Starting phenix.real_space_refine on Sat Mar 16 03:01:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8l_0371/03_2024/6n8l_0371.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8l_0371/03_2024/6n8l_0371.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/6n8l_0371/03_2024/6n8l_0371.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8l_0371/03_2024/6n8l_0371.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8l_0371/03_2024/6n8l_0371.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8l_0371/03_2024/6n8l_0371.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: 5 Type Number sf(0) Gaussians P 3479 5.49 5 S 122 5.16 5 C 68274 2.51 5 N 23904 2.21 5 O 34147 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "v ARG 63": "NH1" <-> "NH2" Residue "v ARG 73": "NH1" <-> "NH2" Residue "v ARG 113": "NH1" <-> "NH2" Residue "v ARG 162": "NH1" <-> "NH2" Residue "v TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ARG 303": "NH1" <-> "NH2" 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 TYR 133": "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 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 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 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 229": "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 ARG 166": "NH1" <-> "NH2" Residue "H ARG 168": "NH1" <-> "NH2" Residue "H ARG 173": "NH1" <-> "NH2" Residue "h TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "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 TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 84": "NH1" <-> "NH2" Residue "Z PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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: 129926 Number of models: 1 Model: "" Number of chains: 48 Chain: "v" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2783 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 13, 'TRANS': 348} Chain breaks: 4 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 69 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: "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: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1989 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 239} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 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: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1270 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 151} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 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: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1053 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 131} Chain breaks: 1 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: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1698 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} 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': 335, 'rna2p_pyr': 229, 'rna3p_pur': 1440, 'rna3p_pyr': 1197} Link IDs: {'rna2p': 564, 'rna3p': 2636} 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} 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: 49.46, per 1000 atoms: 0.38 Number of scatterers: 129926 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: 5 Type Number sf(0) S 122 16.00 P 3479 15.00 O 34147 8.00 N 23904 7.00 C 68274 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS v 19 " - pdb=" SG CYS v 22 " distance=2.04 Simple disulfide: pdb=" SG CYS v 19 " - pdb=" SG CYS v 35 " distance=2.04 Simple disulfide: pdb=" SG CYS v 22 " - pdb=" SG CYS v 35 " distance=2.04 Simple disulfide: pdb=" SG CYS v 22 " - pdb=" SG CYS v 38 " distance=2.05 Simple disulfide: pdb=" SG CYS v 58 " - pdb=" SG CYS v 143 " distance=2.03 Simple disulfide: pdb=" SG CYS v 61 " - pdb=" SG CYS v 143 " distance=2.02 Simple disulfide: pdb=" SG CYS v 61 " - pdb=" SG CYS v 146 " distance=2.02 Simple disulfide: pdb=" SG CYS v 143 " - pdb=" SG CYS v 146 " distance=2.05 Simple disulfide: pdb=" SG CYS g 44 " - pdb=" SG CYS g 47 " distance=2.03 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=2.02 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=2.03 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=2.07 Simple disulfide: pdb=" SG CYS u 9 " - pdb=" SG CYS u 32 " distance=2.03 Simple disulfide: pdb=" SG CYS u 9 " - pdb=" SG CYS u 36 " distance=2.00 Simple disulfide: pdb=" SG CYS u 32 " - pdb=" SG CYS u 36 " distance=2.58 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: 46.47 Conformation dependent library (CDL) restraints added in 8.0 seconds 13548 Ramachandran restraints generated. 6774 Oldfield, 0 Emsley, 6774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13308 Finding SS restraints... Secondary structure from input PDB file: 243 helices and 70 sheets defined 37.9% alpha, 13.9% beta 763 base pairs and 1796 stacking pairs defined. Time for finding SS restraints: 39.39 Creating SS restraints... Processing helix chain 'v' and resid 77 through 88 removed outlier: 3.839A pdb=" N LEU v 82 " --> pdb=" O SER v 78 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA v 83 " --> pdb=" O ARG v 79 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS v 85 " --> pdb=" O LEU v 81 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG v 87 " --> pdb=" O ALA v 83 " (cutoff:3.500A) Processing helix chain 'v' and resid 147 through 152 removed outlier: 3.768A pdb=" N THR v 152 " --> pdb=" O SER v 149 " (cutoff:3.500A) Processing helix chain 'v' and resid 168 through 181 removed outlier: 3.698A pdb=" N GLN v 176 " --> pdb=" O LEU v 172 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU v 179 " --> pdb=" O GLU v 175 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS v 181 " --> pdb=" O LEU v 177 " (cutoff:3.500A) Processing helix chain 'v' and resid 204 through 218 removed outlier: 3.782A pdb=" N VAL v 208 " --> pdb=" O LYS v 204 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE v 213 " --> pdb=" O LYS v 209 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA v 216 " --> pdb=" O ASP v 212 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL v 217 " --> pdb=" O PHE v 213 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL v 218 " --> pdb=" O LEU v 214 " (cutoff:3.500A) Processing helix chain 'v' and resid 260 through 265 Processing helix chain 'v' and resid 297 through 302 Processing helix chain 'v' and resid 311 through 315 removed outlier: 3.587A pdb=" N GLN v 314 " --> pdb=" O ASP v 311 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU v 315 " --> pdb=" O VAL v 312 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 311 through 315' Processing helix chain 'v' and resid 343 through 347 removed outlier: 4.228A pdb=" N GLY v 347 " --> pdb=" O THR v 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 343 through 347' Processing helix chain 'v' and resid 381 through 386 Processing helix chain 'v' and resid 388 through 392 Processing helix chain 's' and resid 4 through 14 removed outlier: 3.539A pdb=" N UNK s 11 " --> pdb=" O UNK s 7 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N UNK s 12 " --> pdb=" O UNK s 8 " (cutoff:3.500A) Processing helix chain 's' and resid 66 through 71 Processing helix chain 's' and resid 80 through 86 Processing helix chain 's' and resid 90 through 99 removed outlier: 3.502A pdb=" N UNK s 96 " --> pdb=" O UNK s 92 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N UNK s 99 " --> pdb=" O UNK s 95 " (cutoff:3.500A) Processing helix chain 's' and resid 111 through 116 Processing helix chain 's' and resid 120 through 125 removed outlier: 4.015A pdb=" N UNK s 124 " --> pdb=" O UNK s 120 " (cutoff:3.500A) Processing helix chain 's' and resid 138 through 146 removed outlier: 4.286A pdb=" N UNK s 142 " --> pdb=" O UNK s 138 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N UNK s 146 " --> pdb=" O UNK s 142 " (cutoff:3.500A) Processing helix chain 's' and resid 171 through 175 removed outlier: 3.920A pdb=" N UNK s 174 " --> pdb=" O UNK s 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 11 removed outlier: 3.737A pdb=" N LYS A 10 " --> pdb=" O ASN A 7 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY A 11 " --> pdb=" O GLN A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 39 Processing helix chain 'A' and resid 173 through 177 removed outlier: 3.543A pdb=" N ASP A 176 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS A 177 " --> pdb=" O ARG A 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 173 through 177' Processing helix chain 'A' and resid 181 through 190 removed outlier: 3.533A pdb=" N ALA A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) Processing helix chain 'a' and resid 83 through 92 removed outlier: 4.136A pdb=" N ASP a 88 " --> pdb=" O GLU a 84 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLN a 89 " --> pdb=" O ASP a 85 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU a 91 " --> pdb=" O ARG a 87 " (cutoff:3.500A) Processing helix chain 'a' and resid 104 through 108 Processing helix chain 'a' and resid 131 through 142 removed outlier: 3.528A pdb=" N GLU a 135 " --> pdb=" O SER a 131 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA a 141 " --> pdb=" O LYS a 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 118 removed outlier: 3.559A pdb=" N LYS B 115 " --> pdb=" O SER B 111 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 135 removed outlier: 3.593A pdb=" N ALA B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 154 removed outlier: 3.661A pdb=" N ILE B 151 " --> pdb=" O GLU B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 188 through 197 removed outlier: 3.643A pdb=" N TRP B 194 " --> pdb=" O GLU B 190 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU B 197 " --> pdb=" O ASP B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 234 Processing helix chain 'B' and resid 347 through 351 Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'b' and resid 379 through 385 removed outlier: 3.748A pdb=" N LYS b 383 " --> pdb=" O PRO b 379 " (cutoff:3.500A) Processing helix chain 'b' and resid 398 through 405 removed outlier: 3.801A pdb=" N ILE b 402 " --> pdb=" O LEU b 398 " (cutoff:3.500A) Processing helix chain 'b' and resid 440 through 445 removed outlier: 3.629A pdb=" N PHE b 444 " --> pdb=" O ASN b 440 " (cutoff:3.500A) Processing helix chain 'b' and resid 448 through 465 removed outlier: 3.703A pdb=" N ALA b 455 " --> pdb=" O ALA b 451 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU b 459 " --> pdb=" O ALA b 455 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU b 461 " --> pdb=" O GLU b 457 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU b 463 " --> pdb=" O GLU b 459 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASN b 465 " --> pdb=" O GLU b 461 " (cutoff:3.500A) Processing helix chain 'b' and resid 482 through 512 removed outlier: 3.534A pdb=" N ASP b 487 " --> pdb=" O ALA b 483 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP b 488 " --> pdb=" O SER b 484 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS b 490 " --> pdb=" O VAL b 486 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TRP b 495 " --> pdb=" O GLU b 491 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN b 498 " --> pdb=" O ALA b 494 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASN b 509 " --> pdb=" O ALA b 505 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N SER b 512 " --> pdb=" O ARG b 508 " (cutoff:3.500A) Processing helix chain 'b' and resid 528 through 539 removed outlier: 3.923A pdb=" N GLU b 533 " --> pdb=" O GLY b 529 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET b 535 " --> pdb=" O MET b 531 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU b 538 " --> pdb=" O HIS b 534 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY b 539 " --> pdb=" O MET