 'chain 'A' and resid 103 through 108' Processing helix chain 'A' and resid 181 through 193 removed outlier: 3.531A pdb=" N ALA A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU A 191 " --> pdb=" O HIS A 187 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS A 192 " --> pdb=" O LYS A 188 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG A 193 " --> pdb=" O TYR A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 removed outlier: 3.857A pdb=" N ASP A 176 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS A 177 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Proline residue: A 178 - end of helix No H-bonds generated for 'chain 'A' and resid 173 through 178' Processing helix chain 'a' and resid 64 through 69 removed outlier: 4.537A pdb=" N PHE a 68 " --> pdb=" O GLN a 64 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N TRP a 69 " --> pdb=" O GLN a 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 64 through 69' Processing helix chain 'a' and resid 77 through 83 removed outlier: 6.030A pdb=" N LEU a 81 " --> pdb=" O LYS a 77 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ILE a 82 " --> pdb=" O LEU a 78 " (cutoff:3.500A) Proline residue: a 83 - end of helix No H-bonds generated for 'chain 'a' and resid 77 through 83' Processing helix chain 'a' and resid 84 through 94 removed outlier: 4.318A pdb=" N ASP a 88 " --> pdb=" O GLU a 84 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N GLN a 89 " --> pdb=" O ASP a 85 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER a 93 " --> pdb=" O GLN a 89 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ALA a 94 " --> pdb=" O TYR a 90 " (cutoff:3.500A) Processing helix chain 'a' and resid 103 through 108 removed outlier: 3.732A pdb=" N ALA a 107 " --> pdb=" O ASP a 103 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY a 108 " --> pdb=" O THR a 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 103 through 108' Processing helix chain 'a' and resid 131 through 142 removed outlier: 3.650A pdb=" N ALA a 141 " --> pdb=" O LYS a 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 120 removed outlier: 3.682A pdb=" N LYS B 115 " --> pdb=" O SER B 111 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LYS B 120 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 138 removed outlier: 3.885A pdb=" N ALA B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS B 136 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N TYR B 137 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ALA B 138 " --> pdb=" O SER B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 154 removed outlier: 5.983A pdb=" N GLU B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ARG B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE B 151 " --> pdb=" O GLU B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 170 removed outlier: 3.884A pdb=" N THR B 169 " --> pdb=" O GLN B 165 " (cutoff:3.500A) Proline residue: B 170 - end of helix No H-bonds generated for 'chain 'B' and resid 165 through 170' Processing helix chain 'B' and resid 187 through 199 removed outlier: 3.574A pdb=" N LYS B 191 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TRP B 194 " --> pdb=" O GLU B 190 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU B 197 " --> pdb=" O ASP B 193 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS B 198 " --> pdb=" O TRP B 194 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE B 199 " --> pdb=" O ALA B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 209 removed outlier: 4.637A pdb=" N VAL B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 233 Processing helix chain 'B' and resid 347 through 352 removed outlier: 4.395A pdb=" N LEU B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU B 352 " --> pdb=" O ARG B 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 347 through 352' Processing helix chain 'B' and resid 372 through 381 removed outlier: 3.573A pdb=" N LYS B 376 " --> pdb=" O THR B 372 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY B 381 " --> pdb=" O HIS B 377 " (cutoff:3.500A) Processing helix chain 'b' and resid 13 through 29 removed outlier: 3.639A pdb=" N VAL b 21 " --> pdb=" O LEU b 17 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR b 29 " --> pdb=" O THR b 25 " (cutoff:3.500A) Processing helix chain 'b' and resid 38 through 69 removed outlier: 3.679A pdb=" N ARG b 48 " --> pdb=" O ALA b 44 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS b 49 " --> pdb=" O PHE b 45 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR b 53 " --> pdb=" O LYS b 49 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL b 58 " --> pdb=" O GLY b 54 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS b 60 " --> pdb=" O GLY b 56 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP b 63 " --> pdb=" O GLU b 59 " (cutoff:3.500A) Proline residue: b 69 - end of helix Processing helix chain 'b' and resid 75 through 86 removed outlier: 3.878A pdb=" N ASP b 80 " --> pdb=" O PRO b 76 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N MET b 82 " --> pdb=" O HIS b 78 " (cutoff:3.500A) Processing helix chain 'b' and resid 87 through 119 removed outlier: 3.779A pdb=" N SER b 94 " --> pdb=" O HIS b 90 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU b 95 " --> pdb=" O TYR b 91 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER b 99 " --> pdb=" O LEU b 95 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG b 114 " --> pdb=" O ARG b 110 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS b 117 " --> pdb=" O VAL b 113 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N PHE b 118 " --> pdb=" O ARG b 114 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY b 119 " --> pdb=" O LEU b 115 " (cutoff:3.500A) Processing helix chain 'b' and resid 121 through 144 removed outlier: 3.582A pdb=" N CYS b 125 " --> pdb=" O SER b 121 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL b 140 " --> pdb=" O MET b 136 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG b 144 " --> pdb=" O VAL b 140 " (cutoff:3.500A) Processing helix chain 'b' and resid 145 through 160 removed outlier: 3.767A pdb=" N TYR b 149 " --> pdb=" O ASP b 145 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLN b 152 " --> pdb=" O ALA b 148 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN b 155 " --> pdb=" O GLU b 151 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N HIS b 156 " --> pdb=" O GLN b 152 " (cutoff:3.500A) Processing helix chain 'b' and resid 179 through 188 removed outlier: 3.692A pdb=" N LEU b 184 " --> pdb=" O LYS b 180 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N CYS b 186 " --> pdb=" O SER b 182 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR b 188 " --> pdb=" O LEU b 184 " (cutoff:3.500A) Processing helix chain 'b' and resid 233 through 246 removed outlier: 3.923A pdb=" N GLN b 238 " --> pdb=" O ASN b 234 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N SER b 239 " --> pdb=" O ILE b 235 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE b 240 " --> pdb=" O GLU b 236 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TYR b 241 " --> pdb=" O MET b 237 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU b 246 " --> pdb=" O ALA b 242 " (cutoff:3.500A) Processing helix chain 'b' and resid 263 through 279 removed outlier: 3.654A pdb=" N GLN b 267 " --> pdb=" O THR b 263 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL b 268 " --> pdb=" O ILE b 264 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS b 269 " --> pdb=" O GLU b 265 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE b 271 " --> pdb=" O GLN b 267 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS b 272 " --> pdb=" O VAL b 268 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER b 273 " --> pdb=" O LYS b 269 " (cutoff:3.500A) Proline residue: b 276 - end of helix removed outlier: 3.792A pdb=" N ALA b 279 " --> pdb=" O LYS b 275 " (cutoff:3.500A) Processing helix chain 'b' and resid 289 through 294 removed outlier: 3.869A pdb=" N ILE b 293 " --> pdb=" O LYS b 289 " (cutoff:3.500A) Processing helix chain 'b' and resid 299 through 312 removed outlier: 3.571A pdb=" N GLN b 304 " --> pdb=" O GLU b 300 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU b 305 " --> pdb=" O GLU b 301 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU b 306 " --> pdb=" O ARG b 302 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU b 311 " --> pdb=" O GLU b 307 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N VAL b 312 " --> pdb=" O SER b 308 " (cutoff:3.500A) Processing helix chain 'b' and resid 324 through 346 removed outlier: 4.333A pdb=" N VAL b 328 " --> pdb=" O LEU b 324 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N MET b 329 " --> pdb=" O GLU b 325 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG b 332 " --> pdb=" O VAL b 328 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS b 334 " --> pdb=" O GLU b 330 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU b 339 " --> pdb=" O ALA b 335 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER b 342 " --> pdb=" O LYS b 338 " (cutoff:3.500A) Processing helix chain 'b' and resid 355 through 362 removed outlier: 3.822A pdb=" N LYS b 360 " --> pdb=" O ASN b 356 " (cutoff:3.500A) Processing helix chain 'b' and resid 379 through 385 removed outlier: 3.761A pdb=" N LYS b 383 " --> pdb=" O PRO b 379 " (cutoff:3.500A) Processing helix chain 'b' and resid 398 through 407 removed outlier: 4.264A pdb=" N ILE b 402 " --> pdb=" O LEU b 398 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU b 405 " --> pdb=" O ASP b 401 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASN b 406 " --> pdb=" O ILE b 402 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY b 407 " --> pdb=" O GLU b 403 " (cutoff:3.500A) Processing helix chain 'b' and resid 424 through 429 removed outlier: 4.244A pdb=" N LYS b 428 " --> pdb=" O ASP b 424 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ASN b 429 " --> pdb=" O ASP b 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 424 through 429' Processing helix chain 'b' and resid 440 through 445 removed outlier: 4.328A pdb=" N PHE b 444 " --> pdb=" O ASN b 440 " (cutoff:3.500A) Processing helix chain 'b' and resid 448 through 467 removed outlier: 3.746A pdb=" N LYS b 452 " --> pdb=" O GLU b 448 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA b 455 " --> pdb=" O ALA b 451 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU b 456 " --> pdb=" O LYS b 452 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU b 459 " --> pdb=" O ALA b 455 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU b 461 " --> pdb=" O GLU b 457 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU b 463 " --> pdb=" O GLU b 459 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN b 465 " --> pdb=" O GLU b 461 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU b 466 " --> pdb=" O LYS b 462 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY b 467 " --> pdb=" O LEU b 463 " (cutoff:3.500A) Processing helix chain 'b' and resid 482 through 511 removed outlier: 3.563A pdb=" N ARG b 497 " --> pdb=" O ALA b 493 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASN b 509 " --> pdb=" O ALA b 505 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG b 510 " --> pdb=" O GLU b 506 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS b 511 " --> pdb=" O ALA b 507 " (cutoff:3.500A) Processing helix chain 'b' and resid 520 through 525 removed outlier: 4.939A pdb=" N THR b 525 " --> pdb=" O ARG b 521 " (cutoff:3.500A) Processing helix chain 'b' and resid 527 through 539 removed outlier: 4.005A pdb=" N MET b 531 " --> pdb=" O SER b 527 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU b 533 " --> pdb=" O GLY b 529 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR b 537 " --> pdb=" O GLU b 533 " (cutoff:3.500A) Processing helix chain 'b' and resid 542 through 550 removed outlier: 3.623A pdb=" N ASP b 547 " --> pdb=" O SER b 543 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS b 548 " --> pdb=" O ALA b 544 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN b 549 " --> pdb=" O LEU b 545 " (cutoff:3.500A) Processing helix chain 'b' and resid 595 through 617 removed outlier: 3.690A pdb=" N MET b 605 " --> pdb=" O LYS b 601 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG b 611 " --> pdb=" O LYS b 607 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N GLU b 612 " --> pdb=" O MET b 608 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ARG b 613 " --> pdb=" O GLU b 609 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N HIS b 616 " --> pdb=" O GLU b 612 " (cutoff:3.500A) Processing helix chain 'b' and resid 631 through 636 removed outlier: 3.987A pdb=" N PHE b 635 " --> pdb=" O SER b 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 46 removed outlier: 3.629A pdb=" N SER C 41 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS C 44 " --> pdb=" O THR C 40 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASN C 45 " --> pdb=" O SER C 41 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N LYS C 46 " --> pdb=" O VAL C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 132 removed outlier: 3.521A pdb=" N ILE C 126 " --> pdb=" O THR C 122 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA C 130 " --> pdb=" O ILE C 126 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL C 131 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ALA C 132 " --> pdb=" O ALA C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 139 Processing helix chain 'C' and resid 153 through 159 removed outlier: 4.820A pdb=" N GLU C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER C 158 " --> pdb=" O THR C 154 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE C 159 " --> pdb=" O ASP C 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 153 through 159' Processing helix chain 'C' and resid 161 through 173 Processing helix chain 'C' and resid 174 through 185 removed outlier: 4.611A pdb=" N LEU C 182 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS C 183 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER C 184 " --> pdb=" O LYS C 180 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LYS C 185 " --> pdb=" O VAL C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 196 removed outlier: 4.408A pdb=" N ARG C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ASN C 196 " --> pdb=" O GLY C 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 191 through 196' Processing helix chain 'C' and resid 214 through 221 removed outlier: 3.551A pdb=" N ARG C 220 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ASN C 221 " --> pdb=" O LYS C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 240 Proline residue: C 240 - end of helix Processing helix chain 'C' and resid 251 through 261 removed outlier: 3.548A pdb=" N LEU C 258 " --> pdb=" O ALA C 254 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ASP C 259 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLN C 260 " --> pdb=" O THR C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 292 removed outlier: 3.812A pdb=" N ILE C 289 " --> pdb=" O ASP C 285 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN C 291 " --> pdb=" O THR C 287 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER C 292 " --> pdb=" O ARG C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 300 removed outlier: 3.770A pdb=" N ALA C 298 " --> pdb=" O GLU C 294 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ARG C 300 " --> pdb=" O GLN C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 328 removed outlier: 3.859A pdb=" N LEU C 327 " --> pdb=" O VAL C 323 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASN C 328 " --> pdb=" O LEU C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 338 removed outlier: 4.471A pdb=" N VAL C 333 " --> pdb=" O PRO C 329 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA C 335 " --> pdb=" O ALA C 331 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA C 336 " --> pdb=" O LYS C 332 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU C 337 " --> pdb=" O VAL C 333 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS C 338 " --> pdb=" O PHE C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 361 removed outlier: 3.623A pdb=" N THR C 356 " --> pdb=" O ALA C 352 " (cutoff:3.500A) Processing helix chain 'c' and resid 9 through 21 removed outlier: 3.558A pdb=" N LEU c 16 " --> pdb=" O GLN c 12 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL c 17 " --> pdb=" O LYS c 13 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS c 19 " --> pdb=" O ALA c 15 " (cutoff:3.500A) Processing helix chain 'c' and resid 26 through 37 removed outlier: 3.638A pdb=" N LYS c 32 " --> pdb=" O LYS c 28 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER c 33 " --> pdb=" O SER c 29 " (cutoff:3.500A) Processing helix chain 'c' and resid 49 through 64 removed outlier: 3.640A pdb=" N LEU c 56 " --> pdb=" O ARG c 52 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET c 61 " --> pdb=" O GLU c 57 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU c 62 " --> pdb=" O TYR c 58 " (cutoff:3.500A) Processing helix chain 'c' and resid 73 through 82 removed outlier: 3.660A pdb=" N GLY c 78 " --> pdb=" O ASN c 74 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR c 79 " --> pdb=" O ASN c 75 " (cutoff:3.500A) Processing helix chain 'd' and resid 15 through 21 removed outlier: 3.888A pdb=" N ARG d 19 " --> pdb=" O ASN d 15 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS d 21 " --> pdb=" O HIS d 17 " (cutoff:3.500A) Processing helix chain 'd' and resid 27 through 44 removed outlier: 3.651A pdb=" N ARG d 31 " --> pdb=" O LYS d 27 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL d 33 " --> pdb=" O ALA d 29 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS d 34 " --> pdb=" O PRO d 30 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE d 36 " --> pdb=" O ALA d 32 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS d 38 " --> pdb=" O LYS d 34 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS d 43 " --> pdb=" O PHE d 39 " (cutoff:3.500A) Processing helix chain 'd' and resid 52 through 61 removed outlier: 3.503A pdb=" N ALA d 58 " --> pdb=" O GLU d 54 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP d 60 " --> pdb=" O ASN d 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 107 removed outlier: 4.053A pdb=" N PHE E 106 " --> pdb=" O ASN E 102 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA E 107 " --> pdb=" O VAL E 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 102 through 107' Processing helix chain 'E' and resid 131 through 150 removed outlier: 3.651A pdb=" N ALA E 144 " --> pdb=" O VAL E 140 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA E 147 " --> pdb=" O LYS E 143 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU E 148 " --> pdb=" O ALA E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 162 removed outlier: 3.553A pdb=" N SER E 160 " --> pdb=" O LYS E 156 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA E 161 " --> pdb=" O GLN E 157 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N SER E 162 " --> pdb=" O TYR E 158 " (cutoff:3.500A) Processing helix chain 'e' and resid 21 through 26 removed outlier: 4.305A pdb=" N TYR e 25 " --> pdb=" O HIS e 21 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N HIS e 26 " --> pdb=" O SER e 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 21 through 26' Processing helix chain 'e' and resid 40 through 45 Processing helix chain 'e' and resid 78 through 87 removed outlier: 3.780A pdb=" N THR e 84 " --> pdb=" O LYS e 80 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LEU e 85 " --> pdb=" O ASP e 81 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N THR e 86 " --> pdb=" O LEU e 82 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N MET e 87 " --> pdb=" O GLU e 83 " (cutoff:3.500A) Processing helix chain 'e' and resid 101 through 116 removed outlier: 3.890A pdb=" N VAL e 106 " --> pdb=" O ALA e 102 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL e 107 " --> pdb=" O LYS e 103 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA e 114 " --> pdb=" O ALA e 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 73 removed outlier: 3.921A pdb=" N ALA F 35 " --> pdb=" O ALA F 31 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE F 44 " --> pdb=" O LYS F 40 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA F 49 " --> pdb=" O LEU F 45 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN F 61 " --> pdb=" O THR F 57 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE F 63 " --> pdb=" O GLU F 59 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA F 72 " --> pdb=" O ASP F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 107 removed outlier: 4.056A pdb=" N VAL F 102 " --> pdb=" O LYS F 98 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG F 107 " --> pdb=" O LEU F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 131 removed outlier: 3.805A pdb=" N GLU F 125 " --> pdb=" O LYS F 121 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE F 130 " --> pdb=" O LEU F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 151 removed outlier: 3.582A pdb=" N ILE F 144 " --> pdb=" O SER F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 173 removed outlier: 4.120A pdb=" N ILE F 169 " --> pdb=" O ASP F 165 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN F 172 " --> pdb=" O ILE F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 190 Processing helix chain 'F' and resid 194 through 203 removed outlier: 3.508A pdb=" N LEU F 202 " --> pdb=" O ALA F 198 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N TRP F 203 " --> pdb=" O ASN F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 244 removed outlier: 4.541A pdb=" N LYS F 238 " --> pdb=" O GLU F 234 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS F 241 " --> pdb=" O ASN F 237 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER F 242 " --> pdb=" O LYS F 238 " (cutoff:3.500A) Processing helix chain 'f' and resid 37 through 45 removed outlier: 4.911A pdb=" N PHE f 43 " --> pdb=" O GLN f 39 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYR f 44 " --> pdb=" O ASP f 40 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU f 45 " --> pdb=" O ALA f 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 69 removed outlier: 3.891A pdb=" N LYS G 63 " --> pdb=" O GLN G 59 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE G 64 " --> pdb=" O ARG G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 81 removed outlier: 4.333A pdb=" N ALA G 76 " --> pdb=" O PRO G 72 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLN G 77 " --> pdb=" O PRO G 73 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N PHE G 78 " --> pdb=" O THR G 74 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N GLN G 79 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N TYR G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N THR G 81 " --> pdb=" O GLN G 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 72 through 81' Processing helix chain 'G' and resid 83 through 98 removed outlier: 4.001A pdb=" N GLU G 89 " --> pdb=" O ASN G 85 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS G 96 " --> pdb=" O LYS G 92 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N TYR G 97 " --> pdb=" O LEU G 93 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ARG G 98 " --> pdb=" O PHE G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 119 removed outlier: 4.452A pdb=" N THR G 110 " --> pdb=" O LYS G 106 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA G 115 " --> pdb=" O LYS G 111 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA G 117 " --> pdb=" O ALA G 113 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU G 118 " --> pdb=" O ALA G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 146 removed outlier: 3.556A pdb=" N ALA G 141 " --> pdb=" O ASN G 137 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLU G 144 " --> pdb=" O VAL G 140 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ASN G 145 " --> pdb=" O ALA G 141 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS G 146 " --> pdb=" O LEU G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 174 removed outlier: 4.730A pdb=" N VAL G 163 " --> pdb=" O PRO G 159 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL G 164 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N PHE G 165 " --> pdb=" O GLU G 161 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LEU G 166 " --> pdb=" O LEU G 162 " (cutoff:3.500A) Proline residue: G 167 - end of helix removed outlier: 3.600A pdb=" N LYS G 171 " --> pdb=" O PRO G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 191 removed outlier: 3.945A pdb=" N LEU G 186 " --> pdb=" O GLY G 182 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR G 188 " --> pdb=" O ALA G 184 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU G 189 " --> pdb=" O ARG G 185 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL G 190 " --> pdb=" O LEU G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 222 removed outlier: 4.927A pdb=" N ALA G 209 " --> pdb=" O ALA G 205 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ALA G 210 " --> pdb=" O GLU G 206 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU G 211 " --> pdb=" O ASP G 207 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER G 216 " --> pdb=" O ALA G 212 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR G 217 " --> pdb=" O LYS G 213 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA G 220 " --> pdb=" O SER G 216 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN G 221 " --> pdb=" O THR G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 232 removed outlier: 5.107A pdb=" N ASP G 227 " --> pdb=" O ALA G 223 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLU G 228 " --> pdb=" O ASP G 224 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS G 230 " --> pdb=" O TYR G 226 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LYS G 231 " --> pdb=" O ASP G 227 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N HIS G 232 " --> pdb=" O GLU G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 253 removed outlier: 3.539A pdb=" N ARG G 249 " --> pdb=" O LYS G 245 " (cutoff:3.500A) Processing helix chain 'g' and resid 58 through 66 removed outlier: 3.859A pdb=" N TYR g 62 " --> pdb=" O ARG g 58 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ALA g 63 " --> pdb=" O PRO g 59 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N THR g 64 " --> pdb=" O ARG g 60 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL g 65 " --> pdb=" O GLN g 61 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N SER g 66 " --> pdb=" O TYR g 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 58 through 66' Processing helix chain 'g' and resid 81 through 113 removed outlier: 6.085A pdb=" N VAL g 85 " --> pdb=" O CYS g 81 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS g 86 " --> pdb=" O ALA g 82 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ARG g 88 " --> pdb=" O CYS g 84 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE g 90 " --> pdb=" O LYS g 86 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA g 92 " --> pdb=" O ARG g 88 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU g 96 " --> pdb=" O ALA g 92 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE g 100 " --> pdb=" O GLU g 96 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL g 101 " --> pdb=" O GLU g 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 9 removed outlier: 4.236A pdb=" N VAL I 6 " --> pdb=" O GLY I 2 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 27 removed outlier: 3.616A pdb=" N ILE I 21 " --> pdb=" O ASP I 17 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR I 22 " --> pdb=" O LEU I 18 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU I 25 " --> pdb=" O ILE I 21 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR I 27 " --> pdb=" O ASN I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 37 removed outlier: 3.546A pdb=" N GLN I 32 " --> pdb=" O LYS I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 70 removed outlier: 3.614A pdb=" N LEU I 64 " --> pdb=" O THR I 60 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS I 65 " --> pdb=" O ALA I 61 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N HIS I 67 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS I 69 " --> pdb=" O LYS I 65 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLY I 70 " --> pdb=" O THR I 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 82 removed outlier: 3.526A pdb=" N ARG I 76 " --> pdb=" O VAL I 72 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N GLY I 82 " --> pdb=" O LYS I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 95 removed outlier: 4.147A pdb=" N SER I 90 " --> pdb=" O THR I 86 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA I 94 " --> pdb=" O SER I 90 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY I 95 " --> pdb=" O ASP I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 131 removed outlier: 3.582A pdb=" N ARG I 104 " --> pdb=" O LYS I 100 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N GLY I 113 " --> pdb=" O THR I 109 " (cutoff:3.500A) Proline residue: I 114 - end of helix removed outlier: 3.641A pdb=" N GLU I 125 " --> pdb=" O ALA I 121 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP I 128 " --> pdb=" O LYS I 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 84 removed outlier: 3.566A pdb=" N ALA H 67 " --> pdb=" O LYS H 63 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU H 68 " --> pdb=" O HIS H 64 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG H 69 " --> pdb=" O VAL H 65 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N THR H 70 " --> pdb=" O ALA H 66 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS H 72 " --> pdb=" O LEU H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 166 removed outlier: 3.572A pdb=" N GLN H 156 " --> pdb=" O GLU H 152 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN H 157 " --> pdb=" O ASP H 153 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN H 162 " --> pdb=" O ALA H 158 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE H 164 " --> pdb=" O ASP H 160 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N CYS H 165 " --> pdb=" O LEU H 161 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG H 166 " --> pdb=" O GLN H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 176 removed outlier: 4.454A pdb=" N LEU H 176 " --> pdb=" O ILE H 172 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 13 removed outlier: 3.896A pdb=" N LEU h 9 " --> pdb=" O LYS h 5 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG h 10 " --> pdb=" O ALA h 6 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR h 11 " --> pdb=" O TYR h 7 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS h 12 " --> pdb=" O GLU h 8 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N SER h 13 " --> pdb=" O LEU h 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 5 through 13' Processing helix chain 'h' and resid 14 through 38 removed outlier: 3.659A pdb=" N LEU h 21 " --> pdb=" O LEU h 17 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL h 22 " --> pdb=" O ALA h 18 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP h 23 " --> pdb=" O SER h 19 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU h 27 " --> pdb=" O ASP h 23 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL h 33 " --> pdb=" O ALA h 29 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU h 36 " --> pdb=" O LYS h 32 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER h 37 " --> pdb=" O VAL h 33 " (cutoff:3.500A) Processing helix chain 'h' and resid 42 through 71 removed outlier: 4.644A pdb=" N THR h 46 " --> pdb=" O PRO h 42 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL h 47 " --> pdb=" O LYS h 43 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE h 51 " --> pdb=" O VAL h 47 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA h 52 " --> pdb=" O ARG h 48 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL h 57 " --> pdb=" O CYS h 53 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL h 66 " --> pdb=" O GLN h 62 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN h 68 " --> pdb=" O GLU h 64 " (cutoff:3.500A) Processing helix chain 'h' and resid 77 through 82 removed outlier: 5.592A pdb=" N ALA h 82 " --> pdb=" O LYS h 78 " (cutoff:3.500A) Processing helix chain 'h' and resid 85 through 92 removed outlier: 3.542A pdb=" N ARG h 89 " --> pdb=" O THR h 85 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA h 91 " --> pdb=" O ALA h 87 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LEU h 92 " --> pdb=" O LEU h 88 " (cutoff:3.500A) Processing helix chain 'h' and resid 93 through 99 removed outlier: 3.562A pdb=" N SER h 98 " --> pdb=" O LYS h 94 " (cutoff:3.500A) Processing helix chain 'h' and resid 101 through 111 removed outlier: 3.501A pdb=" N LYS h 106 " --> pdb=" O GLU h 102 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS h 107 " --> pdb=" O LYS h 103 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE h 109 " --> pdb=" O ARG h 105 " (cutoff:3.500A) Processing helix chain 'i' and resid 25 through 30 removed outlier: 4.802A pdb=" N LYS i 29 " --> pdb=" O LYS i 25 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LYS i 30 " --> pdb=" O ILE i 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 25 through 30' Processing helix chain 'i' and resid 34 through 49 removed outlier: 4.472A pdb=" N LYS i 38 " --> pdb=" O SER i 34 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU i 46 " --> pdb=" O SER i 42 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE i 47 " --> pdb=" O LEU i 43 " (cutoff:3.500A) Processing helix chain 'i' and resid 51 through 64 removed outlier: 3.913A pdb=" N LEU i 60 " --> pdb=" O ARG i 56 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG i 62 " --> pdb=" O ILE i 58 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN i 63 " --> pdb=" O ASP i 59 " (cutoff:3.500A) Processing helix chain 'i' and resid 65 through 77 removed outlier: 3.801A pdb=" N ALA i 69 " --> pdb=" O GLY i 65 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG i 70 " --> pdb=" O GLU i 66 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS i 71 " --> pdb=" O LYS i 67 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS i 75 " --> pdb=" O LYS i 71 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU i 77 " --> pdb=" O ALA i 73 " (cutoff:3.500A) Processing helix chain 'i' and resid 79 through 98 removed outlier: 3.792A pdb=" N ALA i 83 " --> pdb=" O SER i 79 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA i 85 " --> pdb=" O THR i 81 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU i 89 " --> pdb=" O ALA i 85 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN i 92 " --> pdb=" O GLU i 88 " (cutoff:3.500A) Processing helix chain 'j' and resid 4 through 11 removed outlier: 3.530A pdb=" N PHE j 8 " --> pdb=" O GLY j 4 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY j 9 " --> pdb=" O THR j 5 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LYS j 10 " --> pdb=" O PRO j 6 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ARG j 11 " --> pdb=" O SER j 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 4 through 11' Processing helix chain 'j' and resid 50 through 58 removed outlier: 3.688A pdb=" N LYS j 54 " --> pdb=" O GLY j 50 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG j 55 " --> pdb=" O ALA j 51 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG j 56 " --> pdb=" O LYS j 52 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N HIS j 57 " --> pdb=" O ALA j 53 " (cutoff:3.500A) Processing helix chain 'j' and resid 64 through 77 removed outlier: 3.686A pdb=" N LYS j 68 " --> pdb=" O MET j 64 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N HIS j 69 " --> pdb=" O ARG j 65 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL j 70 " --> pdb=" O TYR j 66 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER j 71 " --> pdb=" O LEU j 67 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ARG j 72 " --> pdb=" O LYS j 68 " (cutoff:3.500A) Processing helix chain 'k' and resid 7 through 18 removed outlier: 3.553A pdb=" N GLU k 13 " --> pdb=" O LYS k 9 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU k 14 " --> pdb=" O GLN k 10 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR k 15 " --> pdb=" O PHE k 11 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG k 16 " --> pdb=" O LEU k 12 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ALA k 18 " --> pdb=" O LEU k 14 " (cutoff:3.500A) Processing helix chain 'k' and resid 58 through 69 removed outlier: 3.897A pdb=" N ALA k 62 " --> pdb=" O ASP k 58 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS k 63 " --> pdb=" O ALA k 59 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS k 64 " --> pdb=" O GLY k 60 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLN k 67 " --> pdb=" O LYS k 63 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER k 68 " --> pdb=" O LYS k 64 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU k 69 " --> pdb=" O LEU k 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 17 through 22 removed outlier: 4.527A pdb=" N ARG L 21 " --> pdb=" O HIS L 17 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL L 22 " --> pdb=" O TRP L 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 17 through 22' Processing helix chain 'L' and resid 27 through 47 removed outlier: 3.802A pdb=" N VAL L 33 " --> pdb=" O ALA L 29 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA L 47 " --> pdb=" O ALA L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 84 removed outlier: 3.796A pdb=" N VAL L 80 " --> pdb=" O THR L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 94 removed outlier: 3.683A pdb=" N ARG L 91 " --> pdb=" O ALA L 87 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY L 94 " --> pdb=" O ALA L 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 124 removed outlier: 3.568A pdb=" N PHE L 109 " --> pdb=" O ASN L 105 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER L 121 " --> pdb=" O LYS L 117 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ILE L 124 " --> pdb=" O GLN L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 140 through 146 removed outlier: 3.507A pdb=" N THR L 144 " --> pdb=" O SER L 140 " (cutoff:3.500A) Proline residue: L 146 - end of helix Processing helix chain 'L' and resid 165 through 180 removed outlier: 5.419A pdb=" N THR L 169 " --> pdb=" O SER L 165 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU L 170 " --> pdb=" O ALA L 166 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS L 177 " --> pdb=" O ALA L 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 193 removed outlier: 3.586A pdb=" N ALA L 191 " --> pdb=" O ALA L 187 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA L 193 " --> pdb=" O GLU L 189 " (cutoff:3.500A) Processing helix chain 'l' and resid 6 through 21 removed outlier: 3.676A pdb=" N LYS l 12 " --> pdb=" O ARG l 8 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ARG l 21 " --> pdb=" O LYS l 17 " (cutoff:3.500A) Processing helix chain 'l' and resid 24 through 30 removed outlier: 4.246A pdb=" N ARG l 28 " --> pdb=" O PRO l 24 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU l 29 " --> pdb=" O GLN l 25 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG l 30 " --> pdb=" O TRP l 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 24 through 30' Processing helix chain 'M' and resid 59 through 64 removed outlier: 4.089A pdb=" N VAL M 63 " --> pdb=" O ASN M 59 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N VAL M 64 " --> pdb=" O LEU M 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 59 through 64' Processing helix chain 'M' and resid 77 through 89 removed outlier: 3.521A pdb=" N ALA M 86 " --> pdb=" O SER M 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 90 through 98 removed outlier: 4.005A pdb=" N ALA M 95 " --> pdb=" O CYS M 91 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA M 96 " --> pdb=" O GLU M 92 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER M 97 " --> pdb=" O LYS M 93 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N SER M 98 " --> pdb=" O TRP M 94 " (cutoff:3.500A) Processing helix chain 'M' and resid 99 through 112 removed outlier: 3.550A pdb=" N ILE M 103 " --> pdb=" O TRP M 99 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA M 111 " --> pdb=" O GLU M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 136 removed outlier: 3.962A pdb=" N TYR M 129 " --> pdb=" O LYS M 125 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR M 130 " --> pdb=" O GLN M 126 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS M 133 " --> pdb=" O TYR M 129 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ALA M 136 " --> pdb=" O LYS M 132 " (cutoff:3.500A) Processing helix chain 'p' and resid 19 through 35 removed outlier: 3.635A pdb=" N ILE p 31 " --> pdb=" O LYS p 27 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN p 32 " --> pdb=" O LYS p 28 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS p 34 " --> pdb=" O GLU p 30 " (cutoff:3.500A) Processing helix chain 'p' and resid 73 through 92 removed outlier: 3.708A pdb=" N THR p 78 " --> pdb=" O ALA p 74 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL p 79 " --> pdb=" O ALA p 75 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER p 81 " --> pdb=" O ALA p 77 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA p 92 " --> pdb=" O GLU p 88 " (cutoff:3.500A) Processing helix chain 'p' and resid 9 through 14 removed outlier: 3.526A pdb=" N GLY p 12 " --> pdb=" O GLY p 9 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS p 13 " --> pdb=" O ILE p 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 14 removed outlier: 3.974A pdb=" N ARG N 12 " --> pdb=" O GLU N 8 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS N 13 " --> pdb=" O GLU N 9 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N LYS N 14 " --> pdb=" O LEU N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 34 removed outlier: 3.772A pdb=" N PHE N 21 " --> pdb=" O ASP N 17 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TRP N 28 " --> pdb=" O ARG N 24 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG N 31 " --> pdb=" O VAL N 27 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN N 32 " --> pdb=" O TRP N 28 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS N 33 " --> pdb=" O GLU N 29 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ASN N 34 " --> pdb=" O TYR N 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 52 removed outlier: 3.561A pdb=" N LEU N 51 " --> pdb=" O LYS N 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 97 through 111 removed outlier: 3.766A pdb=" N VAL N 106 " --> pdb=" O ALA N 102 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA N 111 " --> pdb=" O GLY N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 139 through 146 removed outlier: 3.589A pdb=" N ARG N 144 " --> pdb=" O LYS N 140 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ASP N 145 " --> pdb=" O ALA N 141 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ALA N 146 " --> pdb=" O ILE N 142 " (cutoff:3.500A) Processing helix chain 'N' and resid 147 through 153 removed outlier: 6.693A pdb=" N ILE N 151 " --> pdb=" O ARG N 147 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N CYS N 152 " --> pdb=" O TYR N 148 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ASP N 153 " --> pdb=" O ASN N 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 147 through 153' Processing helix chain 'N' and resid 158 through 163 removed outlier: 3.671A pdb=" N ARG N 162 " --> pdb=" O HIS N 158 " (cutoff:3.500A) Processing helix chain 'N' and resid 165 through 173 removed outlier: 3.596A pdb=" N LYS N 170 " --> pdb=" O ALA N 166 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY N 173 " --> pdb=" O LYS N 169 " (cutoff:3.500A) Processing helix chain 'N' and resid 186 through 196 removed outlier: 3.910A pdb=" N GLN N 194 " --> pdb=" O THR N 190 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR N 196 " --> pdb=" O LYS N 192 " (cutoff:3.500A) Processing helix chain 'u' and resid 33 through 43 removed outlier: 3.560A pdb=" N ALA u 39 " --> pdb=" O LYS u 35 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG u 43 " --> pdb=" O ALA u 39 " (cutoff:3.500A) Processing helix chain 'u' and resid 45 through 50 removed outlier: 5.972A pdb=" N LYS u 50 " --> pdb=" O PRO u 46 " (cutoff:3.500A) Processing helix chain 'u' and resid 52 through 60 removed outlier: 3.754A pdb=" N ARG u 56 " --> pdb=" O THR u 52 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA u 58 " --> pdb=" O ALA u 54 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY u 60 " --> pdb=" O ARG u 56 " (cutoff:3.500A) Processing helix chain 'u' and resid 66 through 72 removed outlier: 4.186A pdb=" N THR u 70 " --> pdb=" O ASP u 66 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE u 71 " --> pdb=" O SER u 67 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ALA u 72 " --> pdb=" O THR u 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 66 through 72' Processing helix chain 'u' and resid 82 through 131 removed outlier: 3.716A pdb=" N VAL u 86 " --> pdb=" O ASN u 82 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR u 88 " --> pdb=" O GLU u 84 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS u 91 " --> pdb=" O ALA u 87 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA u 94 " --> pdb=" O LEU u 90 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU u 98 " --> pdb=" O ALA u 94 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS u 102 " --> pdb=" O GLU u 98 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN u 110 " --> pdb=" O ALA u 106 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLY u 114 " --> pdb=" O ASN u 110 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN u 115 " --> pdb=" O ARG u 111 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LYS u 116 " --> pdb=" O MET u 112 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N GLU u 117 " --> pdb=" O ARG u 113 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS u 118 " --> pdb=" O GLY u 114 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE u 120 " --> pdb=" O LYS u 116 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS u 125 " --> pdb=" O LEU u 121 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU u 126 " --> pdb=" O ARG u 122 " (cutoff:3.500A) Proline residue: u 131 - end of helix Processing helix chain 'u' and resid 132 through 149 removed outlier: 3.541A pdb=" N ILE u 136 " --> pdb=" O GLU u 132 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU u 138 " --> pdb=" O LEU u 134 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL u 139 " --> pdb=" O ARG u 135 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU u 140 " --> pdb=" O ILE u 136 " (cutoff:3.500A) Processing helix chain 'O' and resid 15 through 30 removed outlier: 3.851A pdb=" N VAL O 22 " --> pdb=" O ARG O 18 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN O 26 " --> pdb=" O VAL O 22 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 61 removed outlier: 3.569A pdb=" N ASN O 50 " --> pdb=" O GLU O 46 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU O 52 " --> pdb=" O PHE O 48 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE O 57 " --> pdb=" O LYS O 53 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS O 60 " --> pdb=" O ASP O 56 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ALA O 61 " --> pdb=" O PHE O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 65 through 70 removed outlier: 4.129A pdb=" N GLY O 69 " --> pdb=" O ASN O 65 " (cutoff:3.500A) Proline residue: O 70 - end of helix No H-bonds generated for 'chain 'O' and resid 65 through 70' Processing helix chain 'O' and resid 75 through 89 removed outlier: 4.283A pdb=" N MET O 87 " --> pdb=" O ALA O 83 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N SER O 89 " --> pdb=" O ARG O 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 103 removed outlier: 4.235A pdb=" N ARG O 101 " --> pdb=" O ALA O 97 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU O 102 " --> pdb=" O ALA O 98 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N LYS O 103 " --> pdb=" O LEU O 99 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 116 removed outlier: 8.156A pdb=" N LYS O 114 " --> pdb=" O PRO O 110 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS O 115 " --> pdb=" O PRO O 111 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N LYS O 116 " --> pdb=" O TYR O 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 110 through 116' Processing helix chain 'O' and resid 124 through 129 Processing helix chain 'O' and resid 137 through 146 removed outlier: 3.671A pdb=" N THR O 143 " --> pdb=" O GLY O 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 151 through 183 removed outlier: 4.345A pdb=" N LYS O 155 " --> pdb=" O ASP O 151 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL O 162 " --> pdb=" O ALA O 158 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER O 163 " --> pdb=" O LYS O 159 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR O 167 " --> pdb=" O SER O 163 " (cutoff:3.500A) Processing helix chain 'O' and resid 188 through 198 Processing helix chain 'P' and resid 25 through 37 removed outlier: 3.855A pdb=" N GLU P 31 " --> pdb=" O LYS P 27 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA P 33 " --> pdb=" O THR P 29 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE P 36 " --> pdb=" O THR P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 54 removed outlier: 3.828A pdb=" N LYS P 46 " --> pdb=" O THR P 42 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU P 52 " --> pdb=" O LEU P 48 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASP P 53 " --> pdb=" O GLU P 49 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS P 54 " --> pdb=" O GLN P 50 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 106 removed outlier: 3.744A pdb=" N PHE P 90 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY P 93 " --> pdb=" O LYS P 89 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU P 103 " --> pdb=" O ALA P 99 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA P 104 " --> pdb=" O ALA P 100 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS P 105 " --> pdb=" O ASN P 101 " (cutoff:3.500A) Processing helix chain 'P' and resid 169 through 183 removed outlier: 3.547A pdb=" N ILE P 176 " --> pdb=" O GLN P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 70 through 76 removed outlier: 4.041A pdb=" N GLY P 73 " --> pdb=" O THR P 70 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLU P 75 " --> pdb=" O GLN P 72 " (cutoff:3.500A) Processing helix chain 'Q' and resid 23 through 40 removed outlier: 3.547A pdb=" N LYS Q 27 " --> pdb=" O ASN Q 23 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE Q 35 " --> pdb=" O LYS Q 31 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG Q 38 " --> pdb=" O THR Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 54 removed outlier: 4.194A pdb=" N LYS Q 46 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL Q 47 " --> pdb=" O PRO Q 43 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU Q 52 " --> pdb=" O VAL Q 48 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU Q 54 " --> pdb=" O LYS Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 55 through 60 Proline residue: Q 60 - end of helix Processing helix chain 'Q' and resid 63 through 73 removed outlier: 3.765A pdb=" N ILE Q 67 " --> pdb=" O SER Q 63 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS Q 72 " --> pdb=" O ALA Q 68 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN Q 73 " --> pdb=" O ARG Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 118 removed outlier: 3.511A pdb=" N ALA Q 112 " --> pdb=" O ALA Q 108 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS Q 113 " --> pdb=" O GLY Q 109 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE Q 114 " --> pdb=" O ALA Q 110 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL Q 115 " --> pdb=" O ARG Q 111 " (cutoff:3.500A) Processing helix chain 'Q' and resid 123 through 131 removed outlier: 3.789A pdb=" N LEU Q 127 " --> pdb=" O THR Q 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 16 removed outlier: 3.508A pdb=" N ALA R 12 " --> pdb=" O LYS R 8 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 36 removed outlier: 3.902A pdb=" N ALA R 33 " --> pdb=" O THR R 29 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN R 34 " --> pdb=" O SER R 30 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA R 35 " --> pdb=" O GLU R 31 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ASN R 36 " --> pdb=" O ILE R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 48 removed outlier: 3.536A pdb=" N ILE R 41 " --> pdb=" O SER R 37 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS R 43 " --> pdb=" O ASN R 39 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY R 48 " --> pdb=" O LEU R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 73 removed outlier: 3.811A pdb=" N SER R 69 " --> pdb=" O ALA R 65 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU R 72 " --> pdb=" O GLN R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 82 removed outlier: 3.599A pdb=" N ARG R 81 " --> pdb=" O GLY R 77 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N LYS R 82 " --> pdb=" O TYR R 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 77 through 82' Processing helix chain 'R' and resid 84 through 113 Proline residue: R 90 - end of helix removed outlier: 6.332A pdb=" N VAL R 93 " --> pdb=" O LEU R 89 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL R 101 " --> pdb=" O ARG R 97 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU R 106 " --> pdb=" O LEU R 102 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP R 111 " --> pdb=" O ALA R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 130 removed outlier: 3.834A pdb=" N VAL R 122 " --> pdb=" O HIS R 118 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS R 125 " --> pdb=" O HIS R 121 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY R 129 " --> pdb=" O LYS R 125 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASN R 130 " --> pdb=" O GLU R 126 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 155 removed outlier: 3.513A pdb=" N HIS R 141 " --> pdb=" O ALA R 137 " (cutoff:3.500A) Processing helix chain 'S' and resid 33 through 49 removed outlier: 3.678A pdb=" N ALA S 37 " --> pdb=" O ASN S 33 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TRP S 42 " --> pdb=" O LYS S 38 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR S 43 " --> pdb=" O SER S 39 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE S 44 " --> pdb=" O ARG S 40 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LYS S 47 " --> pdb=" O TYR S 43 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS S 49 " --> pdb=" O LEU S 45 " (cutoff:3.500A) Processing helix chain 'S' and resid 98 through 114 removed outlier: 3.520A pdb=" N VAL S 103 " --> pdb=" O ARG S 99 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU S 104 " --> pdb=" O VAL S 100 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN S 108 " --> pdb=" O GLU S 104 " (cutoff:3.500A) Processing helix chain 'S' and resid 137 through 145 removed outlier: 3.756A pdb=" N LYS S 141 " --> pdb=" O ARG S 137 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N PHE S 143 " --> pdb=" O TYR S 139 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU S 144 " --> pdb=" O VAL S 140 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N THR S 145 " --> pdb=" O LYS S 141 " (cutoff:3.500A) Processing helix chain 'T' and resid 99 through 123 removed outlier: 4.520A pdb=" N GLN T 103 " --> pdb=" O SER T 99 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG T 116 " --> pdb=" O ASN T 112 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY T 123 " --> pdb=" O ALA T 119 " (cutoff:3.500A) Processing helix chain 'U' and resid 19 through 26 removed outlier: 3.978A pdb=" N ASN U 25 " --> pdb=" O SER U 21 " (cutoff:3.500A) Processing helix chain 'U' and resid 29 through 41 removed outlier: 3.936A pdb=" N TYR U 33 " --> pdb=" O ASP U 29 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS U 35 " --> pdb=" O ALA U 31 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE U 38 " --> pdb=" O ALA U 34 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP U 39 " --> pdb=" O LYS U 35 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N HIS U 40 " --> pdb=" O TYR U 36 " (cutoff:3.500A) Processing helix chain 'U' and resid 72 through 88 removed outlier: 3.636A pdb=" N THR U 80 " --> pdb=" O LEU U 76 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS U 85 " --> pdb=" O LYS U 81 " (cutoff:3.500A) Processing helix chain 'V' and resid 66 through 71 removed outlier: 5.233A pdb=" N LYS V 71 " --> pdb=" O PRO V 67 " (cutoff:3.500A) Processing helix chain 'V' and resid 119 through 127 removed outlier: 3.729A pdb=" N LEU V 125 " --> pdb=" O GLU V 121 " (cutoff:3.500A) Proline residue: V 127 - end of helix Processing helix chain 'V' and resid 128 through 133 Processing helix chain 'W' and resid 19 through 37 removed outlier: 3.855A pdb=" N LYS W 23 " --> pdb=" O GLY W 19 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG W 31 " --> pdb=" O PHE W 27 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU W 32 " --> pdb=" O ASP W 28 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASP W 35 " --> pdb=" O ARG W 31 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR W 36 " --> pdb=" O GLU W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 61 removed outlier: 3.602A pdb=" N ARG W 57 " --> pdb=" O LEU W 53 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA W 61 " --> pdb=" O ARG W 57 " (cutoff:3.500A) Processing helix chain 'W' and resid 69 through 78 Processing helix chain 'W' and resid 89 through 96 removed outlier: 3.850A pdb=" N SER W 93 " --> pdb=" O LEU W 89 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS W 94 " --> pdb=" O TYR W 90 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU W 95 " --> pdb=" O GLN W 91 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N CYS W 96 " --> pdb=" O LEU W 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 89 through 96' Processing helix chain 'W' and resid 108 through 119 removed outlier: 4.175A pdb=" N VAL W 112 " --> pdb=" O ASP W 108 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS W 113 " --> pdb=" O VAL W 109 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS W 117 " --> pdb=" O LYS W 113 " (cutoff:3.500A) Processing helix chain 'W' and resid 150 through 155 removed outlier: 5.273A pdb=" N VAL W 155 " --> pdb=" O ALA W 151 " (cutoff:3.500A) Processing helix chain 'W' and resid 158 through 168 removed outlier: 4.129A pdb=" N GLU W 162 " --> pdb=" O ILE W 158 " (cutoff:3.500A) Proline residue: W 163 - end of helix Processing helix chain 'W' and resid 196 through 207 removed outlier: 3.519A pdb=" N LEU W 201 " --> pdb=" O VAL W 197 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU W 203 " --> pdb=" O GLN W 199 " (cutoff:3.500A) Processing helix chain 'X' and resid 58 through 64 removed outlier: 3.667A pdb=" N ILE X 63 " --> pdb=" O SER X 59 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLU X 64 " --> pdb=" O TYR X 60 " (cutoff:3.500A) Processing helix chain 'X' and resid 69 through 79 removed outlier: 3.612A pdb=" N MET X 73 " --> pdb=" O SER X 69 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS X 74 " --> pdb=" O GLU X 70 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS X 75 " --> pdb=" O THR X 71 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU X 77 " --> pdb=" O MET X 73 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY X 79 " --> pdb=" O LYS X 75 " (cutoff:3.500A) Processing helix chain 'X' and resid 91 through 103 removed outlier: 3.639A pdb=" N LYS X 100 " --> pdb=" O LYS X 96 " (cutoff:3.500A) Processing helix chain 'X' and resid 131 through 140 removed outlier: 3.684A pdb=" N ILE X 135 " --> pdb=" O ASP X 131 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN X 137 " --> pdb=" O LEU X 133 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG X 138 " --> pdb=" O ASP X 134 " (cutoff:3.500A) Processing helix chain 'Y' and resid 11 through 22 removed outlier: 3.636A pdb=" N LYS Y 17 " --> pdb=" O ARG Y 13 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA Y 22 " --> pdb=" O ALA Y 18 " (cutoff:3.500A) Processing helix chain 'Y' and resid 23 through 32 removed outlier: 3.974A pdb=" N VAL Y 29 " --> pdb=" O SER Y 25 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU Y 30 " --> pdb=" O GLN Y 26 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N SER Y 32 " --> pdb=" O ARG Y 28 " (cutoff:3.500A) Processing helix chain 'Y' and resid 36 through 44 removed outlier: 3.597A pdb=" N ALA Y 41 " --> pdb=" O LYS Y 37 " (cutoff:3.500A) Processing helix chain 'Y' and resid 100 through 105 removed outlier: 3.873A pdb=" N LEU Y 104 " --> pdb=" O HIS Y 100 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N VAL Y 105 " --> pdb=" O PRO Y 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 100 through 105' Processing helix chain 'Y' and resid 112 through 123 Processing helix chain 'y' and resid 12 through 17 removed outlier: 4.790A pdb=" N PHE y 16 " --> pdb=" O GLU y 12 " (cutoff:3.500A) Processing helix chain 'y' and resid 32 through 42 removed outlier: 4.229A pdb=" N SER y 36 " --> pdb=" O GLU y 32 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE y 38 " --> pdb=" O PHE y 34 " (cutoff:3.500A) Processing helix chain 'y' and resid 58 through 63 removed outlier: 3.719A pdb=" N MET y 62 " --> pdb=" O ILE y 58 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR y 63 " --> pdb=" O ILE y 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 58 through 63' Processing helix chain 'y' and resid 77 through 88 removed outlier: 3.766A pdb=" N ARG y 85 " --> pdb=" O LEU y 81 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER y 87 " --> pdb=" O HIS y 83 " (cutoff:3.500A) Processing helix chain 'y' and resid 103 through 108 removed outlier: 3.948A pdb=" N VAL y 107 " --> pdb=" O ALA y 103 " (cutoff:3.500A) Processing helix chain 'y' and resid 122 through 133 removed outlier: 4.088A pdb=" N LEU y 128 " --> pdb=" O GLU y 124 " (cutoff:3.500A) Processing helix chain 'y' and resid 147 through 152 removed outlier: 3.649A pdb=" N CYS y 152 " --> pdb=" O VAL y 148 " (cutoff:3.500A) Processing helix chain 'y' and resid 166 through 178 removed outlier: 3.868A pdb=" N SER y 175 " --> pdb=" O GLU y 171 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU y 176 " --> pdb=" O GLU y 172 " (cutoff:3.500A) Processing helix chain 'y' and resid 192 through 197 removed outlier: 3.926A pdb=" N MET y 197 " --> pdb=" O VAL y 193 " (cutoff:3.500A) Processing helix chain 'y' and resid 211 through 223 Processing helix chain 'y' and resid 231 through 237 removed outlier: 4.066A pdb=" N ASN y 235 " --> pdb=" O SER y 231 " (cutoff:3.500A) Processing helix chain 'y' and resid 238 through 243 removed outlier: 3.985A pdb=" N GLU y 242 " --> pdb=" O ASP y 238 " (cutoff:3.500A) Processing helix chain 'Z' and resid 58 through 67 removed outlier: 3.508A pdb=" N ALA Z 63 " --> pdb=" O ALA Z 59 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LYS Z 67 " --> pdb=" O ALA Z 63 " (cutoff:3.500A) Processing helix chain 'Z' and resid 76 through 81 removed outlier: 3.629A pdb=" N LEU Z 80 " --> pdb=" O ASN Z 76 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N LEU Z 81 " --> pdb=" O TYR Z 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 76 through 81' Processing helix chain 'Z' and resid 89 through 97 removed outlier: 3.828A pdb=" N LYS Z 93 " --> pdb=" O VAL Z 89 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N SER Z 94 " --> pdb=" O GLU Z 90 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL Z 95 " --> pdb=" O ALA Z 91 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL Z 96 " --> pdb=" O PHE Z 92 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N SER Z 97 " --> pdb=" O LYS Z 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 89 through 97' Processing helix chain 'Z' and resid 103 through 125 removed outlier: 4.129A pdb=" N ARG Z 107 " --> pdb=" O GLN Z 103 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU Z 108 " --> pdb=" O PRO Z 104 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU Z 109 " --> pdb=" O SER Z 105 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA Z 110 " --> pdb=" O GLN Z 106 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL Z 114 " --> pdb=" O ALA Z 110 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG Z 121 " --> pdb=" O ALA Z 117 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ALA Z 124 " --> pdb=" O GLU Z 120 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLY Z 125 " --> pdb=" O ARG Z 121 " (cutoff:3.500A) Processing helix chain 'Z' and resid 127 through 133 removed outlier: 3.799A pdb=" N PHE Z 131 " --> pdb=" O ASN Z 127 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LYS Z 133 " --> pdb=" O TRP Z 129 " (cutoff:3.500A) Processing helix chain 'z' and resid 7 through 56 removed outlier: 3.916A pdb=" N VAL z 16 " --> pdb=" O ASN z 12 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS z 17 " --> pdb=" O ALA z 13 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL z 21 " --> pdb=" O LYS z 17 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N PHE z 22 " --> pdb=" O ARG z 18 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N GLN z 23 " --> pdb=" O ARG z 19 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS z 24 " --> pdb=" O GLY z 20 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL z 26 " --> pdb=" O PHE z 22 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN z 31 " --> pdb=" O ASP z 27 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER z 34 " --> pdb=" O GLU z 30 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU z 41 " --> pdb=" O LEU z 37 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU z 42 " --> pdb=" O LYS z 38 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS z 43 " --> pdb=" O GLU z 39 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN z 44 " --> pdb=" O ASP z 40 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP z 48 " --> pdb=" O GLN z 44 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS z 51 " --> pdb=" O GLU z 47 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU z 54 " --> pdb=" O LYS z 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 16 removed outlier: 3.550A pdb=" N SER D 13 " --> pdb=" O SER D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 26 removed outlier: 4.936A pdb=" N GLY D 26 " --> pdb=" O ARG D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 38 removed outlier: 3.787A pdb=" N LYS D 34 " --> pdb=" O TYR D 30 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ARG D 35 " --> pdb=" O TYR D 31 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR D 38 " --> pdb=" O LYS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 87 removed outlier: 4.154A pdb=" N LEU D 83 " --> pdb=" O TYR D 79 " (cutoff:3.500A) Proline residue: D 84 - end of helix Processing helix chain 'D' and resid 94 through 114 removed outlier: 3.792A pdb=" N ALA D 106 " --> pdb=" O GLY D 102 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU D 110 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS D 112 " --> pdb=" O ARG D 108 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU D 113 " --> pdb=" O THR D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 170 removed outlier: 4.175A pdb=" N GLY D 161 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA D 162 " --> pdb=" O ARG D 158 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU D 163 " --> pdb=" O VAL D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 201 removed outlier: 3.587A pdb=" N ILE D 199 " --> pdb=" O LEU D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 214 removed outlier: 3.788A pdb=" N TYR D 207 " --> pdb=" O HIS D 203 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP D 213 " --> pdb=" O GLU D 209 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP D 214 " --> pdb=" O GLU D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 223 removed outlier: 3.582A pdb=" N GLU D 221 " --> pdb=" O GLU D 217 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N PHE D 223 " --> pdb=" O PHE D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 230 Processing helix chain 'D' and resid 233 through 250 removed outlier: 4.222A pdb=" N GLU D 237 " --> pdb=" O ALA D 233 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP D 238 " --> pdb=" O ASP D 234 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU D 245 " --> pdb=" O THR D 241 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 274 removed outlier: 3.755A pdb=" N TYR D 265 " --> pdb=" O THR D 261 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU D 268 " --> pdb=" O GLN D 264 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER D 269 " --> pdb=" O TYR D 265 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS D 271 " --> pdb=" O ALA D 267 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR D 272 " --> pdb=" O GLU D 268 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG D 273 " --> pdb=" O SER D 269 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N GLN D 274 " --> pdb=" O LYS D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 285 removed outlier: 3.658A pdb=" N ALA D 284 " --> pdb=" O GLU D 280 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG D 285 " --> pdb=" O GLU D 281 " (cutoff:3.500A) Processing helix chain 'J' and resid 27 through 42 Processing helix chain 'J' and resid 73 through 88 removed outlier: 3.665A pdb=" N GLU J 77 " --> pdb=" O GLY J 73 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU J 78 " --> pdb=" O PRO J 74 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE J 79 " --> pdb=" O LYS J 75 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS J 85 " --> pdb=" O GLU J 81 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL J 86 " --> pdb=" O ARG J 82 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS J 87 " --> pdb=" O GLY J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 113 removed outlier: 4.757A pdb=" N LEU J 112 " --> pdb=" O GLU J 108 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY J 113 " --> pdb=" O HIS J 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 108 through 113' Processing helix chain 'J' and resid 136 through 141 removed outlier: 3.607A pdb=" N ARG J 140 " --> pdb=" O ALA J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 167 removed outlier: 3.948A pdb=" N THR J 159 " --> pdb=" O THR J 155 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TYR J 167 " --> pdb=" O PHE J 163 " (cutoff:3.500A) Processing helix chain 'q' and resid 39 through 46 removed outlier: 4.603A pdb=" N TYR q 43 " --> pdb=" O GLY q 39 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG q 45 " --> pdb=" O ARG q 41 " (cutoff:3.500A) Processing helix chain 'o' and resid 11 through 20 removed outlier: 3.618A pdb=" N ALA o 16 " --> pdb=" O GLN o 12 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG o 18 " --> pdb=" O ARG o 14 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASN o 19 " --> pdb=" O LYS o 15 " (cutoff:3.500A) Processing helix chain 'o' and resid 36 through 57 removed outlier: 3.961A pdb=" N HIS o 45 " --> pdb=" O ARG o 41 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU o 47 " --> pdb=" O HIS o 43 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS o 48 " --> pdb=" O LYS o 44 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR o 50 " --> pdb=" O ALA o 46 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA o 57 " --> pdb=" O ALA o 53 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'v' and resid 188 through 192 removed outlier: 4.090A pdb=" N SER v 189 " --> pdb=" O PHE v 200 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE v 200 " --> pdb=" O SER v 189 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ARG v 156 " --> pdb=" O TYR v 240 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE v 242 " --> pdb=" O ARG v 156 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR v 158 " --> pdb=" O PHE v 242 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'v' and resid 255 through 259 removed outlier: 5.314A pdb=" N ASP v 255 " --> pdb=" O CYS v 276 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N GLN v 272 " --> pdb=" O LEU v 259 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLN v 292 " --> pdb=" O ASP v 287 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'v' and resid 315 through 320 removed outlier: 3.990A pdb=" N ASP v 367 " --> pdb=" O VAL v 320 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'v' and resid 322 through 325 Processing sheet with id= 5, first strand: chain 'A' and resid 41 through 45 removed outlier: 4.876A pdb=" N GLN A 86 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 46 through 50 removed outlier: 3.696A pdb=" N GLN A 47 " --> pdb=" O LYS A 60 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 134 through 137 removed outlier: 6.961A pdb=" N ARG A 147 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ALA A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'B' and resid 41 through 44 removed outlier: 5.365A pdb=" N ALA B 42 " --> pdb=" O ASN B 184 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLN B 182 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ARG B 159 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL B 89 " --> pdb=" O ARG B 159 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU B 161 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'B' and resid 45 through 50 removed outlier: 4.252A pdb=" N ARG B 334 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU B 213 " --> pdb=" O ILE B 282 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'B' and resid 53 through 58 removed outlier: 5.065A pdb=" N ASN B 319 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE B 321 " --> pdb=" O GLY B 286 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'B' and resid 87 through 90 removed outlier: 7.489A pdb=" N VAL B 87 " --> pdb=" O ALA B 107 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 107 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'B' and resid 84 through 87 removed outlier: 4.127A pdb=" N LYS B 201 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'b' and resid 204 through 210 removed outlier: 3.550A pdb=" N TYR b 205 " --> pdb=" O ASP b 220 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ARG b 168 " --> pdb=" O ARG b 215 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN b 217 " --> pdb=" O ARG b 168 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR b 221 " --> pdb=" O ILE b 172 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLY b 174 " --> pdb=" O THR b 221 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N CYS b 249 " --> pdb=" O THR b 169 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N SER b 282 " --> pdb=" O SER b 248 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N VAL b 250 " --> pdb=" O SER b 282 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL b 283 " --> pdb=" O GLY b 314 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLU b 316 " --> pdb=" O VAL b 283 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'C' and resid 5 through 8 removed outlier: 5.720A pdb=" N ASN C 18 " --> pdb=" O VAL C 8 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'C' and resid 224 through 229 removed outlier: 3.621A pdb=" N GLU C 226 " --> pdb=" O PRO C 205 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR C 209 " --> pdb=" O ALA C 228 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N PHE C 247 " --> pdb=" O GLY C 204 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'c' and resid 22 through 25 removed outlier: 6.648A pdb=" N LYS c 22 " --> pdb=" O LEU c 93 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU c 41 " --> pdb=" O ILE c 92 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS c 66 " --> pdb=" O LYS c 40 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'd' and resid 48 through 51 removed outlier: 5.817A pdb=" N ASP d 48 " --> pdb=" O LEU d 89 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG d 77 " --> pdb=" O VAL d 8 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL d 8 " --> pdb=" O ARG d 77 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N THR d 9 " --> pdb=" O VAL d 109 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL d 107 " --> pdb=" O GLU d 11 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'E' and resid 37 through 41 removed outlier: 4.164A pdb=" N THR E 38 " --> pdb=" O TYR E 54 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'e' and resid 71 through 77 Processing sheet with id= 20, first strand: chain 'F' and resid 133 through 138 removed outlier: 7.966A pdb=" N TYR F 133 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY F 137 " --> pdb=" O PHE F 85 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N SER F 113 " --> pdb=" O ARG F 88 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ASN F 112 " --> pdb=" O LEU F 207 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'f' and resid 63 through 71 removed outlier: 5.258A pdb=" N LYS f 63 " --> pdb=" O ALA f 55 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N LYS f 47 " --> pdb=" O VAL f 71 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ARG f 48 " --> pdb=" O PHE f 101 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N VAL f 52 " --> pdb=" O SER f 97 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N SER f 97 " --> pdb=" O VAL f 52 " (cutoff:3.500A) removed outlier: 13.134A pdb=" N ARG f 54 " --> pdb=" O GLY f 95 " (cutoff:3.500A) removed outlier: 15.905A pdb=" N GLY f 95 " --> pdb=" O ARG f 54 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALA f 96 " --> pdb=" O HIS f 13 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU f 29 " --> pdb=" O LEU f 14 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'G' and resid 176 through 181 removed outlier: 3.805A pdb=" N VAL G 151 " --> pdb=" O PRO G 176 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU G 150 " --> pdb=" O LEU G 200 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'g' and resid 19 through 24 removed outlier: 4.716A pdb=" N LYS g 19 " --> pdb=" O VAL g 35 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL g 35 " --> pdb=" O LYS g 19 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'I' and resid 49 through 52 removed outlier: 4.911A pdb=" N HIS I 49 " --> pdb=" O MET I 58 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS I 56 " --> pdb=" O CYS I 51 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'H' and resid 5 through 12 removed outlier: 3.510A pdb=" N GLN H 8 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLN H 51 " --> pdb=" O VAL H 12 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'H' and resid 17 through 20 Processing sheet with id= 27, first strand: chain 'H' and resid 85 through 91 removed outlier: 5.866A pdb=" N GLU H 143 " --> pdb=" O SER H 137 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER H 137 " --> pdb=" O GLU H 143 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'H' and resid 100 through 105 Processing sheet with id= 29, first strand: chain 'k' and resid 2 through 5 removed outlier: 4.450A pdb=" N VAL k 55 " --> pdb=" O ILE k 5 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N THR k 22 " --> pdb=" O ARG k 46 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE k 27 " --> pdb=" O LEU k 78 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'L' and resid 56 through 59 Processing sheet with id= 31, first strand: chain 'M' and resid 19 through 24 removed outlier: 4.645A pdb=" N ARG M 19 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS M 31 " --> pdb=" O ILE M 23 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'M' and resid 36 through 39 removed outlier: 6.736A pdb=" N LYS M 43 " --> pdb=" O ILE M 39 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'p' and resid 53 through 57 removed outlier: 4.453A pdb=" N GLY p 53 " --> pdb=" O GLY p 66 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS p 62 " --> pdb=" O CYS p 57 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'N' and resid 35 through 39 removed outlier: 6.444A pdb=" N VAL N 35 " --> pdb=" O ARG N 65 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLY N 58 " --> pdb=" O ASP N 136 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE N 133 " --> pdb=" O LEU N 116 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'N' and resid 117 through 121 removed outlier: 3.505A pdb=" N TYR N 119 " --> pdb=" O GLU N 131 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL N 121 " --> pdb=" O TYR N 129 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N TYR N 129 " --> pdb=" O VAL N 121 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'u' and resid 18 through 22 removed outlier: 3.887A pdb=" N ILE u 19 " --> pdb=" O PHE u 31 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'O' and resid 6 through 10 Processing sheet with id= 38, first strand: chain 'P' and resid 14 through 20 Processing sheet with id= 39, first strand: chain 'P' and resid 124 through 131 removed outlier: 4.180A pdb=" N GLN P 125 " --> pdb=" O SER P 141 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N SER P 141 " --> pdb=" O GLN P 125 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG P 127 " --> pdb=" O TYR P 139 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ARG P 135 " --> pdb=" O ARG P 131 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'Q' and resid 79 through 83 Processing sheet with id= 41, first strand: chain 'R' and resid 21 through 24 No H-bonds generated for sheet with id= 41 Processing sheet with id= 42, first strand: chain 'S' and resid 24 through 31 removed outlier: 6.653A pdb=" N ILE S 10 " --> pdb=" O VAL S 59 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU S 57 " --> pdb=" O ARG S 12 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'S' and resid 89 through 96 removed outlier: 6.703A pdb=" N TRP S 78 " --> pdb=" O LEU S 124 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'S' and resid 6 through 10 removed outlier: 4.740A pdb=" N GLU S 6 " --> pdb=" O ILE S 64 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER S 60 " --> pdb=" O ILE S 10 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'S' and resid 74 through 78 removed outlier: 4.727A pdb=" N ASN S 74 " --> pdb=" O ILE S 129 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS S 125 " --> pdb=" O TRP S 78 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'U' and resid 54 through 58 removed outlier: 6.337A pdb=" N ASN U 101 " --> pdb=" O THR U 14 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR U 16 " --> pdb=" O ASN U 101 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR U 108 " --> pdb=" O TRP U 92 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N TRP U 92 " --> pdb=" O TYR U 108 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'V' and resid 20 through 24 removed outlier: 4.130A pdb=" N ALA V 21 " --> pdb=" O ILE V 36 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'V' and resid 56 through 60 removed outlier: 4.446A pdb=" N ASP V 56 " --> pdb=" O VAL V 78 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET V 74 " --> pdb=" O ALA V 60 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ASP V 97 " --> pdb=" O ALA V 82 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA V 82 " --> pdb=" O ASP V 97 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG V 80 " --> pdb=" O ALA V 99 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'W' and resid 63 through 67 removed outlier: 4.054A pdb=" N THR W 105 " --> pdb=" O TYR W 39 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR W 39 " --> pdb=" O THR W 105 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N ARG W 38 " --> pdb=" O ASN W 223 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL W 42 " --> pdb=" O ALA W 219 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA W 219 " --> pdb=" O VAL W 42 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR W 220 " --> pdb=" O GLU W 229 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP W 222 " --> pdb=" O THR W 227 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR W 227 " --> pdb=" O ASP W 222 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'W' and resid 120 through 123 Processing sheet with id= 51, first strand: chain 'X' and resid 81 through 86 removed outlier: 3.715A pdb=" N LYS X 120 " --> pdb=" O VAL X 86 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N THR X 119 " --> pdb=" O ARG X 115 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS X 109 " --> pdb=" O ARG X 125 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'Y' and resid 72 through 75 removed outlier: 3.775A pdb=" N SER Y 72 " --> pdb=" O GLN Y 81 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'Y' and resid 86 through 89 removed outlier: 4.648A pdb=" N ALA Y 93 " --> pdb=" O LYS Y 89 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'y' and resid 2 through 5 Processing sheet with id= 55, first strand: chain 'y' and resid 23 through 27 Processing sheet with id= 56, first strand: chain 'y' and resid 69 through 73 removed outlier: 3.578A pdb=" N VAL y 72 " --> pdb=" O GLN y 95 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'y' and resid 114 through 117 Processing sheet with id= 58, first strand: chain 'Z' and resid 9 through 13 removed outlier: 4.954A pdb=" N LYS Z 9 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL Z 13 " --> pdb=" O LYS Z 21 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS Z 21 " --> pdb=" O VAL Z 13 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL Z 24 " --> pdb=" O ALA Z 44 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU Z 42 " --> pdb=" O VAL Z 26 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS Z 40 " --> pdb=" O HIS Z 29 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'Z' and resid 42 through 46 Processing sheet with id= 60, first strand: chain 'D' and resid 72 through 75 removed outlier: 4.296A pdb=" N VAL D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE D 64 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE D 145 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL D 53 " --> pdb=" O ASP D 147 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'J' and resid 45 through 49 removed outlier: 3.548A pdb=" N ALA J 66 " --> pdb=" O SER J 48 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LYS J 16 " --> pdb=" O VAL J 130 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N SER J 22 " --> pdb=" O GLY J 124 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLY J 124 " --> pdb=" O SER J 22 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'q' and resid 7 through 10 1872 hydrogen bonds defined for protein. 5553 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1808 hydrogen bonds 3008 hydrogen bond angles 0 basepair planarities 766 basepair parallelities 1764 stacking parallelities Total time for adding SS restraints: 168.64 Time building geometry restraints manager: 53.