b 535 " (cutoff:3.500A) Processing helix chain 'b' and resid 542 through 550 removed outlier: 4.020A pdb=" N LYS b 548 " --> pdb=" O ALA b 544 " (cutoff:3.500A) Processing helix chain 'b' and resid 595 through 608 removed outlier: 3.704A pdb=" N ARG b 599 " --> pdb=" O ASP b 595 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER b 600 " --> pdb=" O GLY b 596 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS b 607 " --> pdb=" O ASP b 603 " (cutoff:3.500A) Processing helix chain 'b' and resid 610 through 616 removed outlier: 3.600A pdb=" N ASN b 614 " --> pdb=" O ARG b 610 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG b 615 " --> pdb=" O ARG b 611 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N HIS b 616 " --> pdb=" O GLU b 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 610 through 616' Processing helix chain 'b' and resid 631 through 636 removed outlier: 4.217A pdb=" N PHE b 635 " --> pdb=" O SER b 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 43 removed outlier: 3.877A pdb=" N SER C 41 " --> pdb=" O THR C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 132 removed outlier: 3.557A pdb=" N ALA C 128 " --> pdb=" O SER C 124 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N THR C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA C 130 " --> pdb=" O ILE C 126 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL C 131 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 4.085A 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 157 Processing helix chain 'C' and resid 161 through 173 removed outlier: 3.519A pdb=" N ALA C 167 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY C 173 " --> pdb=" O LEU C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 181 removed outlier: 3.871A pdb=" N VAL C 181 " --> pdb=" O ASP C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 219 Processing helix chain 'C' and resid 234 through 239 Processing helix chain 'C' and resid 252 through 263 removed outlier: 3.551A pdb=" N LYS C 257 " --> pdb=" O ALA C 253 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU C 258 " --> pdb=" O ALA C 254 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASP C 259 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLN C 260 " --> pdb=" O THR C 256 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP C 262 " --> pdb=" O LEU C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 291 removed outlier: 3.964A pdb=" N ILE C 289 " --> pdb=" O ASP C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 297 removed outlier: 3.571A pdb=" N GLN C 296 " --> pdb=" O SER C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 325 removed outlier: 3.559A pdb=" N LEU C 324 " --> pdb=" O ASN C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 337 removed outlier: 4.625A pdb=" N VAL C 333 " --> pdb=" O PRO C 329 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA C 335 " --> pdb=" O ALA C 331 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA C 336 " --> pdb=" O LYS C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 360 removed outlier: 3.792A pdb=" N THR C 356 " --> pdb=" O ALA C 352 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR C 358 " --> pdb=" O VAL C 354 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 18 removed outlier: 3.624A pdb=" N LEU c 16 " --> pdb=" O GLN c 12 " (cutoff:3.500A) Processing helix chain 'c' and resid 26 through 37 removed outlier: 3.962A pdb=" N LYS c 32 " --> pdb=" O LYS c 28 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER c 33 " --> pdb=" O SER c 29 " (cutoff:3.500A) Processing helix chain 'c' and resid 49 through 61 removed outlier: 3.512A pdb=" N MET c 61 " --> pdb=" O GLU c 57 " (cutoff:3.500A) Processing helix chain 'c' and resid 74 through 79 removed outlier: 3.838A pdb=" N GLY c 78 " --> pdb=" O ASN c 74 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR c 79 " --> pdb=" O ASN c 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 74 through 79' Processing helix chain 'd' and resid 24 through 27 Processing helix chain 'd' and resid 28 through 45 removed outlier: 3.503A pdb=" N VAL d 33 " --> pdb=" O ALA d 29 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS d 34 " --> pdb=" O PRO d 30 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS d 43 " --> pdb=" O PHE d 39 " (cutoff:3.500A) Processing helix chain 'd' and resid 52 through 60 Processing helix chain 'd' and resid 61 through 63 No H-bonds generated for 'chain 'd' and resid 61 through 63' Processing helix chain 'E' and resid 97 through 101 removed outlier: 4.253A pdb=" N LYS E 100 " --> pdb=" O ASN E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 107 removed outlier: 3.800A pdb=" N ALA E 107 " --> pdb=" O GLU E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 150 removed outlier: 3.622A pdb=" N VAL E 141 " --> pdb=" O ASP E 137 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA E 144 " --> pdb=" O VAL E 140 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU E 145 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ALA E 147 " --> pdb=" O LYS E 143 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU E 148 " --> pdb=" O ALA E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 161 removed outlier: 3.519A 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) Processing helix chain 'e' and resid 54 through 58 Processing helix chain 'e' and resid 78 through 83 Processing helix chain 'e' and resid 84 through 86 No H-bonds generated for 'chain 'e' and resid 84 through 86' Processing helix chain 'e' and resid 101 through 116 removed outlier: 3.778A pdb=" N VAL e 106 " --> pdb=" O ALA e 102 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL e 107 " --> pdb=" O LYS e 103 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA e 114 " --> pdb=" O ALA e 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 72 removed outlier: 3.519A pdb=" N LYS F 38 " --> pdb=" O LYS F 34 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU F 39 " --> pdb=" O ALA F 35 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE F 43 " --> pdb=" O GLU F 39 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE F 44 " --> pdb=" O LYS F 40 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU F 56 " --> pdb=" O GLN F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 106 removed outlier: 3.789A pdb=" N VAL F 102 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 130 removed outlier: 3.541A pdb=" N GLU F 125 " --> pdb=" O LYS F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 152 removed outlier: 3.590A pdb=" N ILE F 144 " --> pdb=" O SER F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 171 removed outlier: 4.435A pdb=" N ILE F 169 " --> pdb=" O ASP F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 177 removed outlier: 3.740A pdb=" N GLY F 177 " --> pdb=" O GLY F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 190 Processing helix chain 'F' and resid 194 through 200 Processing helix chain 'F' and resid 235 through 244 removed outlier: 3.878A pdb=" N LYS F 241 " --> pdb=" O ASN F 237 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER F 242 " --> pdb=" O LYS F 238 " (cutoff:3.500A) Processing helix chain 'f' and resid 37 through 42 Processing helix chain 'f' and resid 43 through 45 No H-bonds generated for 'chain 'f' and resid 43 through 45' Processing helix chain 'G' and resid 53 through 69 removed outlier: 3.511A pdb=" N GLN G 61 " --> pdb=" O ARG G 57 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS G 63 " --> pdb=" O GLN G 59 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE G 67 " --> pdb=" O LYS G 63 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 96 removed outlier: 3.593A pdb=" N ALA G 88 " --> pdb=" O ARG G 84 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU G 89 " --> pdb=" O ASN G 85 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS G 96 " --> pdb=" O LYS G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 120 removed outlier: 3.936A pdb=" N THR G 110 " --> pdb=" O LYS G 106 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA G 115 " --> pdb=" O LYS G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 143 Processing helix chain 'G' and resid 159 through 163 Processing helix chain 'G' and resid 165 through 174 Processing helix chain 'G' and resid 184 through 189 removed outlier: 3.902A pdb=" N LEU G 189 " --> pdb=" O ARG G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 222 removed outlier: 3.587A pdb=" N LEU G 211 " --> pdb=" O ASP G 207 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS G 213 " --> pdb=" O ALA G 209 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU G 214 " --> pdb=" O ALA G 210 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER G 216 " --> pdb=" O ALA G 212 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR G 217 " --> pdb=" O LYS G 213 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA G 220 " --> pdb=" O SER G 216 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN G 221 " --> pdb=" O THR G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 230 removed outlier: 3.910A pdb=" N LYS G 230 " --> pdb=" O TYR G 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 252 removed outlier: 4.033A pdb=" N ASN G 252 " --> pdb=" O LYS G 248 " (cutoff:3.500A) Processing helix chain 'g' and resid 59 through 63 removed outlier: 3.775A pdb=" N TYR g 62 " --> pdb=" O PRO g 59 " (cutoff:3.500A) Processing helix chain 'g' and resid 66 through 70 removed outlier: 3.512A pdb=" N HIS g 69 " --> pdb=" O SER g 66 " (cutoff:3.500A) Processing helix chain 'g' and resid 83 through 111 removed outlier: 3.680A pdb=" N ARG g 88 " --> pdb=" O CYS g 84 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE g 90 " --> pdb=" O LYS g 86 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA g 92 " --> pdb=" O ARG g 88 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU g 96 " --> pdb=" O ALA g 92 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE g 100 " --> pdb=" O GLU g 96 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL g 101 " --> pdb=" O GLU g 97 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR g 109 " --> pdb=" O VAL g 105 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU g 110 " --> pdb=" O LYS g 106 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA g 111 " --> pdb=" O GLU g 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 9 removed outlier: 3.711A pdb=" N LYS I 7 " --> pdb=" O ARG I 3 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG I 8 " --> pdb=" O TYR I 4 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 26 removed outlier: 3.541A pdb=" N TYR I 22 " --> pdb=" O LEU I 18 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN I 23 " --> pdb=" O ASP I 19 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP I 24 " --> pdb=" O LEU I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 27 through 36 removed outlier: 3.553A pdb=" N VAL I 31 " --> pdb=" O THR I 27 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN I 36 " --> pdb=" O GLN I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 69 removed outlier: 3.682A pdb=" N LYS I 65 " --> pdb=" O ALA I 61 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N HIS I 67 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS I 69 " --> pdb=" O LYS I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 80 removed outlier: 3.659A pdb=" N ARG I 76 " --> pdb=" O VAL I 72 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS I 78 " --> pdb=" O LYS I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 93 removed outlier: 4.296A pdb=" N SER I 90 " --> pdb=" O THR I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 111 removed outlier: 3.667A pdb=" N ARG I 104 " --> pdb=" O LYS I 100 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN I 110 " --> pdb=" O GLN I 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 130 removed outlier: 3.935A pdb=" N GLU I 115 " --> pdb=" O SER I 111 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA I 121 " --> pdb=" O GLU I 117 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU I 125 " --> pdb=" O ALA I 121 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP I 128 " --> pdb=" O LYS I 124 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER I 129 " --> pdb=" O GLU I 125 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR I 130 " --> pdb=" O HIS I 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 84 removed outlier: 3.659A pdb=" N ALA H 67 " --> pdb=" O LYS H 63 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU H 68 " --> pdb=" O HIS H 64 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG H 69 " --> pdb=" O VAL H 65 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR H 70 " --> pdb=" O ALA H 66 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS H 72 " --> pdb=" O LEU H 68 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN H 77 " --> pdb=" O SER H 73 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL H 82 " --> pdb=" O MET H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 120 Processing helix chain 'H' and resid 150 through 164 removed outlier: 3.728A pdb=" N GLN H 156 " --> pdb=" O GLU H 152 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN H 157 " --> pdb=" O ASP H 153 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN H 162 " --> pdb=" O ALA H 158 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 10 removed outlier: 3.772A pdb=" N LEU h 9 " --> pdb=" O LYS h 5 " (cutoff:3.500A) Processing helix chain 'h' and resid 13 through 35 removed outlier: 3.657A pdb=" N GLU h 27 " --> pdb=" O ASP h 23 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS h 32 " --> pdb=" O LEU h 28 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL h 33 " --> pdb=" O ALA h 29 " (cutoff:3.500A) Processing helix chain 'h' and resid 43 through 70 removed outlier: 3.607A pdb=" N VAL h 47 " --> pdb=" O LYS h 43 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL h 57 " --> pdb=" O CYS h 53 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG h 67 " --> pdb=" O ARG h 63 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN h 68 " --> pdb=" O GLU h 64 " (cutoff:3.500A) Processing helix chain 'h' and resid 77 through 81 Processing helix chain 'h' and resid 85 through 90 removed outlier: 3.619A pdb=" N ARG h 89 " --> pdb=" O THR h 85 " (cutoff:3.500A) Processing helix chain 'h' and resid 101 through 111 removed outlier: 3.671A pdb=" N LYS h 106 " --> pdb=" O GLU h 102 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE h 109 " --> pdb=" O ARG h 105 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA h 110 " --> pdb=" O LYS h 106 " (cutoff:3.500A) Processing helix chain 'i' and resid 25 through 29 removed outlier: 3.513A pdb=" N TYR i 28 " --> pdb=" O LYS i 25 " (cutoff:3.500A) Processing helix chain 'i' and resid 36 through 49 removed outlier: 4.067A pdb=" N GLU i 46 " --> pdb=" O SER i 42 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE i 47 " --> pdb=" O LEU i 43 " (cutoff:3.500A) Processing helix chain 'i' and resid 51 through 77 removed outlier: 3.540A pdb=" N ARG i 56 " --> pdb=" O PRO i 52 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG i 62 " --> pdb=" O ILE i 58 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN i 63 " --> pdb=" O ASP i 59 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY i 65 " --> pdb=" O ILE i 61 " (cutoff:3.500A) removed outlier: 8.970A pdb=" N GLU i 66 " --> pdb=" O ARG i 62 " (cutoff:3.500A) removed outlier: 9.483A pdb=" N LYS i 67 " --> pdb=" O ASN i 63 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ARG i 68 " --> pdb=" O SER i 64 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA i 69 " --> pdb=" O GLY i 65 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS i 71 " --> pdb=" O LYS i 67 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS i 75 " --> pdb=" O LYS i 71 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU i 77 " --> pdb=" O ALA i 73 " (cutoff:3.500A) Processing helix chain 'i' and resid 80 through 98 removed outlier: 4.254A pdb=" N ALA i 85 " --> pdb=" O THR i 81 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASN i 92 " --> pdb=" O GLU i 88 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE i 93 " --> pdb=" O GLU i 89 " (cutoff:3.500A) Processing helix chain 'j' and resid 51 through 56 Processing helix chain 'j' and resid 66 through 68 No H-bonds generated for 'chain 'j' and resid 66 through 68' Processing helix chain 'j' and resid 69 through 77 removed outlier: 3.684A pdb=" N ARG j 73 " --> pdb=" O HIS j 69 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN j 76 " --> pdb=" O ARG j 72 " (cutoff:3.500A) Processing helix chain 'k' and resid 7 through 15 removed outlier: 3.823A pdb=" N GLU k 13 " --> pdb=" O LYS k 9 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU k 14 " --> pdb=" O GLN k 10 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR k 15 " --> pdb=" O PHE k 11 " (cutoff:3.500A) Processing helix chain 'k' and resid 59 through 68 removed outlier: 3.500A pdb=" N LYS k 63 " --> pdb=" O ALA k 59 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN k 67 " --> pdb=" O LYS k 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 46 removed outlier: 3.544A pdb=" N LYS L 32 " --> pdb=" O GLN L 28 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL L 33 " --> pdb=" O ALA L 29 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA L 38 " --> pdb=" O SER L 34 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA L 44 " --> pdb=" O ALA L 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 66 removed outlier: 3.590A pdb=" N ASN L 66 " --> pdb=" O VAL L 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 84 Processing helix chain 'L' and resid 86 through 94 removed outlier: 3.573A pdb=" N ALA L 90 " --> pdb=" O THR L 86 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG L 91 " --> pdb=" O ALA L 87 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 122 removed outlier: 3.888A pdb=" N SER L 121 " --> pdb=" O LYS L 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 140 through 145 removed outlier: 3.864A pdb=" N THR L 144 " --> pdb=" O SER L 140 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 179 removed outlier: 3.716A pdb=" N LYS L 177 " --> pdb=" O ALA L 173 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS L 178 " --> pdb=" O ARG L 174 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE L 179 " --> pdb=" O SER L 175 " (cutoff:3.500A) Processing helix chain 'L' and resid 179 through 193 removed outlier: 3.604A pdb=" N ARG L 183 " --> pdb=" O PHE L 179 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU L 189 " --> pdb=" O LYS L 185 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA L 191 " --> pdb=" O ALA L 187 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA L 193 " --> pdb=" O GLU L 189 " (cutoff:3.500A) Processing helix chain 'l' and resid 6 through 19 removed outlier: 3.702A pdb=" N LYS l 12 " --> pdb=" O ARG l 8 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS l 15 " --> pdb=" O GLN l 11 " (cutoff:3.500A) Processing helix chain 'l' and resid 24 through 30 removed outlier: 3.619A pdb=" N ILE l 27 " --> pdb=" O PRO l 24 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG l 30 " --> pdb=" O ILE l 27 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 89 removed outlier: 3.716A pdb=" N LYS M 83 " --> pdb=" O ALA M 79 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 96 removed outlier: 3.670A pdb=" N ALA M 95 " --> pdb=" O CYS M 91 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA M 96 " --> pdb=" O GLU M 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 109 removed outlier: 3.728A pdb=" N LYS M 101 " --> pdb=" O SER M 97 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 135 removed outlier: 3.526A pdb=" N MET M 121 " --> pdb=" O ARG M 117 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR M 129 " --> pdb=" O LYS M 125 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR M 130 " --> pdb=" O GLN M 126 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS M 133 " --> pdb=" O TYR M 129 " (cutoff:3.500A) Processing helix chain 'p' and resid 8 through 14 removed outlier: 3.814A pdb=" N GLY p 12 " --> pdb=" O GLY p 9 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS p 13 " --> pdb=" O ILE p 10 " (cutoff:3.500A) Processing helix chain 'p' and resid 21 through 35 removed outlier: 3.661A pdb=" N VAL p 26 " --> pdb=" O LEU p 22 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS p 27 " --> pdb=" O ARG p 23 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU p 29 " --> pdb=" O GLN p 25 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLN p 32 " --> pdb=" O LYS p 28 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS p 34 " --> pdb=" O GLU p 30 " (cutoff:3.500A) Processing helix chain 'p' and resid 73 through 91 removed outlier: 4.000A pdb=" N VAL p 79 " --> pdb=" O ALA p 75 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR p 82 " --> pdb=" O THR p 78 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET p 89 " --> pdb=" O ARG p 85 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL p 90 " --> pdb=" O LEU p 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 13 removed outlier: 3.551A pdb=" N GLN N 11 " --> pdb=" O LEU N 7 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG N 12 " --> pdb=" O GLU N 8 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS N 13 " --> pdb=" O GLU N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 18 through 33 removed outlier: 3.799A pdb=" N TRP N 28 " --> pdb=" O ARG N 24 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG N 31 " --> pdb=" O VAL N 27 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS N 33 " --> pdb=" O GLU N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 50 Processing helix chain 'N' and resid 75 through 79 removed outlier: 4.026A pdb=" N GLY N 78 " --> pdb=" O VAL N 75 " (cutoff:3.500A) Processing helix chain 'N' and resid 97 through 106 removed outlier: 3.596A pdb=" N THR N 101 " --> pdb=" O SER N 97 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 152 removed outlier: 3.737A pdb=" N ILE N 151 " --> pdb=" O TYR N 148 " (cutoff:3.500A) Processing helix chain 'N' and resid 153 through 157 removed outlier: 3.962A pdb=" N LYS N 157 " --> pdb=" O PRO N 154 " (cutoff:3.500A) Processing helix chain 'N' and resid 167 through 172 Processing helix chain 'N' and resid 186 through 195 removed outlier: 3.874A pdb=" N GLN N 194 " --> pdb=" O THR N 190 " (cutoff:3.500A) Processing helix chain 'u' and resid 33 through 42 removed outlier: 3.674A pdb=" N GLN u 42 " --> pdb=" O LYS u 38 " (cutoff:3.500A) Processing helix chain 'u' and resid 52 through 57 Processing helix chain 'u' and resid 66 through 72 removed outlier: 3.609A pdb=" N THR u 70 " --> pdb=" O SER u 67 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE u 71 " --> pdb=" O THR u 68 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA u 72 " --> pdb=" O LEU u 69 " (cutoff:3.500A) Processing helix chain 'u' and resid 82 through 112 removed outlier: 3.669A pdb=" N VAL u 86 " --> pdb=" O ASN u 82 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS u 91 " --> pdb=" O ALA u 87 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA u 94 " --> pdb=" O LEU u 90 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU u 98 " --> pdb=" O ALA u 94 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA u 106 " --> pdb=" O LYS u 102 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN u 110 " --> pdb=" O ALA u 106 " (cutoff:3.500A) Processing helix chain 'u' and resid 114 through 