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 23716 1.33 - 1.46: 56627 1.46 - 1.58: 55249 1.58 - 1.71: 6877 1.71 - 1.84: 207 Bond restraints: 142676 Sorted by residual: bond pdb=" C1' U 12260 " pdb=" N1 U 12260 " ideal model delta sigma weight residual 1.470 1.554 -0.084 1.50e-02 4.44e+03 3.11e+01 bond pdb=" N GLN v 231 " pdb=" CA GLN v 231 " ideal model delta sigma weight residual 1.457 1.512 -0.054 1.29e-02 6.01e+03 1.78e+01 bond pdb=" C1' A 12259 " pdb=" N9 A 12259 " ideal model delta sigma weight residual 1.475 1.412 0.063 1.50e-02 4.44e+03 1.77e+01 bond pdb=" CA PHE B 130 " pdb=" C PHE B 130 " ideal model delta sigma weight residual 1.525 1.474 0.051 1.27e-02 6.20e+03 1.60e+01 bond pdb=" C ASP b 437 " pdb=" N GLY b 438 " ideal model delta sigma weight residual 1.333 1.299 0.034 9.60e-03 1.09e+04 1.26e+01 ... (remaining 142671 not shown) Histogram of bond angle deviations from ideal: 96.64 - 104.89: 16153 104.89 - 113.14: 86224 113.14 - 121.39: 71802 121.39 - 129.64: 33263 129.64 - 137.89: 2268 Bond angle restraints: 209710 Sorted by residual: angle pdb=" N GLN q 82 " pdb=" CA GLN q 82 " pdb=" C GLN q 82 " ideal model delta sigma weight residual 110.19 118.94 -8.75 1.24e+00 6.50e-01 4.98e+01 angle pdb=" C ASN b 515 " pdb=" N LYS b 516 " pdb=" CA LYS b 516 " ideal model delta sigma weight residual 121.90 113.09 8.81 1.26e+00 6.30e-01 4.89e+01 angle pdb=" C ASN F 157 " pdb=" N LYS F 158 " pdb=" CA LYS F 158 " ideal model delta sigma weight residual 121.54 134.15 -12.61 1.91e+00 2.74e-01 4.36e+01 angle pdb=" C THR J 154 " pdb=" N THR J 155 " pdb=" CA THR J 155 " ideal model delta sigma weight residual 121.54 133.94 -12.40 1.91e+00 2.74e-01 4.22e+01 angle pdb=" C LYS S 23 " pdb=" N LEU S 24 " pdb=" CA LEU S 24 " ideal model delta sigma weight residual 121.54 133.16 -11.62 1.91e+00 2.74e-01 3.70e+01 ... (remaining 209705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 81897 35.97 - 71.95: 7627 71.95 - 107.92: 890 107.92 - 143.89: 20 143.89 - 179.87: 66 Dihedral angle restraints: 90500 sinusoidal: 68904 harmonic: 21596 Sorted by residual: dihedral pdb=" CA VAL T 154 " pdb=" C VAL T 154 " pdb=" N PRO T 155 " pdb=" CA PRO T 155 " ideal model delta harmonic sigma weight residual -180.00 -121.38 -58.62 0 5.00e+00 4.00e-02 1.37e+02 dihedral pdb=" CA THR G 30 " pdb=" C THR G 30 " pdb=" N PRO G 31 " pdb=" CA PRO G 31 " ideal model delta harmonic sigma weight residual -180.00 -123.45 -56.55 0 5.00e+00 4.00e-02 1.28e+02 dihedral pdb=" CA LYS v 278 " pdb=" C LYS v 278 " pdb=" N ILE v 279 " pdb=" CA ILE v 279 " ideal model delta harmonic sigma weight residual -180.00 -128.71 -51.29 0 5.00e+00 4.00e-02 1.05e+02 ... (remaining 90497 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 24754 0.088 - 0.176: 1437 0.176 - 0.264: 107 0.264 - 0.352: 36 0.352 - 0.440: 4 Chirality restraints: 26338 Sorted by residual: chirality pdb=" CB THR L 76 " pdb=" CA THR L 76 " pdb=" OG1 THR L 76 " pdb=" CG2 THR L 76 " both_signs ideal model delta sigma weight residual False 2.55 2.11 0.44 2.00e-01 2.50e+01 4.85e+00 chirality pdb=" C3' G 12249 " pdb=" C4' G 12249 " pdb=" O3' G 12249 " pdb=" C2' G 12249 " both_signs ideal model delta sigma weight residual False -2.48 -2.10 -0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CB ILE G 36 " pdb=" CA ILE G 36 " pdb=" CG1 ILE G 36 " pdb=" CG2 ILE G 36 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.24e+00 ... (remaining 26335 not shown) Planarity restraints: 13678 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 140 " 0.080 5.00e-02 4.00e+02 1.23e-01 2.42e+01 pdb=" N PRO D 141 " -0.213 5.00e-02 4.00e+02 pdb=" CA PRO D 141 " 0.067 5.00e-02 4.00e+02 pdb=" CD PRO D 141 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG b 369 " -0.021 2.00e-02 2.50e+03 4.36e-02 1.90e+01 pdb=" C ARG b 369 " 0.075 2.00e-02 2.50e+03 pdb=" O ARG b 369 " -0.029 2.00e-02 2.50e+03 pdb=" N ASP b 370 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR q 43 " -0.020 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C TYR q 43 " 0.068 2.00e-02 2.50e+03 pdb=" O TYR q 43 " -0.025 2.00e-02 2.50e+03 pdb=" N ASP q 44 " -0.023 2.00e-02 2.50e+03 ... (remaining 13675 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 482 2.48 - 3.08: 79914 3.08 - 3.69: 227556 3.69 - 4.29: 333014 4.29 - 4.90: 486300 Nonbonded interactions: 1127266 Sorted by model distance: nonbonded pdb=" O ILE E 130 " pdb=" O LYS E 131 " model vdw 1.873 3.040 nonbonded pdb=" O GLN b 195 " pdb="MG MG b 702 " model vdw 2.153 2.170 nonbonded pdb=" O GLY D 71 " pdb=" O2' G 2 7 " model vdw 2.203 2.440 nonbonded pdb=" O MET B 214 " pdb=" OG SER B 341 " model vdw 2.217 2.440 nonbonded pdb=" OG1 THR h 85 " pdb=" OP2 G 3 36 " model vdw 2.220 2.440 ... (remaining 1127261 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.21 max=1.00 mean=0.99 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: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.130 Extract box with map and model: 16.410 Check model and map are aligned: 1.450 Set scattering table: 0.870 Process input model: 426.670 Find NCS groups from input model: 2.610 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 452.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 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 : 0.006 0.084 142676 Z= 0.397 Angle : 0.910 14.962 209710 Z= 0.486 Chirality : 0.046 0.440 26338 Planarity : 0.006 0.123 13678 Dihedral : 21.808 179.868 76492 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.56 % Favored : 92.99 % Rotamer: Outliers : 0.51 % Allowed : 5.03 % Favored : 94.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 1.50 % Twisted General : 0.48 % 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: -4.28 (0.08), residues: 7123 helix: -4.17 (0.05), residues: 2413 sheet: -1.18 (0.16), residues: 937 loop : -2.32 (0.08), residues: 3773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.004 TRP b 427 HIS 0.019 0.002 HIS q 23 PHE 0.052 0.003 PHE D 253 TYR 0.032 0.003 TYR H 92 ARG 0.026 0.001 ARG q 41 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14246 Ramachandran restraints generated. 7123 Oldfield, 0 Emsley, 7123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14246 Ramachandran restraints generated. 7123 Oldfield, 0 Emsley, 7123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2165 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 2134 time to evaluate : 6.738 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: v 175 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8414 (mt-10) REVERT: v 182 ASN cc_start: 0.8629 (t0) cc_final: 0.7985 (t0) REVERT: v 191 SER cc_start: 0.8555 (m) cc_final: 0.8293 (t) REVERT: v 194 LYS cc_start: 0.8214 (tptp) cc_final: 0.7861 (tttt) REVERT: v 277 SER cc_start: 0.8821 (t) cc_final: 0.8447 (p) REVERT: v 362 ILE cc_start: 0.8242 (pt) cc_final: 0.8021 (mt) REVERT: v 367 ASP cc_start: 0.7955 (t0) cc_final: 0.7628 (t0) REVERT: A 33 ASP cc_start: 0.8661 (p0) cc_final: 0.8379 (p0) REVERT: A 119 LYS cc_start: 0.8416 (mtmt) cc_final: 0.7932 (mtmm) REVERT: A 186 PHE cc_start: 0.8813 (t80) cc_final: 0.8466 (t80) REVERT: A 204 MET cc_start: 0.8868 (mtm) cc_final: 0.8574 (mtm) REVERT: a 84 GLU cc_start: 0.8248 (tp30) cc_final: 0.7818 (mm-30) REVERT: a 86 LYS cc_start: 0.8609 (mmtm) cc_final: 0.8331 (ptpp) REVERT: B 214 MET cc_start: 0.8098 (mmm) cc_final: 0.7490 (mmm) REVERT: B 215 ILE cc_start: 0.9196 (pp) cc_final: 0.8829 (pp) REVERT: B 319 ASN cc_start: 0.8833 (m-40) cc_final: 0.8581 (m110) REVERT: B 333 LYS cc_start: 0.9047 (pttm) cc_final: 0.8760 (ptpt) REVERT: b 62 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7415 (mp0) REVERT: b 110 ARG cc_start: 0.7094 (mtm110) cc_final: 0.5277 (mmt180) REVERT: b 136 MET cc_start: 0.8420 (mtt) cc_final: 0.8097 (mtp) REVERT: b 213 TYR cc_start: 0.7912 (m-80) cc_final: 0.7583 (m-80) REVERT: b 288 ASN cc_start: 0.7433 (OUTLIER) cc_final: 0.7184 (t0) REVERT: b 394 ASN cc_start: 0.8887 (m-40) cc_final: 0.8373 (p0) REVERT: b 491 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7599 (tm-30) REVERT: b 526 LYS cc_start: 0.5125 (mmpt) cc_final: 0.4848 (mptt) REVERT: C 8 VAL cc_start: 0.9399 (t) cc_final: 0.9176 (p) REVERT: C 148 ILE cc_start: 0.8920 (mt) cc_final: 0.8529 (mp) REVERT: C 313 LEU cc_start: 0.8868 (tm) cc_final: 0.8602 (tp) REVERT: c 40 LYS cc_start: 0.9044 (mptm) cc_final: 0.8831 (mttm) REVERT: c 55 GLU cc_start: 0.7909 (tt0) cc_final: 0.7496 (tt0) REVERT: d 67 VAL cc_start: 0.9194 (t) cc_final: 0.8992 (p) REVERT: d 80 ASN cc_start: 0.7530 (t0) cc_final: 0.7289 (t0) REVERT: E 52 VAL cc_start: 0.9214 (t) cc_final: 0.9009 (p) REVERT: E 138 GLN cc_start: 0.8587 (tp40) cc_final: 0.7915 (tp40) REVERT: e 72 LYS cc_start: 0.9095 (mttm) cc_final: 0.8709 (mtpt) REVERT: e 119 VAL cc_start: 0.9262 (t) cc_final: 0.9055 (m) REVERT: f 24 ASN cc_start: 0.8884 (t0) cc_final: 0.8661 (t0) REVERT: f 70 LYS cc_start: 0.9259 (pttt) cc_final: 0.9052 (pttp) REVERT: G 173 MET cc_start: 0.8266 (mmm) cc_final: 0.7945 (mmt) REVERT: G 216 SER cc_start: 0.9227 (t) cc_final: 0.9017 (p) REVERT: G 224 ASP cc_start: 0.8802 (m-30) cc_final: 0.8477 (m-30) REVERT: g 18 ASN cc_start: 0.9016 (t0) cc_final: 0.8777 (t0) REVERT: g 29 ILE cc_start: 0.9072 (pp) cc_final: 0.8834 (pt) REVERT: g 67 LYS cc_start: 0.9262 (tptm) cc_final: 0.8667 (tptp) REVERT: g 93 PHE cc_start: 0.9206 (t80) cc_final: 0.8934 (t80) REVERT: I 16 ARG cc_start: 0.7724 (ttt180) cc_final: 0.7449 (ttm-80) REVERT: I 74 LYS cc_start: 0.8240 (mttt) cc_final: 0.7651 (mttp) REVERT: I 87 GLN cc_start: 0.8605 (tp40) cc_final: 0.7994 (tp-100) REVERT: I 124 LYS cc_start: 0.8305 (mttt) cc_final: 0.8021 (ttmm) REVERT: H 91 ARG cc_start: 0.7457 (mtp-110) cc_final: 0.6479 (ttm-80) REVERT: H 150 SER cc_start: 0.9054 (t) cc_final: 0.8823 (p) REVERT: i 81 THR cc_start: 0.9333 (t) cc_final: 0.9115 (p) REVERT: j 66 TYR cc_start: 0.8996 (t80) cc_final: 0.8537 (t80) REVERT: L 54 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8184 (tp) REVERT: L 86 THR cc_start: 0.9043 (p) cc_final: 0.8828 (t) REVERT: L 114 GLN cc_start: 0.8184 (tp40) cc_final: 0.7883 (tp-100) REVERT: L 172 LEU cc_start: 0.9414 (mt) cc_final: 0.9192 (mt) REVERT: M 77 ARG cc_start: 0.8171 (mtp85) cc_final: 0.7665 (mtt-85) REVERT: p 21 SER cc_start: 0.9354 (m) cc_final: 0.8257 (p) REVERT: p 87 ARG cc_start: 0.9107 (ttp-110) cc_final: 0.8867 (ttm170) REVERT: N 192 LYS cc_start: 0.8619 (tttm) cc_final: 0.8356 (ttmm) REVERT: u 1 MET cc_start: 0.7729 (mtm) cc_final: 0.6890 (mtp) REVERT: u 79 VAL cc_start: 0.8190 (OUTLIER) cc_final: 0.7960 (m) REVERT: u 91 LYS cc_start: 0.8800 (mttt) cc_final: 0.8364 (mmtm) REVERT: u 98 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7824 (mt-10) REVERT: u 122 ARG cc_start: 0.8052 (ttp-170) cc_final: 0.7466 (mmt90) REVERT: Q 89 ASP cc_start: 0.9056 (t0) cc_final: 0.8805 (t0) REVERT: Q 136 ASN cc_start: 0.8511 (t0) cc_final: 0.8144 (t0) REVERT: R 68 GLN cc_start: 0.9057 (tp40) cc_final: 0.8590 (tp40) REVERT: R 111 ASP cc_start: 0.7705 (m-30) cc_final: 0.7480 (m-30) REVERT: R 144 GLN cc_start: 0.8778 (mm-40) cc_final: 0.8532 (mm-40) REVERT: S 36 ILE cc_start: 0.8910 (mt) cc_final: 0.8706 (mt) REVERT: T 112 ASN cc_start: 0.9055 (m-40) cc_final: 0.8804 (m-40) REVERT: T 115 LYS cc_start: 0.9015 (mttt) cc_final: 0.8781 (mmtp) REVERT: U 88 GLN cc_start: 0.8645 (mp10) cc_final: 0.8436 (mt0) REVERT: V 23 MET cc_start: 0.8728 (ptt) cc_final: 0.8478 (ptm) REVERT: V 27 ASP cc_start: 0.8820 (p0) cc_final: 0.8535 (p0) REVERT: W 21 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7558 (pp20) REVERT: W 28 ASP cc_start: 0.7990 (m-30) cc_final: 0.7680 (t0) REVERT: W 83 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7207 (tm-30) REVERT: W 162 GLU cc_start: 0.6397 (tm-30) cc_final: 0.5959 (tm-30) REVERT: W 179 LYS cc_start: 0.4938 (mtmt) cc_final: 0.4479 (mttp) REVERT: W 186 TYR cc_start: 0.7298 (t80) cc_final: 0.7028 (t80) REVERT: W 223 ASN cc_start: 0.6315 (m110) cc_final: 0.5768 (m-40) REVERT: X 106 ASP cc_start: 0.7513 (m-30) cc_final: 0.7307 (m-30) REVERT: Y 105 VAL cc_start: 0.9007 (t) cc_final: 0.8797 (p) REVERT: y 18 LYS cc_start: 0.8930 (tptt) cc_final: 0.8699 (tptm) REVERT: y 59 ILE cc_start: 0.9296 (pt) cc_final: 0.9029 (mp) REVERT: y 169 ASP cc_start: 0.8991 (m-30) cc_final: 0.8254 (m-30) REVERT: y 209 ASP cc_start: 0.8404 (t0) cc_final: 0.7452 (t0) REVERT: z 31 GLN cc_start: 0.8413 (mm-40) cc_final: 0.8178 (mm110) REVERT: D 148 ILE cc_start: 0.8494 (mt) cc_final: 0.7926 (mt) REVERT: D 172 TYR cc_start: 0.8625 (t80) cc_final: 0.8355 (t80) REVERT: J 12 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8053 (tm) REVERT: J 38 GLU cc_start: 0.8447 (tt0) cc_final: 0.8201 (tm-30) REVERT: J 47 GLN cc_start: 0.8732 (mt0) cc_final: 0.7842 (mp-120) REVERT: J 89 TYR cc_start: 0.8132 (m-10) cc_final: 0.7906 (m-80) REVERT: J 93 ASP cc_start: 0.6826 (t0) cc_final: 0.6289 (t0) REVERT: J 101 ASN cc_start: 0.8766 (m-40) cc_final: 0.8397 (m-40) REVERT: J 132 ASN cc_start: 0.8797 (p0) cc_final: 0.8594 (p0) REVERT: o 38 LYS cc_start: 0.9291 (ttmt) cc_final: 0.9067 (ttmm) outliers start: 31 outliers final: 5 residues processed: 2152 average time/residue: 1.2520 time to fit residues: 4517.9942 Evaluate side-chains 1275 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1266 time to evaluate : 6.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain b residue 288 ASN Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain q residue 79 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 905 optimal weight: 10.0000 chunk 812 optimal weight: 9.9990 chunk 450 optimal weight: 0.9980 chunk 277 optimal weight: 2.9990 chunk 548 optimal weight: 8.9990 chunk 434 optimal weight: 0.9990 chunk 840 optimal weight: 10.0000 chunk 325 optimal weight: 5.9990 chunk 510 optimal weight: 4.9990 chunk 625 optimal weight: 10.0000 chunk 973 optimal weight: 20.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: v 203 GLN ** v 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 38 HIS A 132 ASN A 140 ASN a 64 GLN a 74 ASN a 120 ASN B 211 GLN B 293 ASN B 371 GLN b 70 ASN ** b 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 124 GLN b 155 GLN b 177 ASN b 208 HIS b 217 GLN b 288 ASN b 346 ASN b 413 ASN b 415 ASN b 470 ASN C 110 ASN C 114 ASN ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 36 GLN d 57 GLN e 52 GLN ** F 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 GLN ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 244 ASN G 38 GLN G 85 ASN ** G 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 232 HIS g 52 GLN I 36 ASN I 119 ASN H 8 GLN H 9 GLN H 157 ASN H 163 GLN h 16 GLN h 20 GLN h 34 GLN h 59 ASN i 91 ASN j 48 ASN k 67 GLN L 12 ASN L 120 GLN l 11 GLN l 20 ASN l 50 ASN M 41 GLN N 11 GLN N 37 HIS N 57 GLN N 117 ASN ** u 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 45 ASN u 110 ASN u 130 ASN ** O 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 10 HIS Q 126 GLN R 66 HIS ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 46 GLN ** S 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 122 HIS U 25 ASN U 49 ASN U 87 ASN V 47 ASN ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 22 ASN W 54 GLN W 91 GLN W 205 GLN W 232 ASN Y 66 GLN y 140 GLN y 178 GLN Z 57 HIS D 39 GLN D 45 ASN D 244 HIS J 43 GLN q 59 HIS q 90 HIS o 48 HIS Total number of N/Q/H flips: 83 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 142676 Z= 0.225 Angle : 0.652 14.787 209710 Z= 0.338 Chirality : 0.038 0.325 26338 Planarity : 0.005 0.107 13678 Dihedral : 23.152 179.734 62062 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.51 % Favored : 93.22 % Rotamer: Outliers : 3.71 % Allowed : 12.65 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 1.13 % Twisted General : 0.17 % 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: -2.77 (0.08), residues: 7123 helix: -2.00 (0.08), residues: 2530 sheet: -0.86 (0.16), residues: 946 loop : -1.95 (0.09), residues: 3647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP M 99 HIS 0.010 0.001 HIS q 20 PHE 0.022 0.002 PHE q 36 TYR 0.039 0.002 TYR H 92 ARG 0.009 0.001 ARG q 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14246 Ramachandran restraints generated. 7123 Oldfield, 0 Emsley, 7123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14246 Ramachandran restraints generated. 7123 Oldfield, 0 Emsley, 7123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1631 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 1405 time to evaluate : 6.820 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: v 163 GLN cc_start: 0.8598 (tt0) cc_final: 0.8237 (tt0) REVERT: v 164 LYS cc_start: 0.9040 (mmpt) cc_final: 0.8740 (mmtm) REVERT: v 175 GLU cc_start: 0.8414 (mt-10) cc_final: 0.7874 (mt-10) REVERT: v 194 LYS cc_start: 0.8307 (tptp) cc_final: 0.7779 (tttt) REVERT: v 201 TYR cc_start: 0.7750 (m-10) cc_final: 0.7516 (m-80) REVERT: v 278 LYS cc_start: 0.8226 (tttt) cc_final: 0.7986 (tppt) REVERT: A 69 TYR cc_start: 0.8650 (t80) cc_final: 0.8379 (t80) REVERT: A 204 MET cc_start: 0.8863 (mtm) cc_final: 0.8618 (mtm) REVERT: a 135 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7723 (tm-30) REVERT: B 214 MET cc_start: 0.7997 (mmm) cc_final: 0.7580 (mmm) REVERT: B 319 ASN cc_start: 0.8888 (m-40) cc_final: 0.8379 (m110) REVERT: B 333 LYS cc_start: 0.8922 (pttm) cc_final: 0.8576 (ptpt) REVERT: b 136 MET cc_start: 0.8532 (mtt) cc_final: 0.8201 (mtp) REVERT: b 312 VAL cc_start: 0.2599 (OUTLIER) cc_final: 0.2193 (p) REVERT: b 394 ASN cc_start: 0.8934 (m-40) cc_final: 0.8315 (p0) REVERT: C 8 VAL cc_start: 0.9303 (t) cc_final: 0.9048 (p) REVERT: C 76 ARG cc_start: 0.8908 (mpt-90) cc_final: 0.8614 (mmt90) REVERT: C 150 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8447 (tt) REVERT: C 197 ARG cc_start: 0.8540 (mtm180) cc_final: 0.8283 (mtp180) REVERT: C 313 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8512 (tp) REVERT: C 339 LEU cc_start: 0.9000 (mt) cc_final: 0.8748 (mt) REVERT: d 74 ARG cc_start: 0.8527 (ttm170) cc_final: 0.8139 (ttm170) REVERT: d 80 ASN cc_start: 0.7913 (t0) cc_final: 0.7467 (t0) REVERT: E 5 LYS cc_start: 0.8172 (tptt) cc_final: 0.7910 (tppt) REVERT: E 138 GLN cc_start: 0.8157 (tp40) cc_final: 0.7914 (tt0) REVERT: e 23 ASP cc_start: 0.8096 (p0) cc_final: 0.7669 (p0) REVERT: e 72 LYS cc_start: 0.8919 (mttm) cc_final: 0.8577 (mtpt) REVERT: e 119 VAL cc_start: 0.9317 (t) cc_final: 0.9108 (m) REVERT: F 124 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8837 (tm) REVERT: f 24 ASN cc_start: 0.8937 (t0) cc_final: 0.8625 (t0) REVERT: f 31 LYS cc_start: 0.8714 (ttmt) cc_final: 0.8481 (ttmm) REVERT: G 83 ASP cc_start: 0.8530 (p0) cc_final: 0.8292 (p0) REVERT: G 173 MET cc_start: 0.8715 (mmm) cc_final: 0.7879 (mmt) REVERT: G 224 ASP cc_start: 0.8838 (m-30) cc_final: 0.8581 (m-30) REVERT: g 93 PHE cc_start: 0.9213 (t80) cc_final: 0.8995 (t80) REVERT: I 65 LYS cc_start: 0.8398 (mttt) cc_final: 0.8073 (mtpp) REVERT: I 87 GLN cc_start: 0.8628 (tp40) cc_final: 0.7918 (tp-100) REVERT: h 68 GLN cc_start: 0.8148 (pp30) cc_final: 0.7659 (tm-30) REVERT: h 104 GLN cc_start: 0.8451 (mm-40) cc_final: 0.8067 (mp10) REVERT: j 66 TYR cc_start: 0.9116 (t80) cc_final: 0.8659 (t80) REVERT: k 12 LEU cc_start: 0.8837 (mt) cc_final: 0.8410 (mt) REVERT: L 114 GLN cc_start: 0.8189 (tp40) cc_final: 0.7600 (tp-100) REVERT: p 84 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8242 (ttp-110) REVERT: N 5 LYS cc_start: 0.8559 (tptt) cc_final: 0.8053 (tptt) REVERT: N 8 GLU cc_start: 0.8238 (tt0) cc_final: 0.7915 (tt0) REVERT: N 127 TYR cc_start: 0.8507 (m-80) cc_final: 0.8273 (m-80) REVERT: N 192 LYS cc_start: 0.8738 (tttm) cc_final: 0.8382 (ttmm) REVERT: u 3 ILE cc_start: 0.8597 (mm) cc_final: 0.8380 (mm) REVERT: u 82 ASN cc_start: 0.8475 (t0) cc_final: 0.8011 (m-40) REVERT: u 91 LYS cc_start: 0.8662 (mttt) cc_final: 0.8429 (mmtm) REVERT: P 64 ASN cc_start: 0.8943 (p0) cc_final: 0.8651 (p0) REVERT: P 87 SER cc_start: 0.9039 (m) cc_final: 0.8677 (t) REVERT: P 154 GLU cc_start: 0.7334 (mm-30) cc_final: 0.6771 (mp0) REVERT: Q 136 ASN cc_start: 0.8612 (t0) cc_final: 0.8085 (t0) REVERT: R 68 GLN cc_start: 0.9048 (tp40) cc_final: 0.8501 (tp40) REVERT: T 115 LYS cc_start: 0.8844 (mttt) cc_final: 0.8578 (mmtp) REVERT: U 88 GLN cc_start: 0.8881 (mp10) cc_final: 0.8346 (mt0) REVERT: V 128 ARG cc_start: 0.8476 (mmt90) cc_final: 0.8204 (mmt90) REVERT: W 17 LYS cc_start: 0.8016 (mttt) cc_final: 0.7660 (mttm) REVERT: W 21 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7581 (pp20) REVERT: W 28 ASP cc_start: 0.8014 (m-30) cc_final: 0.7738 (t0) REVERT: W 57 ARG cc_start: 0.7035 (mtm-85) cc_final: 0.6623 (ttm-80) REVERT: W 83 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7236 (tm-30) REVERT: W 149 ILE cc_start: 0.4389 (OUTLIER) cc_final: 0.4178 (pp) REVERT: W 162 GLU cc_start: 0.6311 (tm-30) cc_final: 0.6074 (tm-30) REVERT: W 179 LYS cc_start: 0.4934 (mtmt) cc_final: 0.4552 (mttp) REVERT: W 186 TYR cc_start: 0.7342 (t80) cc_final: 0.7070 (t80) REVERT: W 223 ASN cc_start: 0.6023 (m110) cc_final: 0.5658 (m-40) REVERT: X 133 LEU cc_start: 0.8813 (mm) cc_final: 0.8355 (mm) REVERT: Y 11 ASP cc_start: 0.8649 (t0) cc_final: 0.8426 (t0) REVERT: y 18 LYS cc_start: 0.9020 (tptt) cc_final: 0.8778 (tptm) REVERT: y 34 PHE cc_start: 0.9220 (t80) cc_final: 0.8965 (t80) REVERT: y 59 ILE cc_start: 0.9309 (pt) cc_final: 0.9088 (mp) REVERT: y 80 GLU cc_start: 0.7354 (mt-10) cc_final: 0.7029 (mp0) REVERT: y 169 ASP cc_start: 0.8882 (m-30) cc_final: 0.8335 (m-30) REVERT: y 209 ASP cc_start: 0.8070 (t0) cc_final: 0.7754 (t0) REVERT: Z 106 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.8040 (tm-30) REVERT: Z 108 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8492 (mm-30) REVERT: Z 121 ARG cc_start: 0.8418 (tpp80) cc_final: 0.8157 (tpp-160) REVERT: z 27 ASP cc_start: 0.7698 (m-30) cc_final: 0.7437 (m-30) REVERT: D 57 ASN cc_start: 0.8028 (m110) cc_final: 0.7828 (m110) REVERT: J 30 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8695 (tm) REVERT: J 47 GLN cc_start: 0.8662 (mt0) cc_final: 0.8000 (mp10) REVERT: J 93 ASP cc_start: 0.6753 (t0) cc_final: 0.6452 (t0) REVERT: J 101 ASN cc_start: 0.8813 (m-40) cc_final: 0.8501 (m-40) REVERT: J 132 ASN cc_start: 0.8835 (p0) cc_final: 0.8134 (p0) REVERT: J 172 LEU cc_start: 0.6554 (mt) cc_final: 0.6075 (mt) REVERT: o 19 ASN cc_start: 0.8533 (m-40) cc_final: 0.8205 (m110) outliers start: 226 outliers final: 125 residues processed: 1530 average time/residue: 1.1592 time to fit residues: 3098.8129 Evaluate side-chains 1353 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 1220 time to evaluate : 6.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain v residue 170 THR Chi-restraints excluded: chain v residue 255 ASP Chi-restraints excluded: chain v residue 279 ILE Chi-restraints excluded: chain v residue 328 ILE Chi-restraints excluded: chain v residue 348 VAL Chi-restraints excluded: chain v residue 363 CYS Chi-restraints excluded: chain v residue 392 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 130 VAL Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain b residue 250 VAL Chi-restraints excluded: chain b residue 312 VAL Chi-restraints excluded: chain b residue 435 ILE Chi-restraints excluded: chain b residue 524 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain c residue 18 ILE Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 63 SER Chi-restraints excluded: chain d residue 20 LEU Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain e residue 4 LEU Chi-restraints excluded: chain e residue 14 THR Chi-restraints excluded: chain e residue 51 SER Chi-restraints excluded: chain e residue 86 THR Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 74 THR Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain G residue 219 ASP Chi-restraints excluded: chain G residue 246 MET Chi-restraints excluded: chain g residue 55 SER Chi-restraints excluded: chain g residue 79 SER Chi-restraints excluded: chain I residue 60 THR Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain h residue 37 SER Chi-restraints excluded: chain h residue 47 VAL Chi-restraints excluded: chain h residue 98 SER Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 61 ILE Chi-restraints excluded: chain i residue 93 ILE Chi-restraints excluded: chain j residue 11 ARG Chi-restraints excluded: chain j residue 33 THR Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain L residue 9 ILE Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain l residue 32 ASN Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain M residue 62 GLN Chi-restraints excluded: chain M residue 74 ARG Chi-restraints excluded: chain M residue 82 SER Chi-restraints excluded: chain M residue 91 CYS Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain p residue 84 ARG Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 171 SER Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain u residue 9 CYS Chi-restraints excluded: chain u residue 32 CYS Chi-restraints excluded: chain u residue 34 SER Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 77 SER Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 86 THR Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain X residue 75 LYS Chi-restraints excluded: chain X residue 87 SER Chi-restraints excluded: chain Y residue 7 ASP Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 90 VAL Chi-restraints excluded: chain y residue 5 THR Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 97 SER Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain Z residue 106 GLN Chi-restraints excluded: chain z residue 41 LEU Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 41 SER Chi-restraints excluded: chain J residue 43 GLN Chi-restraints excluded: chain J residue 85 LYS Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 79 THR Chi-restraints excluded: chain o residue 8 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 541 optimal weight: 1.9990 chunk 302 optimal weight: 0.3980 chunk 810 optimal weight: 10.0000 chunk 662 optimal weight: 3.9990 chunk 268 optimal weight: 7.9990 chunk 975 optimal weight: 10.0000 chunk 1053 optimal weight: 10.0000 chunk 868 optimal weight: 10.0000 chunk 967 optimal weight: 10.0000 chunk 332 optimal weight: 1.9990 chunk 782 optimal weight: 10.0000 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** v 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 64 GLN a 120 ASN B 211 GLN ** b 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN C 260 GLN C 320 ASN d 57 GLN F 25 GLN ** F 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 77 ASN ** G 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 145 ASN G 232 HIS g 108 GLN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 9 GLN H 183 HIS h 108 GLN i 91 ASN k 67 GLN l 11 GLN l 50 ASN M 105 GLN u 37 HIS ** O 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 137 ASN Q 45 ASN R 134 HIS ** S 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 65 ASN S 157 GLN T 112 ASN U 25 ASN V 47 ASN ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 205 GLN y 83 HIS ** y 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 36 HIS Z 127 ASN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 ASN J 62 ASN ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 165 GLN o 12 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 142676 Z= 0.216 Angle : 0.597 15.604 209710 Z= 0.308 Chirality : 0.036 0.412 26338 Planarity : 0.005 0.104 13678 Dihedral : 23.011 179.774 62057 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.94 % Favored : 92.91 % Rotamer: Outliers : 4.68 % Allowed : 15.03 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 1.13 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.09), residues: 7123 helix: -0.75 (0.10), residues: 2557 sheet: -0.66 (0.16), residues: 955 loop : -1.75 (0.09), residues: 3611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP M 99 HIS 0.008 0.001 HIS q 20 PHE 0.020 0.002 PHE q 36 TYR 0.035 0.002 TYR F 176 ARG 0.010 0.001 ARG I 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14246 Ramachandran restraints generated. 7123 Oldfield, 0 Emsley, 7123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14246 Ramachandran restraints generated. 