129 removed outlier: 3.516A pdb=" N LYS u 118 " --> pdb=" O GLY u 114 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE u 120 " --> pdb=" O LYS u 116 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP u 123 " --> pdb=" O ASP u 119 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS u 125 " --> pdb=" O LEU u 121 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU u 126 " --> pdb=" O ARG u 122 " (cutoff:3.500A) Processing helix chain 'u' and resid 132 through 149 removed outlier: 3.655A pdb=" N ILE u 136 " --> pdb=" O GLU u 132 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU u 138 " --> pdb=" O LEU u 134 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL u 139 " --> pdb=" O ARG u 135 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU u 140 " --> pdb=" O ILE u 136 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE u 141 " --> pdb=" O ARG u 137 " (cutoff:3.500A) Processing helix chain 'O' and resid 15 through 28 removed outlier: 3.663A pdb=" N VAL O 22 " --> pdb=" O ARG O 18 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN O 26 " --> pdb=" O VAL O 22 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU O 28 " --> pdb=" O ALA O 24 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 40 removed outlier: 3.819A pdb=" N GLU O 40 " --> pdb=" O ARG O 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 37 through 40' Processing helix chain 'O' and resid 46 through 59 removed outlier: 3.845A pdb=" N ASN O 50 " --> pdb=" O GLU O 46 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU O 52 " --> pdb=" O PHE O 48 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N PHE O 57 " --> pdb=" O LYS O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 65 through 69 removed outlier: 3.538A pdb=" N GLY O 69 " --> pdb=" O LYS O 66 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 86 Processing helix chain 'O' and resid 92 through 99 Processing helix chain 'O' and resid 120 through 123 Processing helix chain 'O' and resid 124 through 129 removed outlier: 3.717A pdb=" N ARG O 128 " --> pdb=" O LEU O 124 " (cutoff:3.500A) Processing helix chain 'O' and resid 138 through 145 removed outlier: 3.573A pdb=" N THR O 143 " --> pdb=" O GLY O 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 149 through 186 removed outlier: 3.756A pdb=" N LYS O 155 " --> pdb=" O ASP O 151 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL O 162 " --> pdb=" O ALA O 158 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS O 170 " --> pdb=" O GLU O 166 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE O 174 " --> pdb=" O LYS O 170 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS O 177 " --> pdb=" O ALA O 173 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA O 183 " --> pdb=" O ALA O 179 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR O 184 " --> pdb=" O SER O 180 " (cutoff:3.500A) Processing helix chain 'O' and resid 188 through 198 removed outlier: 3.513A pdb=" N GLN O 193 " --> pdb=" O ASP O 189 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU O 194 " --> pdb=" O VAL O 190 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA O 195 " --> pdb=" O ALA O 191 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA O 196 " --> pdb=" O LYS O 192 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 35 removed outlier: 3.673A pdb=" N GLU P 31 " --> pdb=" O LYS P 27 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR P 32 " --> pdb=" O ASN P 28 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA P 35 " --> pdb=" O GLU P 31 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 52 removed outlier: 3.772A pdb=" N LYS P 46 " --> pdb=" O THR P 42 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU P 49 " --> pdb=" O GLN P 45 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLN P 50 " --> pdb=" O LYS P 46 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU P 52 " --> pdb=" O LEU P 48 " (cutoff:3.500A) Processing helix chain 'P' and resid 71 through 75 removed outlier: 3.665A pdb=" N LYS P 74 " --> pdb=" O ALA P 71 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU P 75 " --> pdb=" O GLN P 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 71 through 75' Processing helix chain 'P' and resid 84 through 106 removed outlier: 3.813A pdb=" N VAL P 88 " --> pdb=" O PRO P 84 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE P 90 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY P 93 " --> pdb=" O LYS P 89 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA P 100 " --> pdb=" O GLN P 96 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS P 105 " --> pdb=" O ASN P 101 " (cutoff:3.500A) Processing helix chain 'P' and resid 132 through 134 No H-bonds generated for 'chain 'P' and resid 132 through 134' Processing helix chain 'P' and resid 169 through 183 removed outlier: 3.722A pdb=" N ILE P 176 " --> pdb=" O GLN P 172 " (cutoff:3.500A) Processing helix chain 'Q' and resid 23 through 40 removed outlier: 3.750A pdb=" N LYS Q 27 " --> pdb=" O ASN Q 23 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE Q 35 " --> pdb=" O LYS Q 31 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG Q 38 " --> pdb=" O THR Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 53 removed outlier: 3.812A pdb=" N VAL Q 47 " --> pdb=" O PRO Q 43 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N PHE Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 71 Processing helix chain 'Q' and resid 107 through 118 removed outlier: 3.662A pdb=" N ILE Q 114 " --> pdb=" O ALA Q 110 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL Q 115 " --> pdb=" O ARG Q 111 " (cutoff:3.500A) Processing helix chain 'Q' and resid 123 through 131 Processing helix chain 'R' and resid 4 through 16 removed outlier: 3.652A pdb=" N ALA R 12 " --> pdb=" O LYS R 8 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER R 13 " --> pdb=" O ARG R 9 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 33 removed outlier: 3.654A pdb=" N ILE R 32 " --> pdb=" O GLU R 28 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA R 33 " --> pdb=" O THR R 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 28 through 33' Processing helix chain 'R' and resid 37 through 47 removed outlier: 3.760A pdb=" N LYS R 43 " --> pdb=" O ASN R 39 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN R 47 " --> pdb=" O LYS R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 72 Processing helix chain 'R' and resid 84 through 89 Processing helix chain 'R' and resid 90 through 112 removed outlier: 3.662A pdb=" N LEU R 102 " --> pdb=" O ARG R 98 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG R 103 " --> pdb=" O LEU R 99 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU R 106 " --> pdb=" O LEU R 102 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS R 108 " --> pdb=" O ARG R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 129 removed outlier: 3.949A pdb=" N LYS R 125 " --> pdb=" O HIS R 121 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY R 129 " --> pdb=" O LYS R 125 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 155 removed outlier: 3.512A pdb=" N LEU R 138 " --> pdb=" O HIS R 134 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS R 141 " --> pdb=" O ALA R 137 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE R 143 " --> pdb=" O VAL R 139 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU R 155 " --> pdb=" O ARG R 151 " (cutoff:3.500A) Processing helix chain 'S' and resid 33 through 49 removed outlier: 3.593A pdb=" N ALA S 37 " --> pdb=" O ASN S 33 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS S 38 " --> pdb=" O GLU S 34 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER S 39 " --> pdb=" O VAL S 35 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP S 42 " --> pdb=" O LYS S 38 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE S 44 " --> pdb=" O ARG S 40 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN S 46 " --> pdb=" O TRP S 42 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS S 47 " --> pdb=" O TYR S 43 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS S 49 " --> pdb=" O LEU S 45 " (cutoff:3.500A) Processing helix chain 'S' and resid 98 through 114 removed outlier: 3.659A pdb=" N VAL S 103 " --> pdb=" O ARG S 99 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU S 104 " --> pdb=" O VAL S 100 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN S 108 " --> pdb=" O GLU S 104 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP S 109 " --> pdb=" O THR S 105 " (cutoff:3.500A) Processing helix chain 'S' and resid 140 through 144 removed outlier: 3.525A pdb=" N PHE S 143 " --> pdb=" O VAL S 140 " (cutoff:3.500A) Processing helix chain 'T' and resid 100 through 122 removed outlier: 3.992A pdb=" N LYS T 110 " --> pdb=" O LEU T 106 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG T 116 " --> pdb=" O ASN T 112 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA T 121 " --> pdb=" O ALA T 117 " (cutoff:3.500A) Processing helix chain 'U' and resid 19 through 25 removed outlier: 3.737A pdb=" N ASN U 25 " --> pdb=" O SER U 21 " (cutoff:3.500A) Processing helix chain 'U' and resid 30 through 41 removed outlier: 3.846A pdb=" N LYS U 35 " --> pdb=" O ALA U 31 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU U 37 " --> pdb=" O TYR U 33 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE U 38 " --> pdb=" O ALA U 34 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP U 39 " --> pdb=" O LYS U 35 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N HIS U 40 " --> pdb=" O TYR U 36 " (cutoff:3.500A) Processing helix chain 'U' and resid 72 through 87 removed outlier: 3.692A pdb=" N THR U 80 " --> pdb=" O LEU U 76 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS U 81 " --> pdb=" O LYS U 77 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS U 85 " --> pdb=" O LYS U 81 " (cutoff:3.500A) Processing helix chain 'V' and resid 119 through 126 removed outlier: 3.894A pdb=" N LEU V 125 " --> pdb=" O GLU V 121 " (cutoff:3.500A) Processing helix chain 'V' and resid 126 through 132 removed outlier: 3.621A pdb=" N ALA V 130 " --> pdb=" O TRP V 126 " (cutoff:3.500A) Processing helix chain 'W' and resid 20 through 32 removed outlier: 3.924A pdb=" N ASP W 28 " --> pdb=" O GLU W 24 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU W 29 " --> pdb=" O ARG W 25 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL W 30 " --> pdb=" O ILE W 26 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG W 31 " --> pdb=" O PHE W 27 " (cutoff:3.500A) Processing helix chain 'W' and resid 32 through 37 removed outlier: 4.192A pdb=" N THR W 36 " --> pdb=" O GLU W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 59 removed outlier: 3.516A pdb=" N GLU W 55 " --> pdb=" O PRO W 51 " (cutoff:3.500A) Processing helix chain 'W' and resid 69 through 78 Processing helix chain 'W' and resid 89 through 95 removed outlier: 4.027A pdb=" N SER W 93 " --> pdb=" O LEU W 89 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS W 94 " --> pdb=" O TYR W 90 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU W 95 " --> pdb=" O GLN W 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 89 through 95' Processing helix chain 'W' and resid 108 through 119 removed outlier: 4.416A pdb=" N VAL W 112 " --> pdb=" O ASP W 108 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS W 113 " --> pdb=" O VAL W 109 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS W 117 " --> pdb=" O LYS W 113 " (cutoff:3.500A) Processing helix chain 'X' and resid 58 through 62 Processing helix chain 'X' and resid 69 through 78 removed outlier: 4.207A pdb=" N LYS X 75 " --> pdb=" O THR X 71 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL X 76 " --> pdb=" O ALA X 72 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU X 77 " --> pdb=" O MET X 73 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASP X 78 " --> pdb=" O LYS X 74 " (cutoff:3.500A) Processing helix chain 'X' and resid 91 through 104 removed outlier: 3.885A pdb=" N LYS X 100 " --> pdb=" O LYS X 96 " (cutoff:3.500A) Processing helix chain 'X' and resid 131 through 140 removed outlier: 3.784A pdb=" N ILE X 135 " --> pdb=" O ASP X 131 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG X 138 " --> pdb=" O ASP X 134 " (cutoff:3.500A) Processing helix chain 'Y' and resid 11 through 21 removed outlier: 3.663A pdb=" N LYS Y 17 " --> pdb=" O ARG Y 13 " (cutoff:3.500A) Processing helix chain 'Y' and resid 25 through 31 removed outlier: 4.277A pdb=" N VAL Y 29 " --> pdb=" O SER Y 25 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU Y 30 " --> pdb=" O GLN Y 26 " (cutoff:3.500A) Processing helix chain 'Y' and resid 36 through 44 removed outlier: 3.560A pdb=" N ALA Y 41 " --> pdb=" O LYS Y 37 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN Y 42 " --> pdb=" O GLU Y 38 " (cutoff:3.500A) Processing helix chain 'Y' and resid 112 through 123 removed outlier: 3.545A pdb=" N LYS Y 116 " --> pdb=" O ASP Y 112 " (cutoff:3.500A) Processing helix chain 'y' and resid 33 through 42 removed outlier: 3.633A pdb=" N ALA y 37 " --> pdb=" O ASN y 33 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE y 38 " --> pdb=" O PHE y 34 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU y 41 " --> pdb=" O ALA y 37 " (cutoff:3.500A) Processing helix chain 'y' and resid 58 through 63 removed outlier: 3.793A pdb=" N MET y 62 " --> pdb=" O ILE y 58 " (cutoff:3.500A) Processing helix chain 'y' and resid 77 through 88 Processing helix chain 'y' and resid 122 through 133 removed outlier: 3.877A pdb=" N LEU y 128 " --> pdb=" O GLU y 124 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER y 130 " --> pdb=" O GLU y 126 " (cutoff:3.500A) Processing helix chain 'y' and resid 166 through 178 removed outlier: 3.573A pdb=" N GLU y 171 " --> pdb=" O VAL y 167 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU y 172 " --> pdb=" O GLN y 168 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU y 176 " --> pdb=" O GLU y 172 " (cutoff:3.500A) Processing helix chain 'y' and resid 192 through 197 removed outlier: 3.561A pdb=" N GLY y 196 " --> pdb=" O VAL y 192 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N MET y 197 " --> pdb=" O VAL y 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 192 through 197' Processing helix chain 'y' and resid 211 through 223 removed outlier: 3.542A pdb=" N SER y 220 " --> pdb=" O SER y 216 " (cutoff:3.500A) Processing helix chain 'Z' and resid 58 through 66 removed outlier: 4.207A pdb=" N ALA Z 63 " --> pdb=" O ALA Z 59 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS Z 64 " --> pdb=" O LYS Z 60 " (cutoff:3.500A) Processing helix chain 'Z' and resid 98 through 102 removed outlier: 3.634A pdb=" N GLU Z 102 " --> pdb=" O GLU Z 99 " (cutoff:3.500A) Processing helix chain 'Z' and resid 105 through 123 removed outlier: 3.905A pdb=" N GLU Z 109 " --> pdb=" O SER Z 105 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA Z 110 " --> pdb=" O GLN Z 106 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU Z 120 " --> pdb=" O LYS Z 116 " (cutoff:3.500A) Processing helix chain 'Z' and resid 127 through 132 removed outlier: 3.874A pdb=" N PHE Z 131 " --> pdb=" O ASN Z 127 " (cutoff:3.500A) Processing helix chain 'z' and resid 7 through 20 removed outlier: 4.058A pdb=" N VAL z 16 " --> pdb=" O ASN z 12 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS z 17 " --> pdb=" O ALA z 13 " (cutoff:3.500A) Processing helix chain 'z' and resid 20 through 56 removed outlier: 3.945A pdb=" N LYS z 24 " --> pdb=" O GLY z 20 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL z 26 " --> pdb=" O PHE z 22 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN z 31 " --> pdb=" O ASP z 27 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG z 32 " --> pdb=" O ALA z 28 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS z 36 " --> pdb=" O ARG z 32 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS z 38 " --> pdb=" O SER z 34 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU z 41 " --> pdb=" O LEU z 37 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU z 47 " --> pdb=" O LYS z 43 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP z 48 " --> pdb=" O GLN z 44 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU z 53 " --> pdb=" O LEU z 49 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU z 54 " --> pdb=" O LYS z 50 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN z 55 " --> pdb=" O LYS z 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 16 removed outlier: 3.555A pdb=" N SER D 14 " --> pdb=" O SER D 10 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE D 16 " --> pdb=" O TYR D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 25 removed outlier: 3.562A pdb=" N GLU D 25 " --> pdb=" O ARG D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 38 removed outlier: 4.023A pdb=" N ARG D 35 " --> pdb=" O TYR D 31 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR D 38 " --> pdb=" O LYS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 87 removed outlier: 3.792A pdb=" N GLY D 87 " --> pdb=" O PRO D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 112 removed outlier: 3.572A pdb=" N ALA D 106 " --> pdb=" O GLY D 102 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU D 110 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS D 112 " --> pdb=" O ARG D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 170 removed outlier: 4.231A pdb=" N ALA D 162 " --> pdb=" O ARG D 158 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU D 163 " --> pdb=" O VAL D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 200 removed outlier: 3.626A pdb=" N SER D 197 " --> pdb=" O GLU D 193 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE D 199 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE D 200 " --> pdb=" O ARG D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 211 removed outlier: 3.822A pdb=" N GLU D 209 " --> pdb=" O SER D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 222 Processing helix chain 'D' and resid 223 through 229 Processing helix chain 'D' and resid 235 through 250 removed outlier: 3.584A pdb=" N ILE D 239 " --> pdb=" O SER D 235 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU D 245 " --> pdb=" O THR D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 273 removed outlier: 4.124A pdb=" N LYS D 271 " --> pdb=" O ALA D 267 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TYR D 272 " --> pdb=" O GLU D 268 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG D 273 " --> pdb=" O SER D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 285 removed outlier: 3.530A pdb=" N ARG D 282 " --> pdb=" O SER D 278 " (cutoff:3.500A) Processing helix chain 'J' and resid 27 through 42 removed outlier: 3.813A pdb=" N VAL J 36 " --> pdb=" O ARG J 32 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU J 37 " --> pdb=" O ALA J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 85 removed outlier: 4.044A pdb=" N GLU J 77 " --> pdb=" O GLY J 73 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU J 78 " --> pdb=" O PRO J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 112 removed outlier: 3.521A pdb=" N LEU J 112 " --> pdb=" O HIS J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 141 removed outlier: 3.611A pdb=" N ARG J 140 " --> pdb=" O ALA J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 166 removed outlier: 4.044A pdb=" N THR J 159 " --> pdb=" O THR J 155 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL J 160 " --> pdb=" O LYS J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 169 No H-bonds generated for 'chain 'J' and resid 167 through 169' Processing helix chain 'q' and resid 41 through 46 Processing helix chain 'o' and resid 12 through 17 Processing helix chain 'o' and resid 36 through 57 removed outlier: 3.610A pdb=" N ASN o 42 " --> pdb=" O LYS o 38 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N HIS o 45 " --> pdb=" O ARG o 41 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY o 49 " --> pdb=" O HIS o 45 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS o 52 " --> pdb=" O HIS o 48 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU o 54 " --> pdb=" O THR o 50 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'v' and resid 100 through 102 Processing sheet with id=AA2, first strand: chain 'v' and resid 187 through 192 removed outlier: 6.930A pdb=" N PHE v 200 " --> pdb=" O ILE v 188 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ILE v 190 " --> pdb=" O ASP v 198 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASP v 198 " --> pdb=" O ILE v 190 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N GLU v 192 " --> pdb=" O GLY v 196 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLY v 196 " --> pdb=" O GLU v 192 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR v 158 " --> pdb=" O TYR v 244 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL v 246 " --> pdb=" O THR v 158 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N GLN v 160 " --> pdb=" O VAL v 246 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER v 243 " --> pdb=" O SER v 225 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS v 223 " --> pdb=" O SER v 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'v' and resid 256 through 258 Processing sheet with id=AA4, first strand: chain 'v' and resid 352 through 357 removed outlier: 3.595A pdb=" N SER v 357 " --> pdb=" O ALA v 336 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASP v 337 " --> pdb=" O VAL v 323 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N VAL v 323 " --> pdb=" O ASP v 337 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR v 339 " --> pdb=" O LEU v 321 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TYR v 372 " --> pdb=" O LEU v 397 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N LEU v 397 " --> pdb=" O TYR v 372 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 's' and resid 28 through 29 Processing sheet with id=AA6, first strand: chain 's' and resid 199 through 200 removed outlier: 3.875A pdb=" N UNK s 200 " --> pdb=" O UNK s 208 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N UNK s 208 " --> pdb=" O UNK s 200 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 71 through 77 removed outlier: 3.584A pdb=" N GLN A 47 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL A 62 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N VAL A 45 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ARG A 64 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N GLY A 43 " --> pdb=" O ARG A 64 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 101 through 103 removed outlier: 5.997A pdb=" N ILE A 136 " --> pdb=" O ARG A 149 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ARG A 149 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY A 138 " --> pdb=" O ARG A 147 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS A 145 " --> pdb=" O ASN A 140 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'a' and resid 72 through 73 Processing sheet with id=AB1, first strand: chain 'a' and resid 145 through 147 removed outlier: 6.674A pdb=" N VAL a 125 " --> pdb=" O GLU a 146 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 356 through 359 removed outlier: 6.873A pdb=" N VAL B 57 " --> pdb=" O LYS B 357 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ILE B 359 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N THR B 55 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG B 334 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE B 