7123 Oldfield, 0 Emsley, 7123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1601 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 1316 time to evaluate : 6.554 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: v 156 ARG cc_start: 0.7191 (mmm160) cc_final: 0.6140 (tpt-90) REVERT: v 163 GLN cc_start: 0.8631 (tt0) cc_final: 0.8163 (tt0) REVERT: v 164 LYS cc_start: 0.9012 (mmpt) cc_final: 0.8727 (mmtm) REVERT: v 194 LYS cc_start: 0.8371 (tptp) cc_final: 0.7816 (ttmt) REVERT: v 278 LYS cc_start: 0.8459 (tttt) cc_final: 0.8238 (tppt) REVERT: v 348 VAL cc_start: 0.8948 (OUTLIER) cc_final: 0.8735 (p) REVERT: v 378 ASN cc_start: -0.0480 (OUTLIER) cc_final: -0.1132 (p0) REVERT: A 204 MET cc_start: 0.8848 (mtm) cc_final: 0.8594 (mtm) REVERT: a 120 ASN cc_start: 0.8674 (OUTLIER) cc_final: 0.8333 (t0) REVERT: a 135 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7716 (tm-30) REVERT: B 319 ASN cc_start: 0.8883 (m-40) cc_final: 0.8475 (m-40) REVERT: B 325 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8848 (ttmt) REVERT: B 333 LYS cc_start: 0.8941 (pttm) cc_final: 0.8448 (ptpt) REVERT: b 106 GLU cc_start: 0.7514 (tp30) cc_final: 0.7286 (tp30) REVERT: b 136 MET cc_start: 0.8389 (mtt) cc_final: 0.8166 (mtp) REVERT: b 394 ASN cc_start: 0.8890 (m-40) cc_final: 0.8320 (p0) REVERT: b 495 TRP cc_start: 0.8362 (t60) cc_final: 0.8045 (t60) REVERT: b 548 LYS cc_start: 0.6257 (mmtm) cc_final: 0.5575 (ptmt) REVERT: C 8 VAL cc_start: 0.9326 (t) cc_final: 0.9053 (p) REVERT: C 63 GLU cc_start: 0.7395 (pm20) cc_final: 0.7033 (pm20) REVERT: C 76 ARG cc_start: 0.8814 (mpt-90) cc_final: 0.8498 (mmt90) REVERT: C 150 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8515 (tt) REVERT: C 313 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8524 (tp) REVERT: c 99 ASP cc_start: 0.7538 (p0) cc_final: 0.7321 (t0) REVERT: d 80 ASN cc_start: 0.8102 (t0) cc_final: 0.7795 (t0) REVERT: E 5 LYS cc_start: 0.8114 (tptt) cc_final: 0.7796 (tppt) REVERT: E 138 GLN cc_start: 0.8162 (tp40) cc_final: 0.7837 (tt0) REVERT: e 23 ASP cc_start: 0.8211 (p0) cc_final: 0.7826 (p0) REVERT: e 72 LYS cc_start: 0.8873 (mttm) cc_final: 0.8624 (mtpt) REVERT: e 119 VAL cc_start: 0.9336 (t) cc_final: 0.9132 (m) REVERT: F 124 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8890 (tm) REVERT: f 24 ASN cc_start: 0.9012 (t0) cc_final: 0.8707 (t0) REVERT: G 83 ASP cc_start: 0.8523 (p0) cc_final: 0.8280 (p0) REVERT: G 202 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7419 (mm-30) REVERT: G 224 ASP cc_start: 0.8864 (m-30) cc_final: 0.8631 (m-30) REVERT: I 58 MET cc_start: 0.8783 (mmt) cc_final: 0.8182 (mmt) REVERT: I 65 LYS cc_start: 0.8440 (mttt) cc_final: 0.8167 (mtpt) REVERT: I 87 GLN cc_start: 0.8614 (tp40) cc_final: 0.7944 (tp-100) REVERT: H 8 GLN cc_start: 0.8586 (mm110) cc_final: 0.8380 (mm110) REVERT: H 143 GLU cc_start: 0.8124 (tp30) cc_final: 0.7880 (mm-30) REVERT: H 162 GLN cc_start: 0.8463 (tm-30) cc_final: 0.8116 (tm-30) REVERT: h 104 GLN cc_start: 0.8401 (mm-40) cc_final: 0.8049 (mp10) REVERT: j 66 TYR cc_start: 0.9183 (t80) cc_final: 0.8670 (t80) REVERT: L 110 ASP cc_start: 0.8009 (m-30) cc_final: 0.7781 (m-30) REVERT: L 114 GLN cc_start: 0.8139 (tp40) cc_final: 0.7444 (tp-100) REVERT: p 32 GLN cc_start: 0.8930 (mt0) cc_final: 0.8720 (mt0) REVERT: p 84 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.8348 (ttp-170) REVERT: p 86 LEU cc_start: 0.9355 (mt) cc_final: 0.9118 (mt) REVERT: N 5 LYS cc_start: 0.8551 (tptt) cc_final: 0.8033 (tptt) REVERT: N 192 LYS cc_start: 0.8801 (tttm) cc_final: 0.8490 (ttmt) REVERT: u 82 ASN cc_start: 0.8446 (t0) cc_final: 0.8079 (m-40) REVERT: u 91 LYS cc_start: 0.8701 (mttt) cc_final: 0.8485 (mmtm) REVERT: O 100 GLU cc_start: 0.7194 (tp30) cc_final: 0.6854 (tp30) REVERT: O 150 GLU cc_start: 0.7955 (tp30) cc_final: 0.7741 (tp30) REVERT: P 64 ASN cc_start: 0.8818 (p0) cc_final: 0.8536 (p0) REVERT: P 108 ASP cc_start: 0.7713 (p0) cc_final: 0.7436 (p0) REVERT: P 154 GLU cc_start: 0.7289 (mm-30) cc_final: 0.6829 (mp0) REVERT: Q 17 THR cc_start: 0.8876 (m) cc_final: 0.8493 (t) REVERT: Q 136 ASN cc_start: 0.8712 (t0) cc_final: 0.8219 (t0) REVERT: R 68 GLN cc_start: 0.9088 (tp40) cc_final: 0.8548 (tp40) REVERT: R 92 GLN cc_start: 0.8798 (tt0) cc_final: 0.8409 (tt0) REVERT: U 41 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8968 (mp) REVERT: U 44 GLU cc_start: 0.7670 (pp20) cc_final: 0.7439 (pp20) REVERT: U 88 GLN cc_start: 0.8626 (mp10) cc_final: 0.8146 (mt0) REVERT: W 17 LYS cc_start: 0.8159 (mttt) cc_final: 0.7809 (mttp) REVERT: W 21 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7566 (pp20) REVERT: W 22 ASN cc_start: 0.7893 (t0) cc_final: 0.7481 (t0) REVERT: W 28 ASP cc_start: 0.7944 (m-30) cc_final: 0.7718 (t0) REVERT: W 57 ARG cc_start: 0.6933 (mtm-85) cc_final: 0.6732 (ttm-80) REVERT: W 67 MET cc_start: 0.7138 (mmm) cc_final: 0.6517 (mmm) REVERT: W 83 GLU cc_start: 0.8416 (mt-10) cc_final: 0.7540 (tm-30) REVERT: W 149 ILE cc_start: 0.5017 (OUTLIER) cc_final: 0.4792 (pp) REVERT: W 161 LEU cc_start: 0.5779 (OUTLIER) cc_final: 0.5428 (mt) REVERT: W 162 GLU cc_start: 0.6550 (tm-30) cc_final: 0.6128 (tm-30) REVERT: W 179 LYS cc_start: 0.4756 (mtmt) cc_final: 0.4449 (mttp) REVERT: W 186 TYR cc_start: 0.7462 (t80) cc_final: 0.7255 (t80) REVERT: W 223 ASN cc_start: 0.6063 (m110) cc_final: 0.5704 (m-40) REVERT: Y 11 ASP cc_start: 0.8683 (t0) cc_final: 0.8479 (t0) REVERT: y 18 LYS cc_start: 0.9032 (tptt) cc_final: 0.8756 (tptm) REVERT: y 34 PHE cc_start: 0.9221 (t80) cc_final: 0.8950 (t80) REVERT: y 59 ILE cc_start: 0.9278 (pt) cc_final: 0.9057 (mp) REVERT: y 80 GLU cc_start: 0.7286 (mt-10) cc_final: 0.6989 (mp0) REVERT: y 169 ASP cc_start: 0.8919 (m-30) cc_final: 0.8236 (m-30) REVERT: y 173 LEU cc_start: 0.9456 (tt) cc_final: 0.9111 (mt) REVERT: y 209 ASP cc_start: 0.8223 (t0) cc_final: 0.7866 (t0) REVERT: Z 106 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7795 (tm-30) REVERT: Z 121 ARG cc_start: 0.8470 (tpp80) cc_final: 0.8206 (tpp-160) REVERT: Z 134 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8756 (tp) REVERT: D 57 ASN cc_start: 0.7975 (m-40) cc_final: 0.7639 (m110) REVERT: D 72 ASP cc_start: 0.7492 (m-30) cc_final: 0.7250 (m-30) REVERT: J 30 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8671 (tm) REVERT: J 47 GLN cc_start: 0.8648 (mt0) cc_final: 0.7996 (mp10) REVERT: J 89 TYR cc_start: 0.8098 (m-80) cc_final: 0.7881 (m-80) REVERT: J 101 ASN cc_start: 0.8735 (m-40) cc_final: 0.8341 (m110) REVERT: q 47 GLN cc_start: -0.1500 (OUTLIER) cc_final: -0.2123 (tt0) REVERT: o 19 ASN cc_start: 0.8465 (m-40) cc_final: 0.8150 (m110) REVERT: o 40 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8423 (ttp-110) outliers start: 285 outliers final: 170 residues processed: 1471 average time/residue: 1.1492 time to fit residues: 2976.3611 Evaluate side-chains 1369 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 1183 time to evaluate : 6.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain v residue 170 THR Chi-restraints excluded: chain v residue 255 ASP Chi-restraints excluded: chain v residue 279 ILE Chi-restraints excluded: chain v residue 348 VAL Chi-restraints excluded: chain v residue 363 CYS Chi-restraints excluded: chain v residue 378 ASN Chi-restraints excluded: chain v residue 392 VAL Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain a residue 64 GLN Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 120 ASN Chi-restraints excluded: chain a residue 130 VAL Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain b residue 15 ASN Chi-restraints excluded: chain b residue 250 VAL Chi-restraints excluded: chain b residue 434 GLU Chi-restraints excluded: chain b residue 435 ILE Chi-restraints excluded: chain b residue 445 LEU Chi-restraints excluded: chain b residue 535 MET Chi-restraints excluded: chain b residue 634 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain c residue 10 ILE Chi-restraints excluded: chain c residue 18 ILE Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 63 SER Chi-restraints excluded: chain d residue 20 LEU Chi-restraints excluded: chain d residue 104 LEU Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain e residue 4 LEU Chi-restraints excluded: chain e residue 14 THR Chi-restraints excluded: chain e residue 51 SER Chi-restraints excluded: chain e residue 86 THR Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain e residue 115 LEU Chi-restraints excluded: chain e residue 126 LEU Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 74 THR Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 219 ASP Chi-restraints excluded: chain G residue 246 MET Chi-restraints excluded: chain g residue 15 THR Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 49 SER Chi-restraints excluded: chain g residue 55 SER Chi-restraints excluded: chain g residue 71 THR Chi-restraints excluded: chain g residue 79 SER Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 60 THR Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 92 TYR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain H residue 183 HIS Chi-restraints excluded: chain h residue 37 SER Chi-restraints excluded: chain h residue 76 GLN Chi-restraints excluded: chain h residue 98 SER Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 42 SER Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 61 ILE Chi-restraints excluded: chain i residue 93 ILE Chi-restraints excluded: chain j residue 11 ARG Chi-restraints excluded: chain j residue 17 THR Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain k residue 50 SER Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 182 ILE Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain M residue 91 CYS Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain p residue 84 ARG Chi-restraints excluded: chain p residue 89 MET Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain u residue 9 CYS Chi-restraints excluded: chain u residue 32 CYS Chi-restraints excluded: chain u residue 34 SER Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 89 SER Chi-restraints excluded: chain O residue 188 SER Chi-restraints excluded: chain P residue 75 GLU Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 141 SER Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 71 LEU Chi-restraints excluded: chain Q residue 86 THR Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 150 VAL Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain S residue 49 HIS Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain T residue 122 GLN Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain U residue 41 ILE Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain W residue 53 LEU Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain W residue 161 LEU Chi-restraints excluded: chain W residue 222 ASP Chi-restraints excluded: chain X residue 67 ILE Chi-restraints excluded: chain X residue 75 LYS Chi-restraints excluded: chain X residue 87 SER Chi-restraints excluded: chain X residue 129 ASP Chi-restraints excluded: chain Y residue 7 ASP Chi-restraints excluded: chain Y residue 76 LEU Chi-restraints excluded: chain Y residue 90 VAL Chi-restraints excluded: chain y residue 5 THR Chi-restraints excluded: chain y residue 177 LEU Chi-restraints excluded: chain y residue 201 ASP Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 97 SER Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain Z residue 106 GLN Chi-restraints excluded: chain Z residue 132 SER Chi-restraints excluded: chain Z residue 134 LEU Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 41 SER Chi-restraints excluded: chain J residue 52 TYR Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 115 LYS Chi-restraints excluded: chain q residue 47 GLN Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 79 THR Chi-restraints excluded: chain o residue 40 ARG Chi-restraints excluded: chain o residue 47 LEU Chi-restraints excluded: chain o residue 52 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 963 optimal weight: 10.0000 chunk 733 optimal weight: 10.0000 chunk 506 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 465 optimal weight: 9.9990 chunk 654 optimal weight: 4.9990 chunk 978 optimal weight: 10.0000 chunk 1036 optimal weight: 10.0000 chunk 511 optimal weight: 10.0000 chunk 927 optimal weight: 10.0000 chunk 279 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** v 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 79 ASN A 132 ASN ** a 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 GLN B 256 HIS d 57 GLN ** F 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 232 HIS ** g 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 20 GLN j 48 ASN l 50 ASN M 105 GLN ** O 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 137 ASN S 142 GLN T 112 ASN T 127 GLN ** U 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 47 ASN ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 ASN ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 165 GLN ** q 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 48 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 142676 Z= 0.391 Angle : 0.703 15.140 209710 Z= 0.357 Chirality : 0.040 0.344 26338 Planarity : 0.005 0.101 13678 Dihedral : 23.018 179.738 62057 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.88 % Favored : 91.93 % Rotamer: Outliers : 5.62 % Allowed : 15.72 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 1.13 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.09), residues: 7123 helix: -0.40 (0.10), residues: 2547 sheet: -0.75 (0.16), residues: 936 loop : -1.73 (0.10), residues: 3640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP M 99 HIS 0.022 0.002 HIS H 183 PHE 0.026 0.002 PHE q 36 TYR 0.029 0.002 TYR Z 49 ARG 0.009 0.001 ARG B 10 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14246 Ramachandran restraints generated. 7123 Oldfield, 0 Emsley, 7123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14246 Ramachandran restraints generated. 7123 Oldfield, 0 Emsley, 7123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1524 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 342 poor density : 1182 time to evaluate : 6.741 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: v 163 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8361 (tt0) REVERT: v 164 LYS cc_start: 0.9001 (mmpt) cc_final: 0.8620 (mmtm) REVERT: v 175 GLU cc_start: 0.8381 (mt-10) cc_final: 0.7788 (mt-10) REVERT: v 247 GLU cc_start: 0.7576 (tt0) cc_final: 0.7088 (tt0) REVERT: v 278 LYS cc_start: 0.8651 (tttt) cc_final: 0.8418 (tppt) REVERT: v 348 VAL cc_start: 0.8942 (OUTLIER) cc_final: 0.8723 (p) REVERT: v 378 ASN cc_start: -0.0099 (OUTLIER) cc_final: -0.0433 (p0) REVERT: A 48 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8813 (mp) REVERT: A 144 ASN cc_start: 0.8075 (m110) cc_final: 0.7406 (p0) REVERT: A 194 ASN cc_start: 0.9226 (t0) cc_final: 0.8692 (t0) REVERT: A 204 MET cc_start: 0.8906 (mtm) cc_final: 0.8611 (mtm) REVERT: a 135 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7813 (tm-30) REVERT: B 17 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8808 (mp) REVERT: B 171 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9105 (mp) REVERT: B 255 TRP cc_start: 0.8543 (t60) cc_final: 0.8240 (t60) REVERT: B 325 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8785 (ttmt) REVERT: b 59 GLU cc_start: 0.8691 (tt0) cc_final: 0.8341 (tt0) REVERT: b 62 GLU cc_start: 0.7611 (mp0) cc_final: 0.6381 (tp30) REVERT: b 136 MET cc_start: 0.8511 (mtt) cc_final: 0.8229 (mtp) REVERT: b 213 TYR cc_start: 0.7730 (m-80) cc_final: 0.7467 (m-80) REVERT: b 254 MET cc_start: 0.6271 (tpp) cc_final: 0.5957 (tpt) REVERT: b 336 CYS cc_start: 0.8239 (m) cc_final: 0.7910 (m) REVERT: b 394 ASN cc_start: 0.8904 (m-40) cc_final: 0.8280 (p0) REVERT: b 395 ARG cc_start: 0.6835 (OUTLIER) cc_final: 0.5848 (pmt100) REVERT: b 595 ASP cc_start: 0.6089 (OUTLIER) cc_final: 0.5502 (p0) REVERT: b 605 MET cc_start: 0.7904 (mtt) cc_final: 0.7679 (mtp) REVERT: b 608 MET cc_start: 0.6190 (mmt) cc_final: 0.5847 (mmt) REVERT: C 8 VAL cc_start: 0.9367 (t) cc_final: 0.9090 (p) REVERT: C 63 GLU cc_start: 0.7596 (pm20) cc_final: 0.6943 (pm20) REVERT: C 99 MET cc_start: 0.8902 (ptm) cc_final: 0.8695 (ptm) REVERT: C 150 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8524 (tt) REVERT: C 313 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8429 (tp) REVERT: c 100 ILE cc_start: 0.9219 (OUTLIER) cc_final: 0.8920 (tt) REVERT: d 80 ASN cc_start: 0.8135 (t0) cc_final: 0.7813 (t0) REVERT: E 5 LYS cc_start: 0.8180 (tptt) cc_final: 0.7771 (tppt) REVERT: E 138 GLN cc_start: 0.8231 (tp40) cc_final: 0.7979 (tt0) REVERT: e 19 ARG cc_start: 0.9318 (OUTLIER) cc_final: 0.9079 (ttt180) REVERT: e 23 ASP cc_start: 0.8324 (p0) cc_final: 0.7890 (p0) REVERT: e 72 LYS cc_start: 0.8870 (mttm) cc_final: 0.8646 (mtpt) REVERT: F 53 LYS cc_start: 0.8717 (tptt) cc_final: 0.8192 (mtmm) REVERT: F 54 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8300 (tt0) REVERT: F 74 SER cc_start: 0.8730 (m) cc_final: 0.7937 (p) REVERT: F 124 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8863 (tm) REVERT: F 233 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7727 (mt-10) REVERT: f 24 ASN cc_start: 0.9073 (t0) cc_final: 0.8707 (t0) REVERT: G 38 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.7980 (pt0) REVERT: G 79 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8273 (pt0) REVERT: G 83 ASP cc_start: 0.8502 (p0) cc_final: 0.8270 (p0) REVERT: G 219 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8289 (p0) REVERT: G 224 ASP cc_start: 0.8923 (m-30) cc_final: 0.8715 (m-30) REVERT: g 18 ASN cc_start: 0.9188 (t0) cc_final: 0.8881 (t0) REVERT: I 58 MET cc_start: 0.8667 (mmt) cc_final: 0.8120 (mmt) REVERT: I 65 LYS cc_start: 0.8505 (mttt) cc_final: 0.8217 (mttt) REVERT: I 87 GLN cc_start: 0.8663 (tp40) cc_final: 0.8008 (tp-100) REVERT: H 171 ASP cc_start: 0.8167 (OUTLIER) cc_final: 0.7210 (t70) REVERT: h 20 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8116 (tp-100) REVERT: h 104 GLN cc_start: 0.8361 (mm-40) cc_final: 0.7996 (mp10) REVERT: L 114 GLN cc_start: 0.8252 (tp40) cc_final: 0.7653 (tp-100) REVERT: L 161 ASP cc_start: 0.7072 (m-30) cc_final: 0.6820 (m-30) REVERT: p 84 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8332 (ttp-110) REVERT: N 5 LYS cc_start: 0.8495 (tptt) cc_final: 0.8256 (tptt) REVERT: N 192 LYS cc_start: 0.8905 (tttm) cc_final: 0.8607 (ttmt) REVERT: u 82 ASN cc_start: 0.8441 (t0) cc_final: 0.8188 (m-40) REVERT: O 150 GLU cc_start: 0.8074 (tp30) cc_final: 0.7856 (tp30) REVERT: P 137 ASN cc_start: 0.8884 (OUTLIER) cc_final: 0.8628 (m110) REVERT: P 154 GLU cc_start: 0.7280 (mm-30) cc_final: 0.6910 (mp0) REVERT: Q 136 ASN cc_start: 0.8814 (t0) cc_final: 0.8251 (t0) REVERT: R 52 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8260 (ttmp) REVERT: R 68 GLN cc_start: 0.9186 (tp40) cc_final: 0.8639 (tp40) REVERT: T 112 ASN cc_start: 0.9042 (m-40) cc_final: 0.8681 (m110) REVERT: U 33 TYR cc_start: 0.9113 (t80) cc_final: 0.8828 (t80) REVERT: U 44 GLU cc_start: 0.7878 (pp20) cc_final: 0.6932 (pp20) REVERT: U 88 GLN cc_start: 0.8710 (mp10) cc_final: 0.8309 (mt0) REVERT: W 17 LYS cc_start: 0.8173 (mttt) cc_final: 0.7848 (mttm) REVERT: W 21 GLU cc_start: 0.8404 (mm-30) cc_final: 0.7539 (pp20) REVERT: W 22 ASN cc_start: 0.7982 (t0) cc_final: 0.7452 (t0) REVERT: W 41 TRP cc_start: 0.6169 (m100) cc_final: 0.5526 (m100) REVERT: W 57 ARG cc_start: 0.6853 (mtm-85) cc_final: 0.6566 (ttm-80) REVERT: W 67 MET cc_start: 0.7445 (mmm) cc_final: 0.6717 (mmm) REVERT: W 149 ILE cc_start: 0.5100 (OUTLIER) cc_final: 0.4872 (pp) REVERT: W 161 LEU cc_start: 0.5934 (OUTLIER) cc_final: 0.5596 (mt) REVERT: W 162 GLU cc_start: 0.6497 (tm-30) cc_final: 0.5914 (tm-30) REVERT: W 179 LYS cc_start: 0.4701 (mtmt) cc_final: 0.4358 (mttp) REVERT: W 223 ASN cc_start: 0.6620 (m110) cc_final: 0.6252 (m-40) REVERT: X 113 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9113 (pp) REVERT: X 115 ARG cc_start: 0.9398 (OUTLIER) cc_final: 0.9158 (mtm180) REVERT: y 18 LYS cc_start: 0.9064 (tptt) cc_final: 0.8773 (tptm) REVERT: y 34 PHE cc_start: 0.9317 (t80) cc_final: 0.9071 (t80) REVERT: y 39 GLU cc_start: 0.8206 (tt0) cc_final: 0.7713 (tt0) REVERT: y 146 ILE cc_start: 0.9257 (tp) cc_final: 0.8835 (tp) REVERT: y 173 LEU cc_start: 0.9468 (tt) cc_final: 0.9144 (mt) REVERT: y 209 ASP cc_start: 0.8230 (t0) cc_final: 0.7985 (t0) REVERT: Z 106 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7717 (tm-30) REVERT: Z 121 ARG cc_start: 0.8558 (tpp80) cc_final: 0.8261 (tpp-160) REVERT: Z 134 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8753 (tp) REVERT: J 30 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8682 (tm) REVERT: J 47 GLN cc_start: 0.8648 (mt0) cc_final: 0.8033 (mp10) REVERT: J 65 ILE cc_start: 0.7924 (tp) cc_final: 0.7631 (tt) REVERT: J 101 ASN cc_start: 0.8877 (m-40) cc_final: 0.8539 (m110) REVERT: q 9 LYS cc_start: 0.3159 (OUTLIER) cc_final: 0.1869 (tttm) REVERT: q 47 GLN cc_start: -0.0797 (OUTLIER) cc_final: -0.1778 (tt0) REVERT: o 19 ASN cc_start: 0.8547 (m-40) cc_final: 0.8219 (m110) REVERT: o 40 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8567 (ttp-110) outliers start: 342 outliers final: 247 residues processed: 1389 average time/residue: 1.1189 time to fit residues: 2737.1063 Evaluate side-chains 1399 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 279 poor density : 1120 time to evaluate : 6.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain v residue 163 GLN Chi-restraints excluded: chain v residue 170 THR Chi-restraints excluded: chain v residue 255 ASP Chi-restraints excluded: chain v residue 279 ILE Chi-restraints excluded: chain v residue 328 ILE Chi-restraints excluded: chain v residue 348 VAL Chi-restraints excluded: chain v residue 362 ILE Chi-restraints excluded: chain v residue 363 CYS Chi-restraints excluded: chain v residue 378 ASN Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain a residue 70 LYS Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 130 VAL Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain b residue 15 ASN Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 164 ASP Chi-restraints excluded: chain b residue 186 CYS Chi-restraints excluded: chain b residue 250 VAL Chi-restraints excluded: chain b residue 312 VAL Chi-restraints excluded: chain b residue 395 ARG Chi-restraints excluded: chain b residue 416 LEU Chi-restraints excluded: chain b residue 434 GLU Chi-restraints excluded: chain b residue 435 ILE Chi-restraints excluded: chain b residue 440 ASN Chi-restraints excluded: chain b residue 445 LEU Chi-restraints excluded: chain b residue 502 THR Chi-restraints excluded: chain b residue 524 LEU Chi-restraints excluded: chain b residue 595 ASP Chi-restraints excluded: chain b residue 634 LEU Chi-restraints excluded: chain b residue 644 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain c residue 11 ASN Chi-restraints excluded: chain c residue 18 ILE Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 63 SER Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain d residue 20 LEU Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 87 ASN Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 104 LEU Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain e residue 4 LEU Chi-restraints excluded: chain e residue 14 THR Chi-restraints excluded: chain e residue 19 ARG Chi-restraints excluded: chain e residue 51 SER Chi-restraints excluded: chain e residue 86 THR Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain e residue 115 LEU Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 31 LYS Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 57 LYS Chi-restraints excluded: chain f residue 74 THR Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 219 ASP Chi-restraints excluded: chain G residue 246 MET Chi-restraints excluded: chain g residue 15 THR Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 29 ILE Chi-restraints excluded: chain g residue 49 SER Chi-restraints excluded: chain g residue 55 SER Chi-restraints excluded: chain g residue 66 SER Chi-restraints excluded: chain g residue 71 THR Chi-restraints excluded: chain g residue 79 SER Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 60 THR Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 92 TYR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain H residue 183 HIS Chi-restraints excluded: chain h residue 11 THR Chi-restraints excluded: chain h residue 20 GLN Chi-restraints excluded: chain h residue 37 SER Chi-restraints excluded: chain h residue 47 VAL Chi-restraints excluded: chain h residue 76 GLN Chi-restraints excluded: chain h residue 98 SER Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 42 SER Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 61 ILE Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain i residue 93 ILE Chi-restraints excluded: chain j residue 7 SER Chi-restraints excluded: chain j residue 11 ARG Chi-restraints excluded: chain j residue 33 THR Chi-restraints excluded: chain j residue 43 LYS Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 50 SER Chi-restraints excluded: chain L residue 9 ILE Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 152 THR Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain l residue 32 ASN Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 62 GLN Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 82 SER Chi-restraints excluded: chain M residue 91 CYS Chi-restraints excluded: chain p residue 10 ILE Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain p residue 59 CYS Chi-restraints excluded: chain p residue 84 ARG Chi-restraints excluded: chain p residue 89 MET Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain u residue 9 CYS Chi-restraints excluded: chain u residue 32 CYS Chi-restraints excluded: chain u residue 34 SER Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain u residue 145 LEU Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 89 SER Chi-restraints excluded: chain O residue 124 LEU Chi-restraints excluded: chain O residue 143 THR Chi-restraints excluded: chain O residue 151 ASP Chi-restraints excluded: chain O residue 188 SER Chi-restraints excluded: chain O residue 189 ASP Chi-restraints excluded: chain P residue 75 GLU Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 137 ASN Chi-restraints excluded: chain P residue 166 VAL Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 57 ILE Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 71 LEU Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 86 THR Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 137 THR Chi-restraints excluded: chain Q residue 150 VAL Chi-restraints excluded: chain R residue 52 LYS Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain S residue 49 HIS Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain T residue 122 GLN Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain T residue 151 LEU Chi-restraints excluded: chain U residue 29 ASP Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain W residue 96 CYS Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain W residue 161 LEU Chi-restraints excluded: chain W residue 217 VAL Chi-restraints excluded: chain W residue 222 ASP Chi-restraints excluded: chain W residue 231 THR Chi-restraints excluded: chain X residue 67 ILE Chi-restraints excluded: chain X residue 75 LYS Chi-restraints excluded: chain X residue 87 SER Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain X residue 113 LEU Chi-restraints excluded: chain X residue 115 ARG Chi-restraints excluded: chain Y residue 7 ASP Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 45 ILE Chi-restraints excluded: chain Y residue 59 VAL Chi-restraints excluded: chain Y residue 76 LEU Chi-restraints excluded: chain Y residue 80 VAL Chi-restraints excluded: chain Y residue 90 VAL Chi-restraints excluded: chain y residue 5 THR Chi-restraints excluded: chain y residue 90 ASP Chi-restraints excluded: chain y residue 101 LEU Chi-restraints excluded: chain y residue 121 ILE Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 97 SER Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain Z residue 106 GLN Chi-restraints excluded: chain Z residue 134 LEU Chi-restraints excluded: chain z residue 41 LEU Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 41 SER Chi-restraints excluded: chain J residue 52 TYR Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 115 LYS Chi-restraints excluded: chain q residue 9 LYS Chi-restraints excluded: chain q residue 47 GLN Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 79 THR Chi-restraints excluded: chain o residue 8 THR Chi-restraints excluded: chain o residue 22 LYS Chi-restraints excluded: chain o residue 40 ARG Chi-restraints excluded: chain o residue 47 LEU Chi-restraints excluded: chain o residue 48 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 862 optimal weight: 10.0000 chunk 588 optimal weight: 10.0000 chunk 15 optimal weight: 30.0000 chunk 771 optimal weight: 10.0000 chunk 427 optimal weight: 7.9990 chunk 884 optimal weight: 10.0000 chunk 716 optimal weight: 0.0770 chunk 1 optimal weight: 40.0000 chunk 529 optimal weight: 8.9990 chunk 930 optimal weight: 10.0000 chunk 261 optimal weight: 10.0000 overall best weight: 7.4150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: v 203 GLN ** v 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 79 ASN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 64 GLN ** a 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 HIS B 211 GLN d 21 HIS d 57 GLN ** E 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 ASN ** G 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 192 GLN G 232 HIS ** g 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 9 GLN H 183 HIS ** L 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 50 ASN M 105 GLN Q 5 HIS S 142 GLN T 127 GLN ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 45 HIS o 48 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 142676 Z= 0.418 Angle : 0.715 14.372 209710 Z= 0.364 Chirality : 0.042 0.352 26338 Planarity : 0.005 0.102 13678 Dihedral : 23.023 179.773 62057 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.10 % Favored : 91.70 % Rotamer: Outliers : 6.41 % Allowed : 16.92 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 1.13 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.10), residues: 7123 helix: -0.25 (0.10), residues: 2542 sheet: -0.87 (0.16), residues: 948 loop : -1.74 (0.10), residues: 3633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP M 99 HIS 0.039 0.002 HIS o 48 PHE 0.032 0.002 PHE q 36 TYR 0.029 0.002 TYR N 129 ARG 0.010 0.001 ARG u 2 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14246 Ramachandran restraints generated. 7123 Oldfield, 0 Emsley, 7123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14246 Ramachandran restraints generated. 