335 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N VAL B 220 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ALA B 217 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ILE B 278 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ALA B 219 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N THR B 276 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR B 221 " --> pdb=" O SER B 274 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N SER B 274 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N LYS B 281 " --> pdb=" O LYS B 325 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N MET B 323 " --> pdb=" O TYR B 283 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL B 285 " --> pdb=" O PHE B 321 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N PHE B 321 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLY B 52 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ASP B 80 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N LYS B 50 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 99 through 106 removed outlier: 7.104A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR B 104 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TRP B 106 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N VAL B 87 " --> pdb=" O TRP B 106 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU B 161 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL B 89 " --> pdb=" O ARG B 159 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ARG B 159 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N GLY B 91 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL B 157 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 99 through 106 removed outlier: 7.104A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR B 104 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TRP B 106 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N VAL B 87 " --> pdb=" O TRP B 106 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS B 201 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 226 through 227 Processing sheet with id=AB6, first strand: chain 'C' and resid 6 through 9 removed outlier: 3.662A pdb=" N VAL C 8 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ASN C 18 " --> pdb=" O VAL C 8 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 150 through 152 removed outlier: 6.371A pdb=" N LEU C 150 " --> pdb=" O TRP C 250 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU C 206 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N THR C 251 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL C 208 " --> pdb=" O THR C 251 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL C 207 " --> pdb=" O ALA C 228 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 186 through 187 Processing sheet with id=AB9, first strand: chain 'c' and resid 22 through 25 removed outlier: 6.802A pdb=" N THR c 24 " --> pdb=" O ILE c 92 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ILE c 92 " --> pdb=" O THR c 24 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU c 41 " --> pdb=" O ILE c 92 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'd' and resid 9 through 15 removed outlier: 6.214A pdb=" N ARG d 50 " --> pdb=" O VAL d 93 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 77 through 79 removed outlier: 3.506A pdb=" N LYS E 56 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N SER E 66 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N TYR E 54 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR E 38 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N VAL E 39 " --> pdb=" O THR E 87 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'e' and resid 72 through 76 removed outlier: 6.482A pdb=" N LYS e 72 " --> pdb=" O ALA e 93 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N GLU e 95 " --> pdb=" O LYS e 72 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N PHE e 74 " --> pdb=" O GLU e 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'F' and resid 74 through 76 Processing sheet with id=AC5, first strand: chain 'F' and resid 205 through 206 removed outlier: 4.565A pdb=" N SER F 113 " --> pdb=" O ARG F 88 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR F 115 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY F 137 " --> pdb=" O PHE F 85 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 153 through 154 Processing sheet with id=AC7, first strand: chain 'f' and resid 8 through 18 removed outlier: 10.045A pdb=" N VAL f 9 " --> pdb=" O ILE f 32 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ILE f 32 " --> pdb=" O VAL f 9 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N GLY f 11 " --> pdb=" O ILE f 30 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N ILE f 30 " --> pdb=" O GLY f 11 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N HIS f 13 " --> pdb=" O SER f 28 " (cutoff:3.500A) removed outlier: 10.090A pdb=" N SER f 28 " --> pdb=" O HIS f 13 " (cutoff:3.500A) removed outlier: 11.358A pdb=" N SER f 15 " --> pdb=" O ASN f 26 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N ASN f 26 " --> pdb=" O SER f 15 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN f 17 " --> pdb=" O ASN f 24 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N ASN f 26 " --> pdb=" O PHE f 85 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N PHE f 85 " --> pdb=" O ASN f 26 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL f 80 " --> pdb=" O THR f 74 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N THR f 74 " --> pdb=" O VAL f 80 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ARG f 82 " --> pdb=" O THR f 72 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR f 72 " --> pdb=" O ARG f 82 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG f 48 " --> pdb=" O PHE f 101 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N VAL f 52 " --> pdb=" O SER f 97 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N SER f 97 " --> pdb=" O VAL f 52 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 150 through 153 removed outlier: 3.789A pdb=" N LEU G 150 " --> pdb=" O LEU G 200 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'g' and resid 21 through 24 Processing sheet with id=AD1, first strand: chain 'I' and resid 50 through 51 removed outlier: 3.676A pdb=" N LYS I 56 " --> pdb=" O CYS I 51 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 3 through 11 removed outlier: 6.957A pdb=" N ILE H 4 " --> pdb=" O ASN H 59 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN H 8 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL H 55 " --> pdb=" O GLN H 8 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 17 through 21 removed outlier: 3.513A pdb=" N LYS H 21 " --> pdb=" O ILE H 24 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 132 through 136 removed outlier: 3.652A pdb=" N LYS H 89 " --> pdb=" O HIS H 183 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N HIS H 183 " --> pdb=" O LYS H 89 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ARG H 91 " --> pdb=" O VAL H 181 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N VAL H 181 " --> pdb=" O ARG H 91 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL H 93 " --> pdb=" O ILE H 179 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ILE H 179 " --> pdb=" O VAL H 93 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 100 through 104 Processing sheet with id=AD6, first strand: chain 'h' and resid 116 through 118 Processing sheet with id=AD7, first strand: chain 'j' and resid 16 through 17 Processing sheet with id=AD8, first strand: chain 'k' and resid 3 through 4 removed outlier: 4.940A pdb=" N THR k 22 " --> pdb=" O ARG k 46 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA k 23 " --> pdb=" O ASN k 76 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 22 through 24 removed outlier: 6.821A pdb=" N LYS L 23 " --> pdb=" O LEU N 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'L' and resid 57 through 59 Processing sheet with id=AE2, first strand: chain 'M' and resid 14 through 15 removed outlier: 3.638A pdb=" N PHE S 150 " --> pdb=" O VAL M 15 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 53 through 59 removed outlier: 5.246A pdb=" N GLY M 48 " --> pdb=" O PRO M 54 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N LYS M 43 " --> pdb=" O ILE M 38 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ILE M 38 " --> pdb=" O LYS M 43 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU M 45 " --> pdb=" O VAL M 36 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ARG M 19 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N VAL M 20 " --> pdb=" O THR M 66 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'p' and resid 47 through 50 removed outlier: 3.667A pdb=" N LYS p 48 " --> pdb=" O THR p 56 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR p 56 " --> pdb=" O LYS p 48 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE p 54 " --> pdb=" O GLY p 50 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 37 through 38 removed outlier: 7.709A pdb=" N TYR N 127 " --> pdb=" O ASN N 122 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ASN N 122 " --> pdb=" O TYR N 127 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N TYR N 129 " --> pdb=" O TRP N 120 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N TRP N 120 " --> pdb=" O TYR N 129 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLU N 131 " --> pdb=" O SER N 118 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N SER N 118 " --> pdb=" O GLU N 131 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE N 133 " --> pdb=" O LEU N 116 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'u' and resid 28 through 30 removed outlier: 3.553A pdb=" N TYR V 94 " --> pdb=" O MET u 20 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU V 93 " --> pdb=" O TRP V 85 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'O' and resid 6 through 10 removed outlier: 6.120A pdb=" N VAL O 7 " --> pdb=" O VAL O 34 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N VAL O 36 " --> pdb=" O VAL O 7 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE O 9 " --> pdb=" O VAL O 36 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 42 through 44 Processing sheet with id=AE9, first strand: chain 'P' and resid 14 through 22 removed outlier: 3.670A pdb=" N TYR P 21 " --> pdb=" O SER P 144 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N SER P 144 " --> pdb=" O TYR P 21 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N THR P 151 " --> pdb=" O VAL P 114 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N VAL P 114 " --> pdb=" O THR P 151 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'P' and resid 58 through 59 Processing sheet with id=AF2, first strand: chain 'P' and resid 128 through 130 removed outlier: 3.564A pdb=" N ASN P 137 " --> pdb=" O THR P 129 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Q' and resid 62 through 63 Processing sheet with id=AF4, first strand: chain 'Q' and resid 121 through 122 removed outlier: 6.118A pdb=" N VAL Q 101 " --> pdb=" O ILE Q 122 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL Q 81 " --> pdb=" O ALA Q 102 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'R' and resid 23 through 24 removed outlier: 3.670A pdb=" N TRP R 23 " --> pdb=" O VAL R 51 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL R 51 " --> pdb=" O TRP R 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'S' and resid 58 through 63 removed outlier: 6.768A pdb=" N ILE S 10 " --> pdb=" O VAL S 59 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE S 61 " --> pdb=" O GLN S 8 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLN S 8 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLN S 63 " --> pdb=" O GLU S 6 