7123 Oldfield, 0 Emsley, 7123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1550 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 390 poor density : 1160 time to evaluate : 8.311 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: v 163 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8272 (tt0) REVERT: v 164 LYS cc_start: 0.8998 (mmpt) cc_final: 0.8616 (mmtm) REVERT: v 175 GLU cc_start: 0.8416 (mt-10) cc_final: 0.7848 (mt-10) REVERT: v 195 ASP cc_start: 0.8270 (t0) cc_final: 0.7816 (t0) REVERT: v 247 GLU cc_start: 0.7613 (tt0) cc_final: 0.7210 (tt0) REVERT: v 278 LYS cc_start: 0.8703 (tttt) cc_final: 0.8499 (tppt) REVERT: A 48 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.8844 (mp) REVERT: A 142 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7485 (p0) REVERT: A 144 ASN cc_start: 0.8087 (m110) cc_final: 0.7338 (p0) REVERT: A 194 ASN cc_start: 0.9249 (t0) cc_final: 0.8729 (t0) REVERT: A 204 MET cc_start: 0.8870 (mtm) cc_final: 0.8555 (mtm) REVERT: a 135 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7788 (tm-30) REVERT: B 17 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8820 (mp) REVERT: B 53 MET cc_start: 0.8387 (mtp) cc_final: 0.8119 (mtm) REVERT: B 255 TRP cc_start: 0.8581 (t60) cc_final: 0.8209 (t60) REVERT: B 325 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8758 (ttmt) REVERT: b 59 GLU cc_start: 0.8507 (tt0) cc_final: 0.8169 (tt0) REVERT: b 62 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.6678 (tp30) REVERT: b 106 GLU cc_start: 0.7707 (tp30) cc_final: 0.7496 (tp30) REVERT: b 136 MET cc_start: 0.8428 (mtt) cc_final: 0.8169 (mtp) REVERT: b 213 TYR cc_start: 0.7862 (m-80) cc_final: 0.7632 (m-80) REVERT: b 336 CYS cc_start: 0.8227 (m) cc_final: 0.8006 (m) REVERT: b 394 ASN cc_start: 0.8903 (m-40) cc_final: 0.8104 (p0) REVERT: b 395 ARG cc_start: 0.6686 (OUTLIER) cc_final: 0.5629 (pmt100) REVERT: b 526 LYS cc_start: 0.5547 (mmpt) cc_final: 0.5331 (mptt) REVERT: b 535 MET cc_start: 0.7402 (OUTLIER) cc_final: 0.7153 (mtt) REVERT: b 595 ASP cc_start: 0.6228 (OUTLIER) cc_final: 0.5614 (p0) REVERT: b 608 MET cc_start: 0.6377 (mmt) cc_final: 0.6073 (mmt) REVERT: C 63 GLU cc_start: 0.7646 (pm20) cc_final: 0.7105 (pm20) REVERT: C 141 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7532 (mmt-90) REVERT: C 150 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8544 (tt) REVERT: C 283 THR cc_start: 0.8991 (OUTLIER) cc_final: 0.8707 (p) REVERT: C 313 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8413 (tp) REVERT: c 100 ILE cc_start: 0.9250 (OUTLIER) cc_final: 0.8752 (tt) REVERT: d 80 ASN cc_start: 0.8094 (t0) cc_final: 0.7683 (t0) REVERT: E 138 GLN cc_start: 0.8217 (tp40) cc_final: 0.7979 (tt0) REVERT: e 19 ARG cc_start: 0.9321 (OUTLIER) cc_final: 0.9089 (ttt180) REVERT: e 23 ASP cc_start: 0.8402 (p0) cc_final: 0.7924 (p0) REVERT: F 53 LYS cc_start: 0.8740 (tptt) cc_final: 0.8313 (mtmm) REVERT: F 54 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8398 (tt0) REVERT: F 124 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8842 (tm) REVERT: f 24 ASN cc_start: 0.9100 (t0) cc_final: 0.8770 (t0) REVERT: G 83 ASP cc_start: 0.8513 (p0) cc_final: 0.8284 (p0) REVERT: G 219 ASP cc_start: 0.8572 (OUTLIER) cc_final: 0.8312 (p0) REVERT: g 18 ASN cc_start: 0.9246 (t0) cc_final: 0.8903 (t0) REVERT: g 96 GLU cc_start: 0.8305 (mm-30) cc_final: 0.8077 (mm-30) REVERT: I 8 ARG cc_start: 0.8824 (ttp80) cc_final: 0.8284 (ttp80) REVERT: I 9 TYR cc_start: 0.9252 (m-10) cc_final: 0.8912 (m-10) REVERT: I 58 MET cc_start: 0.8623 (mmt) cc_final: 0.8124 (mmt) REVERT: I 65 LYS cc_start: 0.8403 (mttt) cc_final: 0.8173 (mttt) REVERT: I 87 GLN cc_start: 0.8590 (tp40) cc_final: 0.7953 (tp-100) REVERT: I 125 GLU cc_start: 0.8053 (tp30) cc_final: 0.7797 (tp30) REVERT: H 162 GLN cc_start: 0.8688 (tm-30) cc_final: 0.8155 (tm-30) REVERT: H 171 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7278 (t70) REVERT: h 71 LYS cc_start: 0.8736 (ptpt) cc_final: 0.8517 (ptpt) REVERT: h 104 GLN cc_start: 0.8366 (mm-40) cc_final: 0.8006 (mp10) REVERT: L 114 GLN cc_start: 0.8279 (tp40) cc_final: 0.7666 (tp-100) REVERT: L 161 ASP cc_start: 0.7107 (m-30) cc_final: 0.6859 (m-30) REVERT: M 128 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8252 (ptp90) REVERT: N 138 GLN cc_start: 0.9061 (mp10) cc_final: 0.8750 (mp10) REVERT: N 192 LYS cc_start: 0.8906 (tttm) cc_final: 0.8614 (ttmt) REVERT: u 82 ASN cc_start: 0.8454 (t0) cc_final: 0.8228 (m-40) REVERT: O 150 GLU cc_start: 0.8097 (tp30) cc_final: 0.7876 (tp30) REVERT: P 154 GLU cc_start: 0.7213 (mm-30) cc_final: 0.7004 (mp0) REVERT: Q 136 ASN cc_start: 0.8844 (t0) cc_final: 0.8289 (t0) REVERT: R 52 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8309 (ttmp) REVERT: R 68 GLN cc_start: 0.9257 (tp40) cc_final: 0.8756 (tp40) REVERT: T 96 ILE cc_start: 0.5275 (tp) cc_final: 0.4929 (tt) REVERT: T 126 VAL cc_start: 0.8705 (t) cc_final: 0.8351 (p) REVERT: T 127 GLN cc_start: 0.8038 (mm110) cc_final: 0.7691 (mm-40) REVERT: T 137 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8326 (mm-30) REVERT: U 33 TYR cc_start: 0.9113 (t80) cc_final: 0.8884 (t80) REVERT: U 41 ILE cc_start: 0.9344 (OUTLIER) cc_final: 0.9095 (mp) REVERT: U 44 GLU cc_start: 0.8680 (pp20) cc_final: 0.7853 (pp20) REVERT: U 88 GLN cc_start: 0.8673 (mp10) cc_final: 0.8389 (mt0) REVERT: W 17 LYS cc_start: 0.8206 (mttt) cc_final: 0.7885 (mttp) REVERT: W 21 GLU cc_start: 0.8465 (mm-30) cc_final: 0.7653 (pp20) REVERT: W 22 ASN cc_start: 0.8296 (t0) cc_final: 0.7833 (m-40) REVERT: W 41 TRP cc_start: 0.6029 (m100) cc_final: 0.5715 (m100) REVERT: W 46 ASP cc_start: 0.8578 (p0) cc_final: 0.8362 (p0) REVERT: W 57 ARG cc_start: 0.6886 (mtm-85) cc_final: 0.6540 (ttm-80) REVERT: W 67 MET cc_start: 0.7569 (mmm) cc_final: 0.6911 (mmm) REVERT: W 149 ILE cc_start: 0.5098 (OUTLIER) cc_final: 0.4879 (pp) REVERT: W 161 LEU cc_start: 0.6308 (OUTLIER) cc_final: 0.6007 (mt) REVERT: W 162 GLU cc_start: 0.6419 (tm-30) cc_final: 0.5878 (tm-30) REVERT: W 179 LYS cc_start: 0.4730 (mtmt) cc_final: 0.4261 (mttp) REVERT: W 223 ASN cc_start: 0.6610 (m110) cc_final: 0.6270 (m-40) REVERT: X 40 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8974 (mm) REVERT: X 113 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9135 (pp) REVERT: X 115 ARG cc_start: 0.9409 (OUTLIER) cc_final: 0.9133 (mtm180) REVERT: X 130 TYR cc_start: 0.8401 (m-80) cc_final: 0.7967 (m-80) REVERT: y 18 LYS cc_start: 0.8988 (tptt) cc_final: 0.8699 (tptm) REVERT: y 34 PHE cc_start: 0.9377 (t80) cc_final: 0.9132 (t80) REVERT: y 39 GLU cc_start: 0.8267 (tt0) cc_final: 0.7769 (tt0) REVERT: y 80 GLU cc_start: 0.7563 (mp0) cc_final: 0.6731 (mp0) REVERT: y 146 ILE cc_start: 0.9289 (tp) cc_final: 0.8708 (tt) REVERT: y 173 LEU cc_start: 0.9475 (tt) cc_final: 0.9144 (mt) REVERT: y 209 ASP cc_start: 0.8237 (t0) cc_final: 0.7984 (t0) REVERT: Z 121 ARG cc_start: 0.8595 (tpp80) cc_final: 0.8202 (tpp-160) REVERT: Z 134 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8734 (tp) REVERT: D 95 TRP cc_start: 0.9241 (OUTLIER) cc_final: 0.7897 (t60) REVERT: J 30 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8702 (tm) REVERT: J 38 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8380 (tm-30) REVERT: J 47 GLN cc_start: 0.8678 (mt0) cc_final: 0.8000 (mp10) REVERT: J 101 ASN cc_start: 0.8859 (m-40) cc_final: 0.8549 (m110) REVERT: J 172 LEU cc_start: 0.7125 (mt) cc_final: 0.6892 (mt) REVERT: q 9 LYS cc_start: 0.2944 (OUTLIER) cc_final: 0.1601 (tttm) REVERT: o 19 ASN cc_start: 0.8572 (m-40) cc_final: 0.8264 (m110) REVERT: o 40 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8610 (ttp-110) outliers start: 390 outliers final: 286 residues processed: 1402 average time/residue: 1.1375 time to fit residues: 2827.4389 Evaluate side-chains 1416 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 317 poor density : 1099 time to evaluate : 6.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain v residue 163 GLN Chi-restraints excluded: chain v residue 170 THR Chi-restraints excluded: chain v residue 197 LEU Chi-restraints excluded: chain v residue 255 ASP Chi-restraints excluded: chain v residue 279 ILE Chi-restraints excluded: chain v residue 328 ILE Chi-restraints excluded: chain v residue 362 ILE Chi-restraints excluded: chain v residue 363 CYS Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain a residue 64 GLN Chi-restraints excluded: chain a residue 70 LYS Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 130 VAL Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain b residue 15 ASN Chi-restraints excluded: chain b residue 62 GLU Chi-restraints excluded: chain b residue 73 ASP Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 164 ASP Chi-restraints excluded: chain b residue 169 THR Chi-restraints excluded: chain b residue 186 CYS Chi-restraints excluded: chain b residue 229 THR Chi-restraints excluded: chain b residue 250 VAL Chi-restraints excluded: chain b residue 312 VAL Chi-restraints excluded: chain b residue 395 ARG Chi-restraints excluded: chain b residue 402 ILE Chi-restraints excluded: chain b residue 434 GLU Chi-restraints excluded: chain b residue 435 ILE Chi-restraints excluded: chain b residue 440 ASN Chi-restraints excluded: chain b residue 445 LEU Chi-restraints excluded: chain b residue 479 ASP Chi-restraints excluded: chain b residue 502 THR Chi-restraints excluded: chain b residue 524 LEU Chi-restraints excluded: chain b residue 535 MET Chi-restraints excluded: chain b residue 538 LEU Chi-restraints excluded: chain b residue 542 MET Chi-restraints excluded: chain b residue 595 ASP Chi-restraints excluded: chain b residue 634 LEU Chi-restraints excluded: chain b residue 644 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain c residue 11 ASN Chi-restraints excluded: chain c residue 18 ILE Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 63 SER Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain d residue 20 LEU Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 87 ASN Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 104 LEU Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain e residue 4 LEU Chi-restraints excluded: chain e residue 14 THR Chi-restraints excluded: chain e residue 19 ARG Chi-restraints excluded: chain e residue 41 VAL Chi-restraints excluded: chain e residue 51 SER Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 86 THR Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain e residue 115 LEU Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 175 LYS Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain f residue 31 LYS Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 57 LYS Chi-restraints excluded: chain f residue 74 THR Chi-restraints excluded: chain f residue 81 VAL Chi-restraints excluded: chain f residue 88 ASN Chi-restraints excluded: chain f residue 97 SER Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 219 ASP Chi-restraints excluded: chain G residue 246 MET Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain g residue 5 VAL Chi-restraints excluded: chain g residue 15 THR Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 29 ILE Chi-restraints excluded: chain g residue 47 CYS Chi-restraints excluded: chain g residue 49 SER Chi-restraints excluded: chain g residue 55 SER Chi-restraints excluded: chain g residue 66 SER Chi-restraints excluded: chain g residue 71 THR Chi-restraints excluded: chain g residue 79 SER Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 60 THR Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain h residue 30 GLU Chi-restraints excluded: chain h residue 37 SER Chi-restraints excluded: chain h residue 47 VAL Chi-restraints excluded: chain h residue 76 GLN Chi-restraints excluded: chain h residue 98 SER Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 26 ILE Chi-restraints excluded: chain i residue 42 SER Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 61 ILE Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain i residue 93 ILE Chi-restraints excluded: chain j residue 7 SER Chi-restraints excluded: chain j residue 11 ARG Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 33 THR Chi-restraints excluded: chain j residue 43 LYS Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 50 SER Chi-restraints excluded: chain k residue 67 GLN Chi-restraints excluded: chain L residue 9 ILE Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 152 THR Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain l residue 9 ILE Chi-restraints excluded: chain l residue 32 ASN Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain M residue 38 ILE Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 62 GLN Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 82 SER Chi-restraints excluded: chain M residue 91 CYS Chi-restraints excluded: chain M residue 128 ARG Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain p residue 59 CYS Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain N residue 171 SER Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain u residue 9 CYS Chi-restraints excluded: chain u residue 19 ILE Chi-restraints excluded: chain u residue 32 CYS Chi-restraints excluded: chain u residue 34 SER Chi-restraints excluded: chain u residue 52 THR Chi-restraints excluded: chain u residue 63 LEU Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain u residue 145 LEU Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 77 SER Chi-restraints excluded: chain O residue 89 SER Chi-restraints excluded: chain O residue 124 LEU Chi-restraints excluded: chain O residue 143 THR Chi-restraints excluded: chain O residue 151 ASP Chi-restraints excluded: chain O residue 182 ASN Chi-restraints excluded: chain O residue 189 ASP Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 75 GLU Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 166 VAL Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 57 ILE Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 71 LEU Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 86 THR Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 137 THR Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain Q residue 150 VAL Chi-restraints excluded: chain R residue 52 LYS Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain S residue 49 HIS Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 88 HIS Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain U residue 29 ASP Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain U residue 41 ILE Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain V residue 11 PHE Chi-restraints excluded: chain V residue 22 ILE Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain W residue 45 LEU Chi-restraints excluded: chain W residue 96 CYS Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain W residue 161 LEU Chi-restraints excluded: chain W residue 217 VAL Chi-restraints excluded: chain W residue 222 ASP Chi-restraints excluded: chain W residue 231 THR Chi-restraints excluded: chain X residue 40 LEU Chi-restraints excluded: chain X residue 75 LYS Chi-restraints excluded: chain X residue 87 SER Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain X residue 113 LEU Chi-restraints excluded: chain X residue 115 ARG Chi-restraints excluded: chain Y residue 7 ASP Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 45 ILE Chi-restraints excluded: chain Y residue 59 VAL Chi-restraints excluded: chain Y residue 76 LEU Chi-restraints excluded: chain Y residue 80 VAL Chi-restraints excluded: chain Y residue 90 VAL Chi-restraints excluded: chain y residue 5 THR Chi-restraints excluded: chain y residue 59 ILE Chi-restraints excluded: chain y residue 90 ASP Chi-restraints excluded: chain y residue 206 THR Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 100 THR Chi-restraints excluded: chain Z residue 106 GLN Chi-restraints excluded: chain Z residue 134 LEU Chi-restraints excluded: chain z residue 41 LEU Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain D residue 95 TRP Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 41 SER Chi-restraints excluded: chain J residue 52 TYR Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain q residue 9 LYS Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 79 THR Chi-restraints excluded: chain o residue 8 THR Chi-restraints excluded: chain o residue 22 LYS Chi-restraints excluded: chain o residue 40 ARG Chi-restraints excluded: chain o residue 47 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 348 optimal weight: 8.9990 chunk 933 optimal weight: 20.0000 chunk 204 optimal weight: 1.9990 chunk 608 optimal weight: 1.9990 chunk 255 optimal weight: 6.9990 chunk 1037 optimal weight: 10.0000 chunk 861 optimal weight: 10.0000 chunk 480 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 343 optimal weight: 0.4980 chunk 544 optimal weight: 4.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** v 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 GLN b 614 ASN C 307 GLN d 57 GLN ** E 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 71 HIS G 232 HIS ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 GLN h 20 GLN ** L 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 GLN N 182 ASN ** P 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 118 HIS V 7 GLN V 98 ASN W 205 GLN W 232 ASN ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 48 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 142676 Z= 0.174 Angle : 0.569 16.317 209710 Z= 0.295 Chirality : 0.035 0.300 26338 Planarity : 0.004 0.099 13678 Dihedral : 22.911 179.927 62057 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.03 % Favored : 92.81 % Rotamer: Outliers : 4.32 % Allowed : 19.68 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 1.13 % 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: -1.17 (0.10), residues: 7123 helix: 0.26 (0.10), residues: 2547 sheet: -0.74 (0.16), residues: 958 loop : -1.55 (0.10), residues: 3618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 23 HIS 0.008 0.001 HIS G 232 PHE 0.020 0.001 PHE q 36 TYR 0.028 0.002 TYR O 168 ARG 0.010 0.000 ARG B 10 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14246 Ramachandran restraints generated. 7123 Oldfield, 0 Emsley, 7123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14246 Ramachandran restraints generated. 7123 Oldfield, 0 Emsley, 7123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1496 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 1233 time to evaluate : 6.425 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: v 163 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8113 (tt0) REVERT: v 164 LYS cc_start: 0.9064 (mmpt) cc_final: 0.8722 (mmtm) REVERT: v 175 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7635 (mt-10) REVERT: v 362 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8133 (mt) REVERT: A 48 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8875 (mp) REVERT: A 142 ASP cc_start: 0.7872 (OUTLIER) cc_final: 0.7586 (p0) REVERT: A 144 ASN cc_start: 0.7935 (m110) cc_final: 0.7330 (p0) REVERT: A 204 MET cc_start: 0.8772 (mtm) cc_final: 0.8441 (mtm) REVERT: a 120 ASN cc_start: 0.8888 (t0) cc_final: 0.8568 (t0) REVERT: a 135 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7682 (tm-30) REVERT: B 171 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8943 (mp) REVERT: B 255 TRP cc_start: 0.8396 (t60) cc_final: 0.7989 (t60) REVERT: B 325 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8779 (ttmt) REVERT: b 59 GLU cc_start: 0.8508 (tt0) cc_final: 0.8235 (tt0) REVERT: b 62 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.6591 (tp30) REVERT: b 136 MET cc_start: 0.8390 (mtt) cc_final: 0.8075 (mtp) REVERT: b 143 LEU cc_start: 0.6681 (mm) cc_final: 0.6460 (tt) REVERT: b 213 TYR cc_start: 0.7900 (m-80) cc_final: 0.7615 (m-80) REVERT: b 394 ASN cc_start: 0.8931 (m-40) cc_final: 0.8226 (p0) REVERT: b 395 ARG cc_start: 0.7050 (OUTLIER) cc_final: 0.6145 (pmt100) REVERT: b 526 LYS cc_start: 0.6220 (mmpt) cc_final: 0.5977 (mptt) REVERT: C 8 VAL cc_start: 0.9327 (t) cc_final: 0.9048 (p) REVERT: C 63 GLU cc_start: 0.7531 (pm20) cc_final: 0.7050 (pm20) REVERT: C 150 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8586 (tt) REVERT: C 283 THR cc_start: 0.8992 (m) cc_final: 0.8673 (p) REVERT: C 321 LYS cc_start: 0.9039 (mppt) cc_final: 0.8825 (mmtm) REVERT: d 44 MET cc_start: 0.8326 (mmm) cc_final: 0.7368 (mmm) REVERT: d 80 ASN cc_start: 0.8087 (t0) cc_final: 0.7694 (t0) REVERT: E 5 LYS cc_start: 0.8078 (tptt) cc_final: 0.7663 (tppt) REVERT: e 23 ASP cc_start: 0.8328 (p0) cc_final: 0.7920 (p0) REVERT: F 30 ARG cc_start: 0.7181 (ttt90) cc_final: 0.6937 (ttt90) REVERT: F 53 LYS cc_start: 0.8616 (tptt) cc_final: 0.8203 (mtmm) REVERT: F 54 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8416 (tt0) REVERT: F 124 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8708 (tm) REVERT: f 24 ASN cc_start: 0.9051 (t0) cc_final: 0.8707 (t0) REVERT: G 83 ASP cc_start: 0.8451 (p0) cc_final: 0.8238 (p0) REVERT: I 8 ARG cc_start: 0.8800 (ttp80) cc_final: 0.8566 (ttt180) REVERT: I 48 GLN cc_start: 0.8083 (mp10) cc_final: 0.7664 (mp10) REVERT: I 58 MET cc_start: 0.8706 (mmt) cc_final: 0.8292 (mmt) REVERT: I 65 LYS cc_start: 0.8370 (mttt) cc_final: 0.8132 (mttt) REVERT: I 87 GLN cc_start: 0.8531 (tp40) cc_final: 0.7933 (tp-100) REVERT: H 7 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7318 (mt-10) REVERT: H 68 LEU cc_start: 0.9620 (OUTLIER) cc_final: 0.9371 (tp) REVERT: H 150 SER cc_start: 0.8569 (OUTLIER) cc_final: 0.8328 (p) REVERT: H 162 GLN cc_start: 0.8519 (tm-30) cc_final: 0.8184 (tm-30) REVERT: H 171 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7275 (t70) REVERT: h 104 GLN cc_start: 0.8413 (mm-40) cc_final: 0.8110 (mp10) REVERT: i 98 ARG cc_start: 0.7827 (mmm160) cc_final: 0.7321 (ttp-110) REVERT: L 114 GLN cc_start: 0.8247 (tp40) cc_final: 0.7580 (tp-100) REVERT: L 161 ASP cc_start: 0.7182 (m-30) cc_final: 0.6885 (m-30) REVERT: M 128 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8116 (ptp90) REVERT: M 135 LEU cc_start: 0.8914 (tt) cc_final: 0.8682 (tt) REVERT: N 138 GLN cc_start: 0.9033 (mp10) cc_final: 0.8732 (mp10) REVERT: N 192 LYS cc_start: 0.8850 (tttm) cc_final: 0.8558 (ttmt) REVERT: u 82 ASN cc_start: 0.8394 (t0) cc_final: 0.8084 (m-40) REVERT: O 65 ASN cc_start: 0.8880 (t0) cc_final: 0.8112 (t0) REVERT: O 187 GLU cc_start: 0.7762 (pm20) cc_final: 0.7542 (pm20) REVERT: Q 136 ASN cc_start: 0.8798 (t0) cc_final: 0.8354 (t0) REVERT: R 25 ASP cc_start: 0.7916 (p0) cc_final: 0.7520 (p0) REVERT: R 28 GLU cc_start: 0.7641 (mp0) cc_final: 0.7187 (mp0) REVERT: R 68 GLN cc_start: 0.9152 (tp40) cc_final: 0.8651 (tp40) REVERT: R 70 LYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8769 (ttmt) REVERT: R 92 GLN cc_start: 0.8832 (tt0) cc_final: 0.8487 (tt0) REVERT: S 90 MET cc_start: 0.8283 (mmm) cc_final: 0.7961 (mmm) REVERT: T 112 ASN cc_start: 0.8902 (m-40) cc_final: 0.8569 (m-40) REVERT: T 127 GLN cc_start: 0.8289 (mm110) cc_final: 0.7835 (mm-40) REVERT: T 137 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8428 (mm-30) REVERT: U 33 TYR cc_start: 0.9079 (t80) cc_final: 0.8858 (t80) REVERT: U 41 ILE cc_start: 0.9311 (OUTLIER) cc_final: 0.9083 (mp) REVERT: U 44 GLU cc_start: 0.8724 (pp20) cc_final: 0.7890 (pp20) REVERT: W 17 LYS cc_start: 0.8275 (mttt) cc_final: 0.7946 (mttm) REVERT: W 21 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7515 (pp20) REVERT: W 22 ASN cc_start: 0.8235 (t0) cc_final: 0.7759 (m-40) REVERT: W 41 TRP cc_start: 0.6063 (m100) cc_final: 0.5817 (m100) REVERT: W 57 ARG cc_start: 0.6863 (mtm-85) cc_final: 0.6538 (ttm-80) REVERT: W 67 MET cc_start: 0.7155 (mmm) cc_final: 0.6448 (mmm) REVERT: W 162 GLU cc_start: 0.6162 (tm-30) cc_final: 0.5830 (tm-30) REVERT: W 179 LYS cc_start: 0.4632 (mtmt) cc_final: 0.4170 (mttp) REVERT: W 223 ASN cc_start: 0.6556 (m110) cc_final: 0.6149 (m-40) REVERT: y 18 LYS cc_start: 0.8982 (tptt) cc_final: 0.8755 (tptm) REVERT: y 34 PHE cc_start: 0.9240 (t80) cc_final: 0.8933 (t80) REVERT: y 39 GLU cc_start: 0.8204 (tt0) cc_final: 0.7787 (tt0) REVERT: y 80 GLU cc_start: 0.7548 (mp0) cc_final: 0.6707 (mp0) REVERT: y 146 ILE cc_start: 0.9233 (tp) cc_final: 0.8642 (tt) REVERT: y 208 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8672 (mm) REVERT: Z 106 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7932 (tm-30) REVERT: Z 121 ARG cc_start: 0.8538 (tpp80) cc_final: 0.8200 (tpp-160) REVERT: Z 134 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8688 (tp) REVERT: D 95 TRP cc_start: 0.9194 (OUTLIER) cc_final: 0.8072 (t60) REVERT: D 199 ILE cc_start: 0.9136 (mt) cc_final: 0.8821 (mt) REVERT: J 30 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8690 (tm) REVERT: J 47 GLN cc_start: 0.8645 (mt0) cc_final: 0.7909 (mp10) REVERT: J 101 ASN cc_start: 0.8629 (m-40) cc_final: 0.8332 (m110) REVERT: J 172 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.6883 (mt) REVERT: q 9 LYS cc_start: 0.2403 (OUTLIER) cc_final: 0.1602 (tttm) REVERT: o 19 ASN cc_start: 0.8490 (m-40) cc_final: 0.8245 (m110) outliers start: 263 outliers final: 169 residues processed: 1395 average time/residue: 1.1280 time to fit residues: 2752.9324 Evaluate side-chains 1352 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1160 time to evaluate : 6.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain v residue 163 GLN Chi-restraints excluded: chain v residue 170 THR Chi-restraints excluded: chain v residue 197 LEU Chi-restraints excluded: chain v residue 255 ASP Chi-restraints excluded: chain v residue 362 ILE Chi-restraints excluded: chain v residue 378 ASN Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain a residue 70 LYS Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain b residue 15 ASN Chi-restraints excluded: chain b residue 62 GLU Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 164 ASP Chi-restraints excluded: chain b residue 169 THR Chi-restraints excluded: chain b residue 229 THR Chi-restraints excluded: chain b residue 250 VAL Chi-restraints excluded: chain b residue 363 VAL Chi-restraints excluded: chain b residue 395 ARG Chi-restraints excluded: chain b residue 416 LEU Chi-restraints excluded: chain b residue 434 GLU Chi-restraints excluded: chain b residue 435 ILE Chi-restraints excluded: chain b residue 445 LEU Chi-restraints excluded: chain b residue 479 ASP Chi-restraints excluded: chain b residue 524 LEU Chi-restraints excluded: chain b residue 532 GLU Chi-restraints excluded: chain b residue 542 MET Chi-restraints excluded: chain b residue 634 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain c residue 11 ASN Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain d residue 20 LEU Chi-restraints excluded: chain d residue 34 LYS Chi-restraints excluded: chain d residue 87 ASN Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain e residue 4 LEU Chi-restraints excluded: chain e residue 14 THR Chi-restraints excluded: chain e residue 51 SER Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain e residue 115 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 165 ASP Chi-restraints excluded: chain F residue 175 LYS Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain f residue 97 SER Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 47 CYS Chi-restraints excluded: chain g residue 49 SER Chi-restraints excluded: chain g residue 55 SER Chi-restraints excluded: chain g residue 74 ARG Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 60 THR Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain H residue 183 HIS Chi-restraints excluded: chain h residue 37 SER Chi-restraints excluded: chain h residue 79 ASP Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 61 ILE Chi-restraints excluded: chain j residue 7 SER Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 43 LYS Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain k residue 50 SER Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain l residue 32 ASN Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 62 GLN Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 128 ARG Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain N residue 171 SER Chi-restraints excluded: chain u residue 9 CYS Chi-restraints excluded: chain u residue 19 ILE Chi-restraints excluded: chain u residue 32 CYS Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain u residue 145 LEU Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 89 SER Chi-restraints excluded: chain O residue 151 ASP Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 166 VAL Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 71 LEU Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain R residue 70 LYS Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain S residue 49 HIS Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 88 HIS Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain T residue 98 HIS Chi-restraints excluded: chain T residue 136 ARG Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain U residue 41 ILE Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain V residue 11 PHE Chi-restraints excluded: chain V residue 22 ILE Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain W residue 96 CYS Chi-restraints excluded: chain X residue 87 SER Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain Y residue 7 ASP Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 59 VAL Chi-restraints excluded: chain Y residue 73 VAL Chi-restraints excluded: chain Y residue 76 LEU Chi-restraints excluded: chain Y residue 80 VAL Chi-restraints excluded: chain y residue 59 ILE Chi-restraints excluded: chain y residue 101 LEU Chi-restraints excluded: chain y residue 106 ASN Chi-restraints excluded: chain y residue 206 THR Chi-restraints excluded: chain y residue 208 LEU Chi-restraints excluded: chain Z residue 5 LEU Chi-restraints excluded: chain Z residue 74 VAL Chi-restraints excluded: chain Z residue 97 SER Chi-restraints excluded: chain Z residue 106 GLN Chi-restraints excluded: chain Z residue 134 LEU Chi-restraints excluded: chain z residue 41 LEU Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 95 TRP Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 52 TYR Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain q residue 9 LYS Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 79 THR Chi-restraints excluded: chain o residue 48 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 999 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 chunk 590 optimal weight: 1.9990 chunk 757 optimal weight: 10.0000 chunk 586 optimal weight: 0.4980 chunk 873 optimal weight: 10.0000 chunk 579 optimal weight: 5.9990 chunk 1033 optimal weight: 20.0000 chunk 646 optimal weight: 20.0000 chunk 629 optimal weight: 8.9990 chunk 477 optimal weight: 0.8980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** v 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 HIS B 211 GLN C 311 HIS d 57 GLN ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 ASN G 232 HIS ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 GLN j 48 ASN ** L 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 GLN O 50 ASN ** P 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 46 GLN ** S 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 131 GLN T 134 GLN V 7 GLN V 47 ASN y 79 GLN J 95 ASN ** q 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 12 GLN o 48 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 142676 Z= 0.184 Angle : 0.566 15.081 209710 Z= 0.292 Chirality : 0.034 0.289 26338 Planarity : 0.004 0.097 13678 Dihedral : 22.852 179.994 62057 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.57 % Favored : 92.28 % Rotamer: Outliers : 4.21 % Allowed : 20.09 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 1.13 % Twisted General : 0.04 % 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: -0.99 (0.10), residues: 7123 helix: 0.49 (0.11), residues: 2538 sheet: -0.64 (0.17), residues: 941 loop : -1.51 (0.10), residues: 3644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP b 427 HIS 0.029 0.001 HIS o 48 PHE 0.020 0.001 PHE q 36 TYR 0.031 0.002 TYR O 167 ARG 0.009 0.000 ARG y 188 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14246 Ramachandran restraints generated. 