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N GLU S 6 " --> pdb=" O GLN S 63 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'S' and resid 88 through 96 removed outlier: 3.637A pdb=" N HIS S 88 " --> pdb=" O TYR S 81 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR S 81 " --> pdb=" O HIS S 88 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ASN S 74 " --> pdb=" O GLU S 128 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N GLU S 128 " --> pdb=" O ASN S 74 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLY S 76 " --> pdb=" O VAL S 126 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N VAL S 126 " --> pdb=" O GLY S 76 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TRP S 78 " --> pdb=" O LEU S 124 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'U' and resid 54 through 58 removed outlier: 7.037A pdb=" N GLU U 102 " --> pdb=" O THR U 98 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'V' and resid 22 through 25 removed outlier: 6.860A pdb=" N MET V 59 " --> pdb=" O ILE V 37 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N VAL V 39 " --> pdb=" O MET V 57 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N MET V 57 " --> pdb=" O VAL V 39 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA V 99 " --> pdb=" O VAL V 79 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N GLY V 100 " --> pdb=" O ILE V 22 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ASN V 24 " --> pdb=" O GLY V 100 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ILE V 102 " --> pdb=" O ASN V 24 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'V' and resid 114 through 118 removed outlier: 5.892A pdb=" N SER V 133 " --> pdb=" O ILE V 114 " (cutoff:3.500A) removed outlier: 9.091A pdb=" N GLY V 116 " --> pdb=" O SER V 133 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL V 135 " --> pdb=" O GLY V 116 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 66 through 67 removed outlier: 3.641A pdb=" N LEU W 43 " --> pdb=" O GLY W 101 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL W 42 " --> pdb=" O ALA W 219 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ALA W 219 " --> pdb=" O VAL W 42 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N HIS W 44 " --> pdb=" O VAL W 217 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N VAL W 217 " --> pdb=" O HIS W 44 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP W 222 " --> pdb=" O THR W 227 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR W 227 " --> pdb=" O ASP W 222 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'W' and resid 121 through 123 removed outlier: 3.865A pdb=" N SER W 211 " --> pdb=" O ASP W 123 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'X' and resid 63 through 66 removed outlier: 3.698A pdb=" N GLN X 65 " --> pdb=" O GLN X 85 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS X 120 " --> pdb=" O VAL X 86 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Y' and resid 32 through 34 Processing sheet with id=AG6, first strand: chain 'Y' and resid 79 through 82 removed outlier: 3.749A pdb=" N SER Y 72 " --> pdb=" O GLN Y 81 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU Y 57 " --> pdb=" O ILE Y 106 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ILE Y 106 " --> pdb=" O LEU Y 57 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Y' and resid 86 through 88 Processing sheet with id=AG8, first strand: chain 'y' and resid 3 through 4 removed outlier: 6.171A pdb=" N THR y 3 " --> pdb=" O THR y 206 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU y 203 " --> pdb=" O ASN y 200 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'y' and resid 17 through 19 Processing sheet with id=AH1, first strand: chain 'y' and resid 64 through 65 removed outlier: 3.554A pdb=" N ALA y 64 " --> pdb=" O LEU y 71 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU y 71 " --> pdb=" O ALA y 64 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'y' and resid 108 through 110 Processing sheet with id=AH3, first strand: chain 'y' and resid 152 through 154 removed outlier: 3.639A pdb=" N VAL y 182 " --> pdb=" O GLY y 159 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Z' and resid 69 through 76 removed outlier: 6.633A pdb=" N LYS Z 69 " --> pdb=" O GLU Z 47 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALA Z 44 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ILE Z 25 " --> pdb=" O ALA Z 44 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ILE Z 46 " --> pdb=" O VAL Z 23 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL Z 23 " --> pdb=" O ILE Z 46 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LYS Z 9 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL Z 10 " --> pdb=" O TYR Z 85 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N TYR Z 85 " --> pdb=" O VAL Z 10 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N VAL Z 12 " --> pdb=" O THR Z 83 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N THR Z 83 " --> pdb=" O VAL Z 12 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'D' and resid 73 through 79 removed outlier: 3.549A pdb=" N VAL D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE D 64 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ALA D 77 " --> pdb=" O CYS D 62 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N CYS D 62 " --> pdb=" O ALA D 77 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N TYR D 79 " --> pdb=" O ILE D 60 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE D 60 " --> pdb=" O TYR D 79 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASP D 59 " --> pdb=" O THR D 56 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL D 53 " --> pdb=" O ASP D 147 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'J' and resid 46 through 48 removed outlier: 3.665A pdb=" N VAL J 67 " --> pdb=" O ILE J 21 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS J 16 " --> pdb=" O VAL J 130 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL J 130 " --> pdb=" O LYS J 16 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'q' and resid 7 through 11 1680 hydrogen bonds defined for protein. 4749 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1817 hydrogen bonds 3032 hydrogen bond angles 0 basepair planarities 763 basepair parallelities 1796 stacking parallelities Total time for adding SS restraints: 173.68 Time building geometry restraints manager: 50.64 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: 27978 1.33 - 1.47: 55119 1.47 - 1.60: 53056 1.60 - 1.73: 3383 1.73 - 1.86: 187 Bond restraints: 139723 Sorted by residual: bond pdb=" CA PHE B 130 " pdb=" C PHE B 130 " ideal model delta sigma weight residual 1.524 1.458 0.066 1.40e-02 5.10e+03 2.22e+01 bond pdb=" CB VAL q 69 " pdb=" CG1 VAL q 69 " ideal model delta sigma weight residual 1.521 1.418 0.103 3.30e-02 9.18e+02 9.70e+00 bond pdb=" CA PHE q 36 " pdb=" C PHE q 36 " ideal model delta sigma weight residual 1.522 1.564 -0.042 1.43e-02 4.89e+03 8.75e+00 bond pdb=" CA ARG D 179 " pdb=" C ARG D 179 " ideal model delta sigma weight residual 1.522 1.483 0.039 1.40e-02 5.10e+03 7.64e+00 bond pdb=" N LYS k 33 " pdb=" CA LYS k 33 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.54e+00 ... (remaining 139718 not shown) Histogram of bond angle deviations from ideal: 96.43 - 104.52: 15525 104.52 - 112.60: 81039 112.60 - 120.69: 66546 120.69 - 128.77: 39264 128.77 - 136.86: 3349 Bond angle restraints: 205723 Sorted by residual: angle pdb=" C ASN b 515 " pdb=" N LYS b 516 " pdb=" CA LYS b 516 " ideal model delta sigma weight residual 122.44 112.82 9.62 1.19e+00 7.06e-01 6.53e+01 angle pdb=" N ALA a 66 " pdb=" CA ALA a 66 " pdb=" C ALA a 66 " ideal model delta sigma weight residual 114.56 105.50 9.06 1.27e+00 6.20e-01 5.09e+01 angle pdb=" C ASN F 157 " pdb=" N LYS F 158 " pdb=" CA LYS F 158 " ideal model delta sigma weight residual 121.54 135.09 -13.55 1.91e+00 2.74e-01 5.04e+01 angle pdb=" CA CYS v 146 " pdb=" CB CYS v 146 " pdb=" SG CYS v 146 " ideal model delta sigma weight residual 114.40 129.92 -15.52 2.30e+00 1.89e-01 4.55e+01 angle pdb=" C THR J 154 " pdb=" N THR J 155 " pdb=" CA THR J 155 " ideal model delta sigma weight residual 121.54 134.12 -12.58 1.91e+00 2.74e-01 4.33e+01 ... (remaining 205718 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 80221 35.99 - 71.97: 7505 71.97 - 107.96: 884 107.96 - 143.94: 14 143.94 - 179.93: 67 Dihedral angle restraints: 88691 sinusoidal: 68122 harmonic: 20569 Sorted by residual: dihedral pdb=" CA PHE b 528 " pdb=" C PHE b 528 " pdb=" N GLY b 529 " pdb=" CA GLY b 529 " ideal model delta harmonic sigma weight residual 180.00 121.67 58.33 0 5.00e+00 4.00e-02 1.36e+02 dihedral pdb=" CA THR q 79 " pdb=" C THR q 79 " pdb=" N ARG q 80 " pdb=" CA ARG q 80 " ideal model delta harmonic sigma weight residual -180.00 -125.65 -54.35 0 5.00e+00 4.00e-02 1.18e+02 dihedral pdb=" CA VAL J 171 " pdb=" C VAL J 171 " pdb=" N LEU J 172 " pdb=" CA LEU J 172 " ideal model delta harmonic sigma weight residual 180.00 125.70 54.30 0 5.00e+00 4.00e-02 1.18e+02 ... (remaining 88688 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 25123 0.112 - 0.225: 706 0.225 - 0.337: 65 0.337 - 0.450: 6 0.450 - 0.562: 1 Chirality restraints: 25901 Sorted by residual: chirality pdb=" C4' G 12770 " pdb=" C5' G 12770 " pdb=" O4' G 12770 " pdb=" C3' G 12770 " both_signs ideal model delta sigma weight residual False -2.50 -1.93 -0.56 2.00e-01 2.50e+01 7.91e+00 chirality pdb=" C3' G 11097 " pdb=" C4' G 11097 " pdb=" O3' G 11097 " pdb=" C2' G 11097 " both_signs ideal model delta sigma weight residual False -2.74 -2.37 -0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" CB ILE X 63 " pdb=" CA ILE X 63 " pdb=" CG1 ILE X 63 " pdb=" CG2 ILE X 63 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.45e+00 ... (remaining 25898 not shown) Planarity restraints: 13168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 140 " 0.082 5.00e-02 4.00e+02 1.26e-01 2.54e+01 pdb=" N PRO D 141 " -0.218 5.00e-02 4.00e+02 pdb=" CA PRO D 141 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO D 141 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS v 278 " 0.019 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C LYS v 278 " -0.067 2.00e-02 2.50e+03 pdb=" O LYS v 278 " 0.025 2.00e-02 2.50e+03 pdb=" N ILE v 279 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG q 71 " 0.111 9.50e-02 1.11e+02 5.95e-02 1.49e+01 pdb=" NE ARG q 71 " -0.028 2.00e-02 2.50e+03 pdb=" CZ ARG q 71 " 0.062 2.00e-02 2.50e+03 pdb=" NH1 ARG q 71 " -0.022 2.00e-02 2.50e+03 pdb=" NH2 ARG q 71 " -0.017 2.00e-02 2.50e+03 ... (remaining 13165 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 18321 2.74 - 3.28: 108650 3.28 - 3.82: 244546 3.82 - 4.36: 301418 4.36 - 4.90: 433480 Nonbonded interactions: 1106415 Sorted by model distance: nonbonded pdb=" O THR q 54 " pdb=" O2' U 1 44 " model vdw 2.200 2.440 nonbonded pdb=" O2' A 3 126 " pdb=" OP2 U 3 128 " model vdw 2.201 2.440 nonbonded pdb=" O2' G 1 978 " pdb=" O2 U 1 979 " model vdw 2.204 2.440 nonbonded pdb=" O GLY D 71 " pdb=" O2' G 2 7 " model vdw 2.206 2.440 nonbonded pdb=" OE2 GLU B 74 " pdb=" OH TYR B 283 " model vdw 2.231 2.440 ... (remaining 1106410 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=0.50 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: 0.010 Normalize map: mean=0, sd=1: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 17.010 Check model and map are aligned: 1.440 Set scattering table: 0.930 Process input model: 401.820 Find NCS groups from input model: 2.810 Set up NCS constraints: 0.300 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:2.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 428.