7123 Oldfield, 0 Emsley, 7123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14246 Ramachandran restraints generated. 7123 Oldfield, 0 Emsley, 7123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1453 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 256 poor density : 1197 time to evaluate : 6.701 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: v 164 LYS cc_start: 0.9138 (mmpt) cc_final: 0.8741 (mmtm) REVERT: v 175 GLU cc_start: 0.8405 (mt-10) cc_final: 0.7773 (mt-10) REVERT: v 362 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8044 (mt) REVERT: A 48 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8933 (mp) REVERT: A 142 ASP cc_start: 0.7867 (OUTLIER) cc_final: 0.7559 (p0) REVERT: A 144 ASN cc_start: 0.7997 (m110) cc_final: 0.7382 (p0) REVERT: a 120 ASN cc_start: 0.8879 (t0) cc_final: 0.8553 (t0) REVERT: a 135 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7682 (tm-30) REVERT: B 171 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9071 (mp) REVERT: B 255 TRP cc_start: 0.8399 (t60) cc_final: 0.8014 (t60) REVERT: B 325 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8761 (ttmt) REVERT: b 136 MET cc_start: 0.8270 (mtt) cc_final: 0.7943 (mtp) REVERT: b 143 LEU cc_start: 0.6604 (mm) cc_final: 0.6386 (tt) REVERT: b 213 TYR cc_start: 0.7902 (m-80) cc_final: 0.7615 (m-80) REVERT: b 394 ASN cc_start: 0.8925 (m-40) cc_final: 0.8209 (p0) REVERT: b 395 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6310 (pmt100) REVERT: b 401 ASP cc_start: 0.7920 (m-30) cc_final: 0.7537 (m-30) REVERT: b 526 LYS cc_start: 0.5924 (mmpt) cc_final: 0.5537 (mptt) REVERT: b 532 GLU cc_start: 0.7408 (pt0) cc_final: 0.7104 (pp20) REVERT: b 595 ASP cc_start: 0.6168 (OUTLIER) cc_final: 0.5375 (p0) REVERT: C 63 GLU cc_start: 0.7521 (pm20) cc_final: 0.7005 (pm20) REVERT: C 99 MET cc_start: 0.8070 (ptp) cc_final: 0.7618 (ptm) REVERT: C 150 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8553 (tt) REVERT: C 283 THR cc_start: 0.9011 (m) cc_final: 0.8686 (p) REVERT: C 321 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8869 (mmtm) REVERT: C 357 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7810 (tm-30) REVERT: d 69 TYR cc_start: 0.8807 (m-80) cc_final: 0.8474 (m-80) REVERT: d 80 ASN cc_start: 0.8102 (t0) cc_final: 0.7680 (t0) REVERT: E 5 LYS cc_start: 0.8091 (tptt) cc_final: 0.7663 (tppt) REVERT: e 23 ASP cc_start: 0.8291 (p0) cc_final: 0.7847 (p0) REVERT: F 53 LYS cc_start: 0.8629 (tptt) cc_final: 0.8206 (mtmm) REVERT: F 54 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8372 (tt0) REVERT: F 124 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8710 (tm) REVERT: f 24 ASN cc_start: 0.9059 (t0) cc_final: 0.8697 (t0) REVERT: G 38 GLN cc_start: 0.8705 (pt0) cc_final: 0.8020 (pt0) REVERT: G 83 ASP cc_start: 0.8495 (p0) cc_final: 0.8261 (p0) REVERT: g 18 ASN cc_start: 0.9133 (t0) cc_final: 0.8781 (t0) REVERT: I 48 GLN cc_start: 0.8182 (mp10) cc_final: 0.7742 (mp10) REVERT: I 58 MET cc_start: 0.8750 (mmt) cc_final: 0.8469 (mmt) REVERT: I 65 LYS cc_start: 0.8333 (mttt) cc_final: 0.8130 (mttt) REVERT: I 87 GLN cc_start: 0.8563 (tp40) cc_final: 0.7994 (tp-100) REVERT: H 8 GLN cc_start: 0.8642 (mm-40) cc_final: 0.8338 (mm110) REVERT: H 68 LEU cc_start: 0.9631 (OUTLIER) cc_final: 0.9393 (tp) REVERT: H 91 ARG cc_start: 0.7826 (mtp-110) cc_final: 0.7526 (ttm-80) REVERT: H 143 GLU cc_start: 0.7960 (tp30) cc_final: 0.7580 (tp30) REVERT: H 150 SER cc_start: 0.8500 (OUTLIER) cc_final: 0.8286 (p) REVERT: H 162 GLN cc_start: 0.8534 (tm-30) cc_final: 0.8196 (tm-30) REVERT: H 171 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7317 (t70) REVERT: h 104 GLN cc_start: 0.8336 (mm-40) cc_final: 0.8007 (mp10) REVERT: L 161 ASP cc_start: 0.7136 (m-30) cc_final: 0.6925 (m-30) REVERT: M 128 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.8145 (ptp90) REVERT: N 138 GLN cc_start: 0.9042 (mp10) cc_final: 0.8715 (mp10) REVERT: N 192 LYS cc_start: 0.8850 (tttm) cc_final: 0.8548 (ttmt) REVERT: u 3 ILE cc_start: 0.9024 (mm) cc_final: 0.8804 (mm) REVERT: u 82 ASN cc_start: 0.8392 (t0) cc_final: 0.8052 (m-40) REVERT: O 65 ASN cc_start: 0.8881 (t0) cc_final: 0.8120 (t0) REVERT: O 100 GLU cc_start: 0.7190 (tp30) cc_final: 0.6907 (tp30) REVERT: O 199 TYR cc_start: 0.8572 (m-80) cc_final: 0.8361 (m-10) REVERT: Q 136 ASN cc_start: 0.8797 (t0) cc_final: 0.8323 (t0) REVERT: R 25 ASP cc_start: 0.7903 (p0) cc_final: 0.7650 (p0) REVERT: R 28 GLU cc_start: 0.7561 (mp0) cc_final: 0.7284 (mp0) REVERT: R 68 GLN cc_start: 0.9156 (tp40) cc_final: 0.8650 (tp40) REVERT: R 70 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8775 (ttmt) REVERT: R 92 GLN cc_start: 0.8826 (tt0) cc_final: 0.8480 (tt0) REVERT: T 112 ASN cc_start: 0.8857 (m-40) cc_final: 0.8427 (m-40) REVERT: T 127 GLN cc_start: 0.8349 (mm110) cc_final: 0.8107 (mm-40) REVERT: T 137 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8479 (mm-30) REVERT: U 41 ILE cc_start: 0.9317 (OUTLIER) cc_final: 0.8989 (mp) REVERT: U 44 GLU cc_start: 0.8717 (pp20) cc_final: 0.7895 (pp20) REVERT: U 75 TYR cc_start: 0.8736 (t80) cc_final: 0.8403 (t80) REVERT: W 17 LYS cc_start: 0.8338 (mttt) cc_final: 0.8010 (mttp) REVERT: W 21 GLU cc_start: 0.8404 (mm-30) cc_final: 0.7567 (pp20) REVERT: W 22 ASN cc_start: 0.8184 (t0) cc_final: 0.7686 (m-40) REVERT: W 41 TRP cc_start: 0.5999 (m100) cc_final: 0.5734 (m100) REVERT: W 57 ARG cc_start: 0.6854 (mtm-85) cc_final: 0.6508 (ttm-80) REVERT: W 67 MET cc_start: 0.7217 (mmm) cc_final: 0.6557 (mmm) REVERT: W 157 MET cc_start: 0.7562 (pmm) cc_final: 0.7360 (pmm) REVERT: W 162 GLU cc_start: 0.5991 (tm-30) cc_final: 0.5655 (tm-30) REVERT: W 179 LYS cc_start: 0.4530 (mtmt) cc_final: 0.4060 (mttp) REVERT: W 223 ASN cc_start: 0.6641 (m110) cc_final: 0.6220 (m-40) REVERT: y 18 LYS cc_start: 0.8992 (tptt) cc_final: 0.8743 (tptm) REVERT: y 34 PHE cc_start: 0.9251 (t80) cc_final: 0.8955 (t80) REVERT: y 39 GLU cc_start: 0.8136 (tt0) cc_final: 0.7764 (tt0) REVERT: y 80 GLU cc_start: 0.7568 (mp0) cc_final: 0.6734 (mp0) REVERT: y 131 ASP cc_start: 0.8475 (m-30) cc_final: 0.8193 (m-30) REVERT: y 146 ILE cc_start: 0.9209 (tp) cc_final: 0.8519 (tt) REVERT: y 169 ASP cc_start: 0.8944 (m-30) cc_final: 0.8470 (m-30) REVERT: y 173 LEU cc_start: 0.9466 (tt) cc_final: 0.9099 (mt) REVERT: Z 106 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7921 (tm-30) REVERT: Z 121 ARG cc_start: 0.8544 (tpp80) cc_final: 0.8208 (tpp-160) REVERT: Z 134 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8683 (tp) REVERT: D 95 TRP cc_start: 0.9199 (OUTLIER) cc_final: 0.8033 (t60) REVERT: D 199 ILE cc_start: 0.9132 (mt) cc_final: 0.8816 (mt) REVERT: J 30 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8715 (tm) REVERT: J 47 GLN cc_start: 0.8648 (mt0) cc_final: 0.7903 (mp10) REVERT: J 101 ASN cc_start: 0.8594 (m-40) cc_final: 0.8387 (m110) REVERT: q 9 LYS cc_start: 0.2410 (OUTLIER) cc_final: 0.1477 (tttm) REVERT: o 7 HIS cc_start: 0.9016 (t70) cc_final: 0.8676 (t-90) REVERT: o 19 ASN cc_start: 0.8496 (m-40) cc_final: 0.8230 (m110) outliers start: 256 outliers final: 186 residues processed: 1347 average time/residue: 1.1821 time to fit residues: 2808.4309 Evaluate side-chains 1363 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 1156 time to evaluate : 6.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain v residue 170 THR Chi-restraints excluded: chain v residue 197 LEU Chi-restraints excluded: chain v residue 255 ASP Chi-restraints excluded: chain v residue 362 ILE Chi-restraints excluded: chain v residue 378 ASN Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain a residue 70 LYS Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain b residue 15 ASN Chi-restraints excluded: chain b residue 16 ASP Chi-restraints excluded: chain b residue 62 GLU Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 164 ASP Chi-restraints excluded: chain b residue 169 THR Chi-restraints excluded: chain b residue 229 THR Chi-restraints excluded: chain b residue 250 VAL Chi-restraints excluded: chain b residue 363 VAL Chi-restraints excluded: chain b residue 385 LEU Chi-restraints excluded: chain b residue 395 ARG Chi-restraints excluded: chain b residue 402 ILE Chi-restraints excluded: chain b residue 434 GLU Chi-restraints excluded: chain b residue 435 ILE Chi-restraints excluded: chain b residue 440 ASN Chi-restraints excluded: chain b residue 445 LEU Chi-restraints excluded: chain b residue 479 ASP Chi-restraints excluded: chain b residue 524 LEU Chi-restraints excluded: chain b residue 595 ASP Chi-restraints excluded: chain b residue 634 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 321 LYS Chi-restraints excluded: chain c residue 11 ASN Chi-restraints excluded: chain c residue 18 ILE Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain d residue 20 LEU Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 87 ASN Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 104 LEU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain e residue 4 LEU Chi-restraints excluded: chain e residue 14 THR Chi-restraints excluded: chain e residue 51 SER Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain e residue 115 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain g residue 20 ILE Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 47 CYS Chi-restraints excluded: chain g residue 49 SER Chi-restraints excluded: chain g residue 55 SER Chi-restraints excluded: chain g residue 71 THR Chi-restraints excluded: chain g residue 74 ARG Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 60 THR Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 142 ASP Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain H residue 183 HIS Chi-restraints excluded: chain h residue 37 SER Chi-restraints excluded: chain h residue 76 GLN Chi-restraints excluded: chain h residue 79 ASP Chi-restraints excluded: chain h residue 98 SER Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain i residue 93 ILE Chi-restraints excluded: chain j residue 7 SER Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain k residue 50 SER Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain l residue 32 ASN Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 62 GLN Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 128 ARG Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain u residue 9 CYS Chi-restraints excluded: chain u residue 19 ILE Chi-restraints excluded: chain u residue 32 CYS Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain u residue 145 LEU Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 89 SER Chi-restraints excluded: chain O residue 151 ASP Chi-restraints excluded: chain P residue 75 GLU Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 166 VAL Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 71 LEU Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 150 VAL Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 70 LYS Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 109 TYR Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain S residue 49 HIS Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 88 HIS Chi-restraints excluded: chain T residue 98 HIS Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain U residue 41 ILE Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain V residue 11 PHE Chi-restraints excluded: chain V residue 22 ILE Chi-restraints excluded: chain V residue 109 MET Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain W residue 96 CYS Chi-restraints excluded: chain X residue 75 LYS Chi-restraints excluded: chain X residue 87 SER Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain Y residue 7 ASP Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 59 VAL Chi-restraints excluded: chain Y residue 73 VAL Chi-restraints excluded: chain Y residue 76 LEU Chi-restraints excluded: chain Y residue 80 VAL Chi-restraints excluded: chain y residue 59 ILE Chi-restraints excluded: chain y residue 101 LEU Chi-restraints excluded: chain y residue 106 ASN Chi-restraints excluded: chain y residue 199 VAL Chi-restraints excluded: chain y residue 206 THR Chi-restraints excluded: chain Z residue 5 LEU Chi-restraints excluded: chain Z residue 106 GLN Chi-restraints excluded: chain Z residue 134 LEU Chi-restraints excluded: chain z residue 41 LEU Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 95 TRP Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 41 SER Chi-restraints excluded: chain J residue 52 TYR Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 95 ASN Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain q residue 9 LYS Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 79 THR Chi-restraints excluded: chain q residue 82 GLN Chi-restraints excluded: chain o residue 48 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 639 optimal weight: 0.1980 chunk 412 optimal weight: 8.9990 chunk 617 optimal weight: 1.9990 chunk 311 optimal weight: 5.9990 chunk 203 optimal weight: 0.6980 chunk 200 optimal weight: 9.9990 chunk 656 optimal weight: 7.9990 chunk 703 optimal weight: 8.9990 chunk 510 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 chunk 812 optimal weight: 10.0000 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** v 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 GLN C 361 HIS d 57 GLN E 138 GLN G 232 HIS I 37 GLN M 105 GLN ** P 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 7 GLN V 47 ASN X 137 ASN ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 47 GLN q 53 GLN ** o 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 48 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 142676 Z= 0.212 Angle : 0.578 14.557 209710 Z= 0.296 Chirality : 0.035 0.291 26338 Planarity : 0.004 0.098 13678 Dihedral : 22.818 179.918 62057 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.58 % Favored : 92.26 % Rotamer: Outliers : 4.44 % Allowed : 20.29 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.04 % 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: -0.89 (0.10), residues: 7123 helix: 0.62 (0.11), residues: 2529 sheet: -0.63 (0.17), residues: 945 loop : -1.48 (0.10), residues: 3649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP b 427 HIS 0.026 0.001 HIS o 48 PHE 0.022 0.001 PHE q 36 TYR 0.033 0.002 TYR U 33 ARG 0.017 0.000 ARG J 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14246 Ramachandran restraints generated. 7123 Oldfield, 0 Emsley, 7123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14246 Ramachandran restraints generated. 7123 Oldfield, 0 Emsley, 7123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1445 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 270 poor density : 1175 time to evaluate : 6.684 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: v 175 GLU cc_start: 0.8593 (mt-10) cc_final: 0.7978 (mt-10) REVERT: v 362 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8136 (mt) REVERT: A 48 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8928 (mp) REVERT: A 142 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7639 (p0) REVERT: A 144 ASN cc_start: 0.8052 (m110) cc_final: 0.7412 (p0) REVERT: a 120 ASN cc_start: 0.8859 (t0) cc_final: 0.8548 (t0) REVERT: a 135 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7701 (tm-30) REVERT: B 171 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.9069 (mp) REVERT: B 255 TRP cc_start: 0.8440 (t60) cc_final: 0.8024 (t60) REVERT: B 325 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8739 (ttmt) REVERT: b 62 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.6763 (tp30) REVERT: b 66 LYS cc_start: 0.6653 (mtpt) cc_final: 0.5485 (mtmt) REVERT: b 136 MET cc_start: 0.8259 (mtt) cc_final: 0.7934 (mtp) REVERT: b 143 LEU cc_start: 0.6564 (mm) cc_final: 0.6329 (tt) REVERT: b 213 TYR cc_start: 0.7917 (m-80) cc_final: 0.7603 (m-80) REVERT: b 361 ILE cc_start: 0.6688 (mt) cc_final: 0.6413 (tt) REVERT: b 394 ASN cc_start: 0.8877 (m-40) cc_final: 0.8155 (p0) REVERT: b 395 ARG cc_start: 0.7202 (OUTLIER) cc_final: 0.6313 (pmt100) REVERT: b 401 ASP cc_start: 0.7912 (m-30) cc_final: 0.7516 (m-30) REVERT: b 595 ASP cc_start: 0.6416 (OUTLIER) cc_final: 0.6070 (p0) REVERT: C 63 GLU cc_start: 0.7489 (pm20) cc_final: 0.6997 (pm20) REVERT: C 99 MET cc_start: 0.8131 (ptp) cc_final: 0.7677 (ptm) REVERT: C 283 THR cc_start: 0.9011 (m) cc_final: 0.8709 (p) REVERT: C 321 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8867 (mmtm) REVERT: C 357 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7766 (tm-30) REVERT: d 44 MET cc_start: 0.8330 (mmm) cc_final: 0.7491 (mmm) REVERT: d 69 TYR cc_start: 0.8833 (m-80) cc_final: 0.8544 (m-80) REVERT: d 80 ASN cc_start: 0.8135 (t0) cc_final: 0.7720 (t0) REVERT: E 5 LYS cc_start: 0.8144 (tptt) cc_final: 0.7696 (tppt) REVERT: E 134 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8342 (ttt-90) REVERT: e 23 ASP cc_start: 0.8359 (p0) cc_final: 0.7824 (p0) REVERT: F 53 LYS cc_start: 0.8640 (tptt) cc_final: 0.8209 (mtmm) REVERT: F 54 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8407 (tt0) REVERT: F 124 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8695 (tm) REVERT: G 38 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.7945 (pt0) REVERT: G 83 ASP cc_start: 0.8497 (p0) cc_final: 0.8262 (p0) REVERT: g 18 ASN cc_start: 0.9167 (t0) cc_final: 0.8734 (t0) REVERT: I 48 GLN cc_start: 0.8224 (mp10) cc_final: 0.7769 (mp10) REVERT: I 58 MET cc_start: 0.8752 (mmt) cc_final: 0.8520 (mmt) REVERT: I 87 GLN cc_start: 0.8555 (tp40) cc_final: 0.8023 (tp-100) REVERT: H 68 LEU cc_start: 0.9627 (OUTLIER) cc_final: 0.9375 (tp) REVERT: H 91 ARG cc_start: 0.7852 (mtp-110) cc_final: 0.7545 (ttm-80) REVERT: H 115 ARG cc_start: 0.8135 (mmt90) cc_final: 0.7635 (mmt90) REVERT: H 143 GLU cc_start: 0.8029 (tp30) cc_final: 0.7654 (tp30) REVERT: H 150 SER cc_start: 0.8546 (OUTLIER) cc_final: 0.8303 (p) REVERT: H 162 GLN cc_start: 0.8615 (tm-30) cc_final: 0.8220 (tm-30) REVERT: H 166 ARG cc_start: 0.8475 (ttp-170) cc_final: 0.8231 (ttp-170) REVERT: H 171 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7337 (t70) REVERT: h 104 GLN cc_start: 0.8353 (mm-40) cc_final: 0.8038 (mp10) REVERT: L 114 GLN cc_start: 0.8429 (tp-100) cc_final: 0.7961 (tp-100) REVERT: N 138 GLN cc_start: 0.9049 (mp10) cc_final: 0.8730 (mp10) REVERT: N 192 LYS cc_start: 0.8904 (tttm) cc_final: 0.8603 (ttmt) REVERT: u 82 ASN cc_start: 0.8375 (t0) cc_final: 0.7996 (m-40) REVERT: O 65 ASN cc_start: 0.8869 (t0) cc_final: 0.8131 (t0) REVERT: O 100 GLU cc_start: 0.7269 (tp30) cc_final: 0.6988 (tp30) REVERT: O 199 TYR cc_start: 0.8610 (m-80) cc_final: 0.8367 (m-10) REVERT: Q 136 ASN cc_start: 0.8801 (t0) cc_final: 0.8297 (t0) REVERT: R 25 ASP cc_start: 0.7887 (p0) cc_final: 0.7531 (p0) REVERT: R 28 GLU cc_start: 0.7581 (mp0) cc_final: 0.7216 (mp0) REVERT: R 68 GLN cc_start: 0.9182 (tp40) cc_final: 0.8678 (tp40) REVERT: R 70 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8771 (ttmt) REVERT: T 112 ASN cc_start: 0.8906 (m-40) cc_final: 0.8565 (m-40) REVERT: T 137 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8501 (tp30) REVERT: U 24 GLU cc_start: 0.8077 (mp0) cc_final: 0.7549 (mp0) REVERT: U 44 GLU cc_start: 0.8734 (pp20) cc_final: 0.7890 (pp20) REVERT: U 75 TYR cc_start: 0.8771 (t80) cc_final: 0.8445 (t80) REVERT: U 92 TRP cc_start: 0.8536 (m100) cc_final: 0.8207 (m100) REVERT: W 17 LYS cc_start: 0.8364 (mttt) cc_final: 0.8082 (mttp) REVERT: W 21 GLU cc_start: 0.8364 (mm-30) cc_final: 0.7594 (pp20) REVERT: W 22 ASN cc_start: 0.8233 (t0) cc_final: 0.7735 (m-40) REVERT: W 41 TRP cc_start: 0.6074 (m100) cc_final: 0.5821 (m100) REVERT: W 57 ARG cc_start: 0.6871 (mtm-85) cc_final: 0.6667 (ttm-80) REVERT: W 67 MET cc_start: 0.7244 (mmm) cc_final: 0.6593 (mmm) REVERT: W 157 MET cc_start: 0.7488 (pmm) cc_final: 0.7247 (pmm) REVERT: W 162 GLU cc_start: 0.5956 (tm-30) cc_final: 0.5601 (tm-30) REVERT: W 179 LYS cc_start: 0.4390 (mtmt) cc_final: 0.3962 (mttp) REVERT: W 223 ASN cc_start: 0.6710 (m110) cc_final: 0.6299 (m-40) REVERT: y 18 LYS cc_start: 0.9002 (tptt) cc_final: 0.8692 (tptm) REVERT: y 34 PHE cc_start: 0.9247 (t80) cc_final: 0.8957 (t80) REVERT: y 39 GLU cc_start: 0.8112 (tt0) cc_final: 0.7771 (tt0) REVERT: y 80 GLU cc_start: 0.7574 (mp0) cc_final: 0.6732 (mp0) REVERT: y 131 ASP cc_start: 0.8486 (m-30) cc_final: 0.8204 (m-30) REVERT: y 146 ILE cc_start: 0.9222 (tp) cc_final: 0.8554 (tt) REVERT: y 169 ASP cc_start: 0.8937 (m-30) cc_final: 0.8269 (m-30) REVERT: y 173 LEU cc_start: 0.9454 (tt) cc_final: 0.9135 (mt) REVERT: Z 106 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7867 (tm-30) REVERT: Z 121 ARG cc_start: 0.8557 (tpp80) cc_final: 0.8233 (tpp-160) REVERT: Z 134 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8670 (tp) REVERT: D 95 TRP cc_start: 0.9232 (OUTLIER) cc_final: 0.8057 (t60) REVERT: D 199 ILE cc_start: 0.9129 (mt) cc_final: 0.8818 (mt) REVERT: J 30 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8713 (tm) REVERT: J 47 GLN cc_start: 0.8691 (mt0) cc_final: 0.7967 (mp10) REVERT: q 9 LYS cc_start: 0.2437 (OUTLIER) cc_final: 0.1492 (tttm) REVERT: o 19 ASN cc_start: 0.8526 (m-40) cc_final: 0.8288 (m110) REVERT: o 44 LYS cc_start: 0.9320 (ttmt) cc_final: 0.9114 (ttmt) outliers start: 270 outliers final: 211 residues processed: 1339 average time/residue: 1.1325 time to fit residues: 2660.1277 Evaluate side-chains 1379 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 1147 time to evaluate : 6.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain v residue 170 THR Chi-restraints excluded: chain v residue 197 LEU Chi-restraints excluded: chain v residue 255 ASP Chi-restraints excluded: chain v residue 362 ILE Chi-restraints excluded: chain v residue 378 ASN Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain a residue 70 LYS Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain b residue 15 ASN Chi-restraints excluded: chain b residue 16 ASP Chi-restraints excluded: chain b residue 62 GLU Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 164 ASP Chi-restraints excluded: chain b residue 169 THR Chi-restraints excluded: chain b residue 229 THR Chi-restraints excluded: chain b residue 363 VAL Chi-restraints excluded: chain b residue 385 LEU Chi-restraints excluded: chain b residue 395 ARG Chi-restraints excluded: chain b residue 402 ILE Chi-restraints excluded: chain b residue 434 GLU Chi-restraints excluded: chain b residue 435 ILE Chi-restraints excluded: chain b residue 440 ASN Chi-restraints excluded: chain b residue 445 LEU Chi-restraints excluded: chain b residue 479 ASP Chi-restraints excluded: chain b residue 524 LEU Chi-restraints excluded: chain b residue 595 ASP Chi-restraints excluded: chain b residue 634 LEU Chi-restraints excluded: chain b residue 644 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 321 LYS Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain c residue 11 ASN Chi-restraints excluded: chain c residue 18 ILE Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 63 SER Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain d residue 20 LEU Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 87 ASN Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 104 LEU Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 134 ARG Chi-restraints excluded: chain E residue 138 GLN Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain e residue 4 LEU Chi-restraints excluded: chain e residue 14 THR Chi-restraints excluded: chain e residue 51 SER Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain e residue 115 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 72 THR Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain g residue 15 THR Chi-restraints excluded: chain g residue 20 ILE Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 47 CYS Chi-restraints excluded: chain g residue 49 SER Chi-restraints excluded: chain g residue 55 SER Chi-restraints excluded: chain g residue 66 SER Chi-restraints excluded: chain g residue 71 THR Chi-restraints excluded: chain g residue 74 ARG Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 60 THR Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 142 ASP Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain H residue 183 HIS Chi-restraints excluded: chain h residue 37 SER Chi-restraints excluded: chain h residue 76 GLN Chi-restraints excluded: chain h residue 79 ASP Chi-restraints excluded: chain h residue 98 SER Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain i residue 93 ILE Chi-restraints excluded: chain j residue 7 SER Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 43 LYS Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain l residue 9 ILE Chi-restraints excluded: chain l residue 32 ASN Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 62 GLN Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain N residue 171 SER Chi-restraints excluded: chain u residue 9 CYS Chi-restraints excluded: chain u residue 19 ILE Chi-restraints excluded: chain u residue 32 CYS Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain u residue 90 LEU Chi-restraints excluded: chain u residue 145 LEU Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 89 SER Chi-restraints excluded: chain O residue 151 ASP Chi-restraints excluded: chain O residue 189 ASP Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain P residue 75 GLU Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 166 VAL Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 49 LEU Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 71 LEU Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 150 VAL Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 70 LYS Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 109 TYR Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain S residue 49 HIS Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 88 HIS Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain T residue 98 HIS Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain V residue 11 PHE Chi-restraints excluded: chain V residue 22 ILE Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain W residue 96 CYS Chi-restraints excluded: chain W residue 217 VAL Chi-restraints excluded: chain X residue 75 LYS Chi-restraints excluded: chain X residue 87 SER Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain Y residue 7 ASP Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 59 VAL Chi-restraints excluded: chain Y residue 73 VAL Chi-restraints excluded: chain Y residue 76 LEU Chi-restraints excluded: chain Y residue 80 VAL Chi-restraints excluded: chain Y residue 90 VAL Chi-restraints excluded: chain y residue 5 THR Chi-restraints excluded: chain y residue 59 ILE Chi-restraints excluded: chain y residue 101 LEU Chi-restraints excluded: chain y residue 106 ASN Chi-restraints excluded: chain y residue 179 VAL Chi-restraints excluded: chain y residue 199 VAL Chi-restraints excluded: chain y residue 206 THR Chi-restraints excluded: chain Z residue 5 LEU Chi-restraints excluded: chain Z residue 106 GLN Chi-restraints excluded: chain Z residue 134 LEU Chi-restraints excluded: chain z residue 4 SER Chi-restraints excluded: chain z residue 41 LEU Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain D residue 95 TRP Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 41 SER Chi-restraints excluded: chain J residue 52 TYR Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain q residue 9 LYS Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 79 THR Chi-restraints excluded: chain q residue 82 GLN Chi-restraints excluded: chain o residue 48 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 939 optimal weight: 10.0000 chunk 989 optimal weight: 50.0000 chunk 903 optimal weight: 10.0000 chunk 962 optimal weight: 20.0000 chunk 579 optimal weight: 4.9990 chunk 419 optimal weight: 10.0000 chunk 756 optimal weight: 10.0000 chunk 295 optimal weight: 4.9990 chunk 870 optimal weight: 10.0000 chunk 910 optimal weight: 10.0000 chunk 959 optimal weight: 30.0000 overall best weight: 7.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** v 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS B 211 GLN b 614 ASN C 58 HIS C 291 ASN d 57 GLN E 126 GLN E 138 GLN ** G 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 232 HIS ** g 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 GLN N 11 GLN ** P 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 46 GLN ** S 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 127 GLN V 47 ASN ** W 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 ASN ** J 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 47 GLN ** o 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 48 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 142676 Z= 0.454 Angle : 0.741 14.745 209710 Z= 0.374 Chirality : 0.042 0.324 26338 Planarity : 0.006 0.101 13678 Dihedral : 22.937 179.747 62057 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.84 % Favored : 90.96 % Rotamer: Outliers : 4.93 % Allowed : 20.08 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.10), residues: 7123 helix: 0.21 (0.10), residues: 2528 sheet: -0.81 (0.17), residues: 942 loop : -1.67 (0.10), residues: 3653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP M 99 HIS 0.020 0.002 HIS o 48 PHE 0.028 0.002 PHE F 229 TYR 0.051 0.003 TYR O 167 ARG 0.011 0.001 ARG l 36 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14246 Ramachandran restraints generated. 7123 Oldfield, 0 Emsley, 7123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14246 Ramachandran restraints generated. 