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 139723 Z= 0.449 Angle : 0.929 15.515 205723 Z= 0.499 Chirality : 0.047 0.562 25901 Planarity : 0.006 0.126 13168 Dihedral : 21.846 179.928 75323 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.31 % Favored : 92.24 % Rotamer: Outliers : 0.64 % Allowed : 4.72 % Favored : 94.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.21 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.56 % 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: -4.50 (0.08), residues: 6774 helix: -4.39 (0.05), residues: 2169 sheet: -1.50 (0.16), residues: 901 loop : -2.49 (0.08), residues: 3704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP b 427 HIS 0.033 0.003 HIS q 90 PHE 0.051 0.004 PHE N 180 TYR 0.039 0.004 TYR H 92 ARG 0.063 0.001 ARG q 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13548 Ramachandran restraints generated. 6774 Oldfield, 0 Emsley, 6774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13548 Ramachandran restraints generated. 6774 Oldfield, 0 Emsley, 6774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2000 residues out of total 5807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 1963 time to evaluate : 6.610 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 34 MET cc_start: 0.7108 (ptp) cc_final: 0.6515 (ptp) REVERT: v 155 TRP cc_start: 0.8537 (p-90) cc_final: 0.8189 (p-90) REVERT: v 226 GLU cc_start: 0.8577 (pm20) cc_final: 0.8234 (pm20) REVERT: v 351 GLN cc_start: 0.8412 (tp-100) cc_final: 0.7926 (mm110) REVERT: v 370 MET cc_start: 0.8588 (mmm) cc_final: 0.8342 (mmt) REVERT: A 33 ASP cc_start: 0.9166 (p0) cc_final: 0.8925 (p0) REVERT: A 52 SER cc_start: 0.9256 (m) cc_final: 0.8998 (p) REVERT: a 70 LYS cc_start: 0.9170 (ttmt) cc_final: 0.8862 (ttpt) REVERT: a 90 TYR cc_start: 0.8666 (m-80) cc_final: 0.8301 (m-80) REVERT: a 132 LYS cc_start: 0.9067 (tttt) cc_final: 0.8852 (tttp) REVERT: B 72 VAL cc_start: 0.8841 (t) cc_final: 0.8624 (m) REVERT: B 74 GLU cc_start: 0.7565 (pt0) cc_final: 0.7314 (pt0) REVERT: B 125 SER cc_start: 0.9255 (p) cc_final: 0.9055 (t) REVERT: B 207 SER cc_start: 0.8789 (p) cc_final: 0.8362 (t) REVERT: B 264 VAL cc_start: 0.9014 (m) cc_final: 0.8809 (p) REVERT: B 319 ASN cc_start: 0.8469 (m-40) cc_final: 0.8235 (m-40) REVERT: b 487 ASP cc_start: 0.7537 (t0) cc_final: 0.7224 (t0) REVERT: b 514 LYS cc_start: 0.7388 (pttp) cc_final: 0.6822 (pttt) REVERT: b 542 MET cc_start: 0.4975 (mmp) cc_final: 0.4307 (ptt) REVERT: b 605 MET cc_start: 0.6445 (mtp) cc_final: 0.5705 (mtp) REVERT: b 613 ARG cc_start: 0.7063 (mtm-85) cc_final: 0.6050 (mtm180) REVERT: C 50 TYR cc_start: 0.9242 (p90) cc_final: 0.9002 (p90) REVERT: C 221 ASN cc_start: 0.8987 (t160) cc_final: 0.8724 (t0) REVERT: C 285 ASP cc_start: 0.8168 (t0) cc_final: 0.7869 (p0) REVERT: c 27 TYR cc_start: 0.8558 (t80) cc_final: 0.8328 (t80) REVERT: c 58 TYR cc_start: 0.9183 (t80) cc_final: 0.8874 (t80) REVERT: E 137 ASP cc_start: 0.8165 (m-30) cc_final: 0.7147 (m-30) REVERT: e 60 ASN cc_start: 0.9000 (t0) cc_final: 0.8749 (t0) REVERT: F 34 LYS cc_start: 0.8930 (mmtt) cc_final: 0.8721 (mtpp) REVERT: F 51 TYR cc_start: 0.9452 (m-10) cc_final: 0.9114 (m-80) REVERT: F 64 GLN cc_start: 0.8646 (tp40) cc_final: 0.7613 (tp40) REVERT: F 68 ASP cc_start: 0.8372 (m-30) cc_final: 0.7717 (m-30) REVERT: F 228 SER cc_start: 0.9364 (m) cc_final: 0.9097 (m) REVERT: f 31 LYS cc_start: 0.8659 (tptt) cc_final: 0.8319 (tttp) REVERT: f 78 SER cc_start: 0.9026 (m) cc_final: 0.8810 (m) REVERT: G 228 GLU cc_start: 0.7942 (pp20) cc_final: 0.7334 (pp20) REVERT: g 11 ASN cc_start: 0.9212 (t0) cc_final: 0.8959 (t0) REVERT: g 31 ARG cc_start: 0.8461 (mtt-85) cc_final: 0.8254 (mtt180) REVERT: g 36 LYS cc_start: 0.8763 (mtmt) cc_final: 0.8468 (mmtt) REVERT: g 54 ILE cc_start: 0.9502 (mm) cc_final: 0.9277 (mm) REVERT: g 55 SER cc_start: 0.9525 (m) cc_final: 0.9276 (m) REVERT: g 98 GLN cc_start: 0.9033 (tp40) cc_final: 0.8688 (tp-100) REVERT: I 43 LYS cc_start: 0.8570 (mtpm) cc_final: 0.8082 (mtmt) REVERT: I 56 LYS cc_start: 0.8227 (tttt) cc_final: 0.8021 (ttmm) REVERT: I 60 THR cc_start: 0.8866 (m) cc_final: 0.8616 (p) REVERT: I 74 LYS cc_start: 0.8602 (mttt) cc_final: 0.8304 (mttp) REVERT: I 78 LYS cc_start: 0.8039 (mttt) cc_final: 0.7111 (ptmt) REVERT: I 116 LYS cc_start: 0.7739 (tmmt) cc_final: 0.7372 (tptp) REVERT: H 46 THR cc_start: 0.9136 (m) cc_final: 0.8766 (p) REVERT: H 90 MET cc_start: 0.7134 (mtp) cc_final: 0.6736 (mtp) REVERT: H 91 ARG cc_start: 0.8816 (mtp-110) cc_final: 0.8573 (ttm-80) REVERT: i 54 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7916 (mt-10) REVERT: i 67 LYS cc_start: 0.8917 (tttm) cc_final: 0.8700 (ttmm) REVERT: L 102 GLN cc_start: 0.8898 (mm-40) cc_final: 0.8652 (mm110) REVERT: l 4 GLN cc_start: 0.8909 (mm110) cc_final: 0.8516 (mm-40) REVERT: l 33 ASN cc_start: 0.8093 (t0) cc_final: 0.7889 (t0) REVERT: M 114 ASP cc_start: 0.7555 (t70) cc_final: 0.7283 (t70) REVERT: p 46 THR cc_start: 0.9288 (p) cc_final: 0.9074 (p) REVERT: u 1 MET cc_start: 0.7907 (mtm) cc_final: 0.7518 (mtp) REVERT: u 10 SER cc_start: 0.8880 (m) cc_final: 0.8488 (t) REVERT: u 27 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8320 (mtpp) REVERT: u 91 LYS cc_start: 0.9049 (mttt) cc_final: 0.8733 (tptm) REVERT: u 112 MET cc_start: 0.8987 (mmt) cc_final: 0.8721 (tpp) REVERT: O 88 VAL cc_start: 0.9105 (t) cc_final: 0.8852 (p) REVERT: P 137 ASN cc_start: 0.9298 (m110) cc_final: 0.8989 (m-40) REVERT: P 168 LEU cc_start: 0.8885 (pp) cc_final: 0.8569 (pp) REVERT: P 169 THR cc_start: 0.8850 (p) cc_final: 0.8591 (t) REVERT: Q 136 ASN cc_start: 0.8398 (t0) cc_final: 0.8082 (t0) REVERT: Q 151 ARG cc_start: 0.7683 (ttm170) cc_final: 0.7379 (mmp-170) REVERT: R 144 GLN cc_start: 0.8064 (mm-40) cc_final: 0.7315 (mm-40) REVERT: T 115 LYS cc_start: 0.9396 (mttt) cc_final: 0.9070 (mtpp) REVERT: T 128 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7900 (tp) REVERT: T 136 ARG cc_start: 0.8249 (pmm-80) cc_final: 0.7989 (mtm110) REVERT: T 156 TYR cc_start: 0.6204 (t80) cc_final: 0.5397 (t80) REVERT: U 33 TYR cc_start: 0.8491 (t80) cc_final: 0.8088 (t80) REVERT: U 36 TYR cc_start: 0.8535 (t80) cc_final: 0.8286 (t80) REVERT: U 43 VAL cc_start: 0.8800 (t) cc_final: 0.8489 (p) REVERT: U 49 ASN cc_start: 0.9028 (t160) cc_final: 0.8825 (t0) REVERT: U 88 GLN cc_start: 0.8679 (mp10) cc_final: 0.8160 (mp10) REVERT: W 72 VAL cc_start: 0.6409 (t) cc_final: 0.6162 (t) REVERT: W 80 LYS cc_start: 0.5836 (mmmt) cc_final: 0.5523 (mmmt) REVERT: X 57 LEU cc_start: 0.8974 (tp) cc_final: 0.8524 (tp) REVERT: X 67 ILE cc_start: 0.9540 (mt) cc_final: 0.9299 (mt) REVERT: y 61 ARG cc_start: 0.8639 (mmp80) cc_final: 0.8353 (mmp80) REVERT: y 215 LEU cc_start: 0.8691 (mt) cc_final: 0.8298 (mt) REVERT: D 57 ASN cc_start: 0.8533 (m110) cc_final: 0.8250 (m110) REVERT: D 69 ILE cc_start: 0.8877 (pp) cc_final: 0.8649 (pt) REVERT: D 196 ARG cc_start: 0.8260 (ttt-90) cc_final: 0.7019 (mmt180) REVERT: J 15 GLU cc_start: 0.7628 (tt0) cc_final: 0.7415 (tt0) REVERT: J 31 THR cc_start: 0.9085 (p) cc_final: 0.8789 (p) REVERT: J 34 SER cc_start: 0.9065 (t) cc_final: 0.8793 (p) REVERT: J 79 ILE cc_start: 0.8969 (mt) cc_final: 0.8399 (mt) REVERT: J 81 GLU cc_start: 0.8806 (tt0) cc_final: 0.8335 (tp30) REVERT: J 89 TYR cc_start: 0.8760 (m-10) cc_final: 0.7832 (m-10) REVERT: J 101 ASN cc_start: 0.8190 (m-40) cc_final: 0.7982 (m-40) REVERT: J 132 ASN cc_start: 0.8104 (p0) cc_final: 0.6885 (p0) REVERT: J 167 TYR cc_start: 0.8042 (m-80) cc_final: 0.7474 (m-80) REVERT: q 29 LYS cc_start: 0.7814 (mmtt) cc_final: 0.7474 (mmtt) outliers start: 37 outliers final: 11 residues processed: 1988 average time/residue: 1.2630 time to fit residues: 4163.0396 Evaluate side-chains 1182 residues out of total 5807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1169 time to evaluate : 5.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain v residue 22 CYS Chi-restraints excluded: chain v residue 143 CYS Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain b residue 445 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain u residue 27 LYS Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain q residue 88 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1037 random chunks: chunk 875 optimal weight: 10.0000 chunk 785 optimal weight: 50.0000 chunk 436 optimal weight: 9.9990 chunk 268 optimal weight: 8.9990 chunk 530 optimal weight: 3.9990 chunk 419 optimal weight: 0.5980 chunk 812 optimal weight: 30.0000 chunk 314 optimal weight: 10.0000 chunk 494 optimal weight: 7.9990 chunk 604 optimal weight: 8.9990 chunk 941 optimal weight: 10.0000 overall best weight: 6.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: v 108 HIS v 349 ASN A 38 HIS A 79 ASN A 140 ASN A 209 HIS a 67 HIS a 120 ASN B 121 ASN b 413 ASN b 415 ASN b 470 ASN b 498 ASN C 48 GLN C 59 GLN C 110 ASN ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 57 GLN ** d 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN E 172 HIS F 186 HIS F 244 ASN G 38 GLN G 85 ASN G 123 GLN G 145 ASN ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 ASN H 183 HIS h 34 GLN h 59 ASN i 91 ASN L 19 GLN L 120 GLN L 162 ASN l 4 GLN l 50 ASN M 27 GLN M 105 GLN N 37 HIS ** u 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 45 ASN u 101 GLN O 55 HIS ** O 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 45 GLN P 118 GLN P 145 HIS Q 10 HIS Q 152 HIS S 63 GLN S 122 HIS S 157 GLN U 49 ASN U 87 ASN W 232 ASN X 94 GLN Y 120 GLN y 86 ASN y 106 ASN ** y 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 44 GLN D 39 GLN D 45 ASN J 95 ASN J 109 HIS ** J 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 20 HIS q 38 GLN ** q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 90 HIS o 11 ASN o 42 ASN Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 139723 Z= 0.373 Angle : 0.721 19.424 205723 Z= 0.368 Chirality : 0.041 0.373 25901 Planarity : 0.006 0.131 13168 Dihedral : 23.170 179.620 61672 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.48 % Favored : 92.21 % Rotamer: Outliers : 3.94 % Allowed : 12.93 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.21 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.09), residues: 6774 helix: -2.37 (0.09), residues: 2255 sheet: -1.21 (0.16), residues: 919 loop : -2.18 (0.09), residues: 3600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP b 427 HIS 0.013 0.001 HIS q 20 PHE 0.027 0.002 PHE D 16 TYR 0.027 0.002 TYR u 4 ARG 0.012 0.001 ARG q 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13548 Ramachandran restraints generated. 6774 Oldfield, 0 Emsley, 6774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13548 Ramachandran restraints generated. 6774 Oldfield, 0 Emsley, 6774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1509 residues out of total 5807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 1282 time to evaluate : 6.706 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 155 TRP cc_start: 0.8659 (p-90) cc_final: 0.8133 (p-90) REVERT: v 215 ASN cc_start: 0.8998 (t0) cc_final: 0.8713 (t0) REVERT: v 224 LYS cc_start: 0.8948 (ptmt) cc_final: 0.8562 (ptmt) REVERT: v 226 GLU cc_start: 0.8668 (pm20) cc_final: 0.8361 (pm20) REVERT: v 240 TYR cc_start: 0.7264 (m-80) cc_final: 0.6798 (m-80) REVERT: a 90 TYR cc_start: 0.8662 (m-80) cc_final: 0.8454 (m-80) REVERT: a 139 ARG cc_start: 0.8509 (mmm-85) cc_final: 0.8196 (mtm180) REVERT: B 7 GLU cc_start: 0.7081 (mm-30) cc_final: 0.6824 (mm-30) REVERT: B 72 VAL cc_start: 0.9072 (t) cc_final: 0.8823 (m) REVERT: B 125 SER cc_start: 0.9232 (p) cc_final: 0.8906 (t) REVERT: B 213 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8112 (tt0) REVERT: b 432 MET cc_start: 0.8271 (ttm) cc_final: 0.7840 (ttp) REVERT: b 487 ASP cc_start: 0.7665 (t0) cc_final: 0.7460 (t70) REVERT: b 503 MET cc_start: 0.7243 (mtp) cc_final: 0.7029 (mtm) REVERT: b 514 LYS cc_start: 0.7432 (pttp) cc_final: 0.7100 (pttt) REVERT: b