7123 Oldfield, 0 Emsley, 7123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1430 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 300 poor density : 1130 time to evaluate : 6.919 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: v 175 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8018 (mt-10) REVERT: A 48 ILE cc_start: 0.9287 (OUTLIER) cc_final: 0.8952 (mp) REVERT: A 142 ASP cc_start: 0.7911 (OUTLIER) cc_final: 0.7606 (p0) REVERT: A 144 ASN cc_start: 0.8194 (m110) cc_final: 0.7418 (p0) REVERT: A 194 ASN cc_start: 0.9257 (t0) cc_final: 0.8760 (t0) REVERT: a 135 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7769 (tm-30) REVERT: B 255 TRP cc_start: 0.8594 (t60) cc_final: 0.8081 (t60) REVERT: B 325 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8796 (ttmt) REVERT: b 62 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.6461 (tp30) REVERT: b 124 GLN cc_start: 0.8469 (tt0) cc_final: 0.8208 (mp10) REVERT: b 136 MET cc_start: 0.8400 (mtt) cc_final: 0.8107 (mtp) REVERT: b 143 LEU cc_start: 0.6663 (OUTLIER) cc_final: 0.6306 (tt) REVERT: b 213 TYR cc_start: 0.7929 (m-80) cc_final: 0.7625 (m-80) REVERT: b 336 CYS cc_start: 0.8326 (m) cc_final: 0.8057 (m) REVERT: b 394 ASN cc_start: 0.8887 (m-40) cc_final: 0.8109 (p0) REVERT: b 395 ARG cc_start: 0.7043 (OUTLIER) cc_final: 0.5924 (pmt100) REVERT: b 401 ASP cc_start: 0.7848 (m-30) cc_final: 0.7521 (m-30) REVERT: b 595 ASP cc_start: 0.6427 (OUTLIER) cc_final: 0.6066 (p0) REVERT: C 63 GLU cc_start: 0.7462 (pm20) cc_final: 0.7065 (pm20) REVERT: C 99 MET cc_start: 0.8207 (ptp) cc_final: 0.7803 (ptm) REVERT: C 357 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7778 (tm-30) REVERT: c 100 ILE cc_start: 0.9275 (OUTLIER) cc_final: 0.8749 (tt) REVERT: d 44 MET cc_start: 0.8391 (mmm) cc_final: 0.7402 (mmm) REVERT: d 80 ASN cc_start: 0.8180 (t0) cc_final: 0.7780 (t0) REVERT: E 134 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8337 (ttt-90) REVERT: e 23 ASP cc_start: 0.8471 (p0) cc_final: 0.7889 (p0) REVERT: F 30 ARG cc_start: 0.7308 (ttt90) cc_final: 0.7050 (ttt90) REVERT: F 53 LYS cc_start: 0.8696 (tptt) cc_final: 0.8248 (mtmm) REVERT: F 54 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8459 (tt0) REVERT: F 124 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8804 (tm) REVERT: f 24 ASN cc_start: 0.9127 (t0) cc_final: 0.8888 (t0) REVERT: f 63 LYS cc_start: 0.8956 (mttp) cc_final: 0.8686 (mttm) REVERT: G 83 ASP cc_start: 0.8494 (p0) cc_final: 0.8282 (p0) REVERT: G 219 ASP cc_start: 0.8589 (p0) cc_final: 0.8283 (p0) REVERT: g 18 ASN cc_start: 0.9335 (t0) cc_final: 0.8859 (t0) REVERT: g 96 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7981 (mm-30) REVERT: I 48 GLN cc_start: 0.8359 (mp10) cc_final: 0.7915 (mp10) REVERT: I 58 MET cc_start: 0.8678 (mmt) cc_final: 0.8451 (mmt) REVERT: I 81 ARG cc_start: 0.8001 (mmm160) cc_final: 0.7450 (mmp-170) REVERT: I 87 GLN cc_start: 0.8595 (tp40) cc_final: 0.8027 (tp-100) REVERT: I 125 GLU cc_start: 0.8149 (tp30) cc_final: 0.7854 (tp30) REVERT: H 91 ARG cc_start: 0.7891 (mtp-110) cc_final: 0.7574 (ttm-80) REVERT: H 150 SER cc_start: 0.8646 (OUTLIER) cc_final: 0.8393 (p) REVERT: H 162 GLN cc_start: 0.8746 (tm-30) cc_final: 0.8489 (tm-30) REVERT: H 171 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.7422 (t70) REVERT: h 104 GLN cc_start: 0.8438 (mm-40) cc_final: 0.8167 (mp10) REVERT: k 31 LEU cc_start: 0.8113 (mm) cc_final: 0.7591 (mt) REVERT: L 114 GLN cc_start: 0.8464 (tp-100) cc_final: 0.7971 (tp-100) REVERT: N 192 LYS cc_start: 0.8954 (tttm) cc_final: 0.8675 (ttmt) REVERT: u 82 ASN cc_start: 0.8506 (t0) cc_final: 0.8229 (m-40) REVERT: Q 136 ASN cc_start: 0.8900 (t0) cc_final: 0.8418 (t0) REVERT: Q 146 SER cc_start: 0.9096 (m) cc_final: 0.8816 (p) REVERT: R 68 GLN cc_start: 0.9232 (tp40) cc_final: 0.8777 (tp40) REVERT: T 112 ASN cc_start: 0.8970 (m-40) cc_final: 0.8669 (m-40) REVERT: T 156 TYR cc_start: 0.6404 (OUTLIER) cc_final: 0.5869 (t80) REVERT: U 24 GLU cc_start: 0.8081 (mp0) cc_final: 0.7757 (mp0) REVERT: U 25 ASN cc_start: 0.8159 (m-40) cc_final: 0.7950 (t0) REVERT: U 44 GLU cc_start: 0.8765 (pp20) cc_final: 0.7944 (pp20) REVERT: U 92 TRP cc_start: 0.8605 (m100) cc_final: 0.8312 (m100) REVERT: W 12 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7327 (mt) REVERT: W 17 LYS cc_start: 0.8434 (mttt) cc_final: 0.8173 (mttp) REVERT: W 57 ARG cc_start: 0.6951 (mtm-85) cc_final: 0.6704 (ttm-80) REVERT: W 67 MET cc_start: 0.7516 (mmm) cc_final: 0.6890 (mmm) REVERT: W 157 MET cc_start: 0.7601 (pmm) cc_final: 0.7198 (pmm) REVERT: W 161 LEU cc_start: 0.6546 (OUTLIER) cc_final: 0.6101 (mt) REVERT: W 162 GLU cc_start: 0.6089 (tm-30) cc_final: 0.5501 (tm-30) REVERT: W 179 LYS cc_start: 0.4733 (mtmt) cc_final: 0.4224 (mttp) REVERT: W 223 ASN cc_start: 0.6559 (m110) cc_final: 0.6210 (m-40) REVERT: X 106 ASP cc_start: 0.7829 (m-30) cc_final: 0.7517 (m-30) REVERT: X 130 TYR cc_start: 0.8422 (m-80) cc_final: 0.7975 (m-80) REVERT: y 18 LYS cc_start: 0.9011 (tptt) cc_final: 0.8693 (tptm) REVERT: y 80 GLU cc_start: 0.7503 (mp0) cc_final: 0.6662 (mp0) REVERT: y 131 ASP cc_start: 0.8544 (m-30) cc_final: 0.8265 (m-30) REVERT: y 169 ASP cc_start: 0.8944 (m-30) cc_final: 0.8441 (m-30) REVERT: y 173 LEU cc_start: 0.9459 (tt) cc_final: 0.9123 (mt) REVERT: Z 31 GLU cc_start: 0.8475 (pm20) cc_final: 0.8050 (pm20) REVERT: Z 121 ARG cc_start: 0.8584 (tpp80) cc_final: 0.8321 (ttm-80) REVERT: Z 134 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8743 (tp) REVERT: z 4 SER cc_start: 0.9257 (OUTLIER) cc_final: 0.8834 (t) REVERT: D 95 TRP cc_start: 0.9338 (OUTLIER) cc_final: 0.8076 (t60) REVERT: D 140 ARG cc_start: 0.7917 (mtm180) cc_final: 0.6042 (tpm170) REVERT: J 30 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8698 (tm) REVERT: J 47 GLN cc_start: 0.8719 (mt0) cc_final: 0.7986 (mp10) REVERT: J 80 LEU cc_start: 0.8825 (tt) cc_final: 0.8115 (pp) REVERT: q 9 LYS cc_start: 0.2473 (OUTLIER) cc_final: 0.1701 (tttm) REVERT: o 7 HIS cc_start: 0.9092 (t-90) cc_final: 0.8775 (t-90) REVERT: o 19 ASN cc_start: 0.8668 (m-40) cc_final: 0.8427 (m110) REVERT: o 44 LYS cc_start: 0.9409 (ttmt) cc_final: 0.9147 (ttmt) outliers start: 300 outliers final: 236 residues processed: 1323 average time/residue: 1.1371 time to fit residues: 2643.0654 Evaluate side-chains 1362 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 256 poor density : 1106 time to evaluate : 6.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain v residue 163 GLN Chi-restraints excluded: chain v residue 170 THR Chi-restraints excluded: chain v residue 255 ASP Chi-restraints excluded: chain v residue 328 ILE Chi-restraints excluded: chain v residue 362 ILE Chi-restraints excluded: chain v residue 378 ASN Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain b residue 16 ASP Chi-restraints excluded: chain b residue 62 GLU Chi-restraints excluded: chain b residue 143 LEU Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 164 ASP Chi-restraints excluded: chain b residue 169 THR Chi-restraints excluded: chain b residue 229 THR Chi-restraints excluded: chain b residue 363 VAL Chi-restraints excluded: chain b residue 395 ARG Chi-restraints excluded: chain b residue 402 ILE Chi-restraints excluded: chain b residue 434 GLU Chi-restraints excluded: chain b residue 435 ILE Chi-restraints excluded: chain b residue 440 ASN Chi-restraints excluded: chain b residue 445 LEU Chi-restraints excluded: chain b residue 479 ASP Chi-restraints excluded: chain b residue 524 LEU Chi-restraints excluded: chain b residue 595 ASP Chi-restraints excluded: chain b residue 634 LEU Chi-restraints excluded: chain b residue 644 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain c residue 11 ASN Chi-restraints excluded: chain c residue 18 ILE Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 63 SER Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain d residue 20 LEU Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 87 ASN Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 104 LEU Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 134 ARG Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain e residue 4 LEU Chi-restraints excluded: chain e residue 14 THR Chi-restraints excluded: chain e residue 15 LYS Chi-restraints excluded: chain e residue 51 SER Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain e residue 115 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 175 LYS Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain f residue 31 LYS Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 72 THR Chi-restraints excluded: chain f residue 74 THR Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain g residue 15 THR Chi-restraints excluded: chain g residue 20 ILE Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 47 CYS Chi-restraints excluded: chain g residue 49 SER Chi-restraints excluded: chain g residue 55 SER Chi-restraints excluded: chain g residue 66 SER Chi-restraints excluded: chain g residue 71 THR Chi-restraints excluded: chain g residue 74 ARG Chi-restraints excluded: chain g residue 79 SER Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 60 THR Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 49 ASN Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 142 ASP Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain h residue 37 SER Chi-restraints excluded: chain h residue 76 GLN Chi-restraints excluded: chain h residue 79 ASP Chi-restraints excluded: chain h residue 98 SER Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 35 ASN Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain i residue 81 THR Chi-restraints excluded: chain i residue 93 ILE Chi-restraints excluded: chain j residue 7 SER Chi-restraints excluded: chain j residue 11 ARG Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 43 LYS Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain l residue 9 ILE Chi-restraints excluded: chain l residue 32 ASN Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 62 GLN Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 82 SER Chi-restraints excluded: chain M residue 97 SER Chi-restraints excluded: chain p residue 10 ILE Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain u residue 9 CYS Chi-restraints excluded: chain u residue 19 ILE Chi-restraints excluded: chain u residue 32 CYS Chi-restraints excluded: chain u residue 34 SER Chi-restraints excluded: chain u residue 63 LEU Chi-restraints excluded: chain u residue 145 LEU Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 89 SER Chi-restraints excluded: chain O residue 143 THR Chi-restraints excluded: chain O residue 151 ASP Chi-restraints excluded: chain O residue 189 ASP Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain P residue 75 GLU Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 166 VAL Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 15 HIS Chi-restraints excluded: chain Q residue 49 LEU Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 71 LEU Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 150 VAL Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 70 LYS Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 109 TYR Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain S residue 49 HIS Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 88 HIS Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain T residue 98 HIS Chi-restraints excluded: chain T residue 126 VAL Chi-restraints excluded: chain T residue 156 TYR Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain V residue 11 PHE Chi-restraints excluded: chain V residue 22 ILE Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain V residue 109 MET Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain W residue 96 CYS Chi-restraints excluded: chain W residue 161 LEU Chi-restraints excluded: chain W residue 217 VAL Chi-restraints excluded: chain W residue 222 ASP Chi-restraints excluded: chain X residue 75 LYS Chi-restraints excluded: chain X residue 87 SER Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain X residue 119 THR Chi-restraints excluded: chain Y residue 7 ASP Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 59 VAL Chi-restraints excluded: chain Y residue 76 LEU Chi-restraints excluded: chain Y residue 80 VAL Chi-restraints excluded: chain Y residue 90 VAL Chi-restraints excluded: chain y residue 5 THR Chi-restraints excluded: chain y residue 59 ILE Chi-restraints excluded: chain y residue 88 LEU Chi-restraints excluded: chain y residue 106 ASN Chi-restraints excluded: chain y residue 179 VAL Chi-restraints excluded: chain y residue 199 VAL Chi-restraints excluded: chain y residue 206 THR Chi-restraints excluded: chain y residue 239 THR Chi-restraints excluded: chain Z residue 5 LEU Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 97 SER Chi-restraints excluded: chain Z residue 106 GLN Chi-restraints excluded: chain Z residue 134 LEU Chi-restraints excluded: chain z residue 4 SER Chi-restraints excluded: chain z residue 41 LEU Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain D residue 95 TRP Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 41 SER Chi-restraints excluded: chain J residue 52 TYR Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain q residue 9 LYS Chi-restraints excluded: chain q residue 79 THR Chi-restraints excluded: chain q residue 82 GLN Chi-restraints excluded: chain o residue 8 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 632 optimal weight: 6.9990 chunk 1018 optimal weight: 10.0000 chunk 621 optimal weight: 3.9990 chunk 483 optimal weight: 4.9990 chunk 707 optimal weight: 3.9990 chunk 1067 optimal weight: 8.9990 chunk 982 optimal weight: 9.9990 chunk 850 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 656 optimal weight: 3.9990 chunk 521 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 GLN ** b 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 57 GLN E 138 GLN G 232 HIS M 105 GLN O 50 ASN ** P 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 46 GLN T 134 GLN ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 199 GLN ** W 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 48 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 142676 Z= 0.219 Angle : 0.602 15.019 209710 Z= 0.310 Chirality : 0.036 0.348 26338 Planarity : 0.004 0.099 13678 Dihedral : 22.866 179.978 62056 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.26 % Favored : 92.63 % Rotamer: Outliers : 4.06 % Allowed : 21.11 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.75 % 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: -1.06 (0.10), residues: 7123 helix: 0.48 (0.11), residues: 2521 sheet: -0.78 (0.17), residues: 940 loop : -1.55 (0.10), residues: 3662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 95 HIS 0.019 0.001 HIS A 218 PHE 0.019 0.001 PHE F 229 TYR 0.034 0.002 TYR F 51 ARG 0.011 0.000 ARG l 36 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14246 Ramachandran restraints generated. 7123 Oldfield, 0 Emsley, 7123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14246 Ramachandran restraints generated. 7123 Oldfield, 0 Emsley, 7123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1404 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 1157 time to evaluate : 6.647 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: v 164 LYS cc_start: 0.9151 (mmpt) cc_final: 0.8796 (mmmt) REVERT: v 175 GLU cc_start: 0.8668 (mt-10) cc_final: 0.7973 (mt-10) REVERT: A 48 ILE cc_start: 0.9205 (OUTLIER) cc_final: 0.8931 (mp) REVERT: A 142 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7648 (p0) REVERT: A 144 ASN cc_start: 0.8077 (m110) cc_final: 0.7448 (p0) REVERT: a 135 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7708 (tm-30) REVERT: B 255 TRP cc_start: 0.8504 (t60) cc_final: 0.8010 (t60) REVERT: b 62 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6676 (tp30) REVERT: b 66 LYS cc_start: 0.6682 (mtpt) cc_final: 0.5513 (mtmt) REVERT: b 124 GLN cc_start: 0.8385 (tt0) cc_final: 0.8067 (mp10) REVERT: b 136 MET cc_start: 0.8303 (mtt) cc_final: 0.7993 (mtp) REVERT: b 143 LEU cc_start: 0.6559 (OUTLIER) cc_final: 0.6334 (tt) REVERT: b 164 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7630 (m-30) REVERT: b 213 TYR cc_start: 0.7904 (m-80) cc_final: 0.7572 (m-80) REVERT: b 336 CYS cc_start: 0.8130 (m) cc_final: 0.7888 (m) REVERT: b 361 ILE cc_start: 0.6761 (mt) cc_final: 0.6513 (tt) REVERT: b 394 ASN cc_start: 0.8838 (m-40) cc_final: 0.8151 (p0) REVERT: b 395 ARG cc_start: 0.7156 (OUTLIER) cc_final: 0.6130 (pmt100) REVERT: b 401 ASP cc_start: 0.7894 (m-30) cc_final: 0.7505 (m-30) REVERT: b 548 LYS cc_start: 0.6261 (mmtm) cc_final: 0.5295 (mtmt) REVERT: b 595 ASP cc_start: 0.6192 (OUTLIER) cc_final: 0.5891 (p0) REVERT: C 63 GLU cc_start: 0.7430 (pm20) cc_final: 0.7001 (pm20) REVERT: C 99 MET cc_start: 0.8128 (ptp) cc_final: 0.7718 (ptm) REVERT: d 31 ARG cc_start: 0.8415 (tpp80) cc_final: 0.8127 (tpp80) REVERT: d 44 MET cc_start: 0.8286 (mmm) cc_final: 0.7391 (mmm) REVERT: d 80 ASN cc_start: 0.8136 (t0) cc_final: 0.7736 (t0) REVERT: E 134 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8376 (ttt-90) REVERT: e 23 ASP cc_start: 0.8428 (p0) cc_final: 0.7870 (p0) REVERT: F 30 ARG cc_start: 0.7236 (ttt90) cc_final: 0.6984 (ttt90) REVERT: F 53 LYS cc_start: 0.8610 (tptt) cc_final: 0.8171 (mtmm) REVERT: F 54 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8417 (tt0) REVERT: F 124 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8696 (tm) REVERT: f 24 ASN cc_start: 0.9040 (t0) cc_final: 0.8776 (t0) REVERT: f 63 LYS cc_start: 0.8958 (mttp) cc_final: 0.8688 (mttm) REVERT: g 18 ASN cc_start: 0.9189 (t0) cc_final: 0.8708 (t0) REVERT: I 48 GLN cc_start: 0.8287 (mp10) cc_final: 0.7850 (mp10) REVERT: I 58 MET cc_start: 0.8685 (mmt) cc_final: 0.8298 (mmt) REVERT: I 87 GLN cc_start: 0.8586 (tp40) cc_final: 0.8029 (tp-100) REVERT: H 91 ARG cc_start: 0.7876 (mtp-110) cc_final: 0.7566 (ttm-80) REVERT: H 143 GLU cc_start: 0.8191 (tp30) cc_final: 0.7845 (tp30) REVERT: H 150 SER cc_start: 0.8615 (OUTLIER) cc_final: 0.8347 (p) REVERT: H 162 GLN cc_start: 0.8620 (tm-30) cc_final: 0.8206 (tm-30) REVERT: H 171 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.7377 (t70) REVERT: h 104 GLN cc_start: 0.8376 (mm-40) cc_final: 0.8027 (mp10) REVERT: k 31 LEU cc_start: 0.7946 (mm) cc_final: 0.7442 (mt) REVERT: k 39 ARG cc_start: 0.8562 (mtp-110) cc_final: 0.8338 (mtm110) REVERT: L 114 GLN cc_start: 0.8435 (tp-100) cc_final: 0.7948 (tp-100) REVERT: N 138 GLN cc_start: 0.9044 (mp10) cc_final: 0.8728 (mp10) REVERT: N 192 LYS cc_start: 0.8881 (tttm) cc_final: 0.8585 (ttmt) REVERT: u 82 ASN cc_start: 0.8394 (t0) cc_final: 0.8071 (m-40) REVERT: O 65 ASN cc_start: 0.8860 (t0) cc_final: 0.8608 (t0) REVERT: Q 136 ASN cc_start: 0.8843 (t0) cc_final: 0.8364 (t0) REVERT: Q 146 SER cc_start: 0.9077 (m) cc_final: 0.8693 (p) REVERT: R 68 GLN cc_start: 0.9166 (tp40) cc_final: 0.8665 (tp40) REVERT: R 70 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8787 (ttmt) REVERT: T 112 ASN cc_start: 0.8940 (m-40) cc_final: 0.8719 (m-40) REVERT: T 156 TYR cc_start: 0.6166 (OUTLIER) cc_final: 0.5363 (t80) REVERT: U 25 ASN cc_start: 0.8196 (m-40) cc_final: 0.7830 (t0) REVERT: U 41 ILE cc_start: 0.9356 (OUTLIER) cc_final: 0.9126 (mp) REVERT: U 44 GLU cc_start: 0.8779 (pp20) cc_final: 0.7933 (pp20) REVERT: U 92 TRP cc_start: 0.8571 (m100) cc_final: 0.8232 (m100) REVERT: W 17 LYS cc_start: 0.8441 (mttt) cc_final: 0.8179 (mttp) REVERT: W 21 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7594 (pp20) REVERT: W 57 ARG cc_start: 0.6910 (mtm-85) cc_final: 0.6530 (ttm-80) REVERT: W 67 MET cc_start: 0.7308 (mmm) cc_final: 0.6720 (mmm) REVERT: W 96 CYS cc_start: 0.4377 (OUTLIER) cc_final: 0.3941 (p) REVERT: W 157 MET cc_start: 0.7597 (pmm) cc_final: 0.7191 (pmm) REVERT: W 161 LEU cc_start: 0.6434 (OUTLIER) cc_final: 0.6096 (mt) REVERT: W 179 LYS cc_start: 0.4472 (mtmt) cc_final: 0.4051 (mttp) REVERT: X 130 TYR cc_start: 0.8358 (m-80) cc_final: 0.7956 (m-80) REVERT: y 18 LYS cc_start: 0.9011 (tptt) cc_final: 0.8703 (tptm) REVERT: y 34 PHE cc_start: 0.9309 (t80) cc_final: 0.9043 (t80) REVERT: y 80 GLU cc_start: 0.7520 (mp0) cc_final: 0.6679 (mp0) REVERT: y 131 ASP cc_start: 0.8570 (m-30) cc_final: 0.8294 (m-30) REVERT: y 146 ILE cc_start: 0.9222 (tp) cc_final: 0.8567 (tt) REVERT: y 169 ASP cc_start: 0.8937 (m-30) cc_final: 0.8428 (m-30) REVERT: y 173 LEU cc_start: 0.9450 (tt) cc_final: 0.9128 (mt) REVERT: Z 106 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7716 (tm-30) REVERT: Z 121 ARG cc_start: 0.8537 (tpp80) cc_final: 0.8194 (tpp-160) REVERT: Z 134 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8690 (tp) REVERT: z 4 SER cc_start: 0.9194 (OUTLIER) cc_final: 0.8856 (m) REVERT: D 95 TRP cc_start: 0.9308 (OUTLIER) cc_final: 0.8013 (t60) REVERT: D 140 ARG cc_start: 0.7682 (mtm180) cc_final: 0.5977 (tpm170) REVERT: D 199 ILE cc_start: 0.9120 (mt) cc_final: 0.8785 (mt) REVERT: J 30 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8712 (tm) REVERT: J 47 GLN cc_start: 0.8723 (mt0) cc_final: 0.8065 (mp10) REVERT: J 101 ASN cc_start: 0.8716 (m110) cc_final: 0.8436 (m-40) REVERT: J 150 ASN cc_start: 0.8349 (t0) cc_final: 0.7737 (t0) REVERT: J 172 LEU cc_start: 0.7379 (mt) cc_final: 0.7104 (mt) REVERT: q 9 LYS cc_start: 0.2240 (OUTLIER) cc_final: 0.1571 (tttm) REVERT: o 44 LYS cc_start: 0.9308 (ttmt) cc_final: 0.9092 (ttmt) outliers start: 247 outliers final: 202 residues processed: 1309 average time/residue: 1.1591 time to fit residues: 2671.6428 Evaluate side-chains 1363 residues out of total 6118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 1139 time to evaluate : 6.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain v residue 170 THR Chi-restraints excluded: chain v residue 255 ASP Chi-restraints excluded: chain v residue 328 ILE Chi-restraints excluded: chain v residue 362 ILE Chi-restraints excluded: chain v residue 378 ASN Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 148 ILE Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain b residue 15 ASN Chi-restraints excluded: chain b residue 62 GLU Chi-restraints excluded: chain b residue 143 LEU Chi-restraints excluded: chain b residue 164 ASP Chi-restraints excluded: chain b residue 169 THR Chi-restraints excluded: chain b residue 229 THR Chi-restraints excluded: chain b residue 363 VAL Chi-restraints excluded: chain b residue 395 ARG Chi-restraints excluded: chain b residue 402 ILE Chi-restraints excluded: chain b residue 435 ILE Chi-restraints excluded: chain b residue 445 LEU Chi-restraints excluded: chain b residue 479 ASP Chi-restraints excluded: chain b residue 524 LEU Chi-restraints excluded: chain b residue 595 ASP Chi-restraints excluded: chain b residue 634 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain c residue 11 ASN Chi-restraints excluded: chain c residue 18 ILE Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain d residue 20 LEU Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 87 ASN Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 104 LEU Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 134 ARG Chi-restraints excluded: chain E residue 138 GLN Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain e residue 4 LEU Chi-restraints excluded: chain e residue 14 THR Chi-restraints excluded: chain e residue 51 SER Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain e residue 115 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 175 LYS Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 72 THR Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain g residue 20 ILE Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 47 CYS Chi-restraints excluded: chain g residue 49 SER Chi-restraints excluded: chain g residue 55 SER Chi-restraints excluded: chain g residue 66 SER Chi-restraints excluded: chain g residue 71 THR Chi-restraints excluded: chain g residue 74 ARG Chi-restraints excluded: chain g residue 79 SER Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 60 THR Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain H residue 183 HIS Chi-restraints excluded: chain h residue 37 SER Chi-restraints excluded: chain h residue 79 ASP Chi-restraints excluded: chain h residue 98 SER Chi-restraints excluded: chain i residue 15 LYS Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain i residue 93 ILE Chi-restraints excluded: chain j residue 7 SER Chi-restraints excluded: chain j residue 11 ARG Chi-restraints excluded: chain j residue 18 LEU Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain k residue 8 ILE Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain l residue 9 ILE Chi-restraints excluded: chain l residue 32 ASN Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 28 SER Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 62 GLN Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain u residue 9 CYS Chi-restraints excluded: chain u residue 32 CYS Chi-restraints excluded: chain u residue 34 SER Chi-restraints excluded: chain u residue 145 LEU Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 89 SER Chi-restraints excluded: chain O residue 151 ASP Chi-restraints excluded: chain O residue 189 ASP Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain P residue 75 GLU Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 166 VAL Chi-restraints excluded: chain P residue 168 LEU Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 71 LEU Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 150 VAL Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 70 LYS Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain S residue 49 HIS Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 88 HIS Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain T residue 98 HIS Chi-restraints excluded: chain T residue 126 VAL Chi-restraints excluded: chain T residue 134 GLN Chi-restraints excluded: chain T residue 136 ARG Chi-restraints excluded: chain T residue 156 TYR Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain U residue 41 ILE Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain V residue 11 PHE Chi-restraints excluded: chain V residue 22 ILE Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 96 CYS Chi-restraints excluded: chain W residue 161 LEU Chi-restraints excluded: chain W residue 217 VAL Chi-restraints excluded: chain X residue 87 SER Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain X residue 119 THR Chi-restraints excluded: chain Y residue 7 ASP Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 59 VAL Chi-restraints excluded: chain Y residue 76 LEU Chi-restraints excluded: chain Y residue 80 VAL Chi-restraints excluded: chain y residue 5 THR Chi-restraints excluded: chain y residue 59 ILE Chi-restraints excluded: chain y residue 88 LEU Chi-restraints excluded: chain y residue 101 LEU Chi-restraints excluded: chain y residue 106 ASN Chi-restraints excluded: chain y residue 179 VAL Chi-restraints excluded: chain y residue 199 VAL Chi-restraints excluded: chain y residue 239 THR Chi-restraints excluded: chain Z residue 5 LEU Chi-restraints excluded: chain Z residue 106 GLN Chi-restraints excluded: chain Z residue 134 LEU Chi-restraints excluded: chain z residue 4 SER Chi-restraints excluded: chain z residue 41 LEU Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 95 TRP Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 41 SER Chi-restraints excluded: chain J residue 52 TYR Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain q residue 9 LYS Chi-restraints excluded: chain q residue 79 THR Chi-restraints excluded: chain q residue 82 GLN Chi-restraints excluded: chain o residue 8 THR Chi-restraints excluded: chain o residue 48 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 675 optimal weight: 6.9990 chunk 905 optimal weight: 10.0000 chunk 260 optimal weight: 0.0050 chunk 784 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 236 optimal weight: 1.9990 chunk 851 optimal weight: 10.0000 chunk 356 optimal weight: 10.0000 chunk 874 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 156 optimal weight: 20.0000 overall best weight: 5.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 120 ASN B 211 GLN ** b 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 614 ASN ** C 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 232 HIS ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 15 HIS ** S 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 ASN ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 ASN ** q 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 12 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.108361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.083274 restraints weight = 296849.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.085611 restraints weight = 125214.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.087027 restraints weight = 78185.780| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3073 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.310 142676 Z= 0.303 Angle : 0.659 59.200 209710 Z= 0.350 Chirality : 0.042 2.965 26338 Planarity : 0.005 0.229 13678 Dihedral : 22.864 179.991 62056 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.43 % Favored : 92.46 % Rotamer: Outliers : 3.98 % Allowed : 21.34 % Favored : 74.68 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.75 % 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: -1.07 (0.10), residues: 7123 helix: 0.46 (0.11), residues: 2521 sheet: -0.78 (0.17), residues: 940 loop : -1.54 (0.10), residues: 3662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 23 HIS 0.381 0.002 HIS o 48 PHE 0.020 0.001 PHE F 229 TYR 0.049 0.002 TYR u 4 ARG 0.009 0.000 ARG l 36 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 38391.48 seconds wall clock time: 667 minutes 40.95 seconds (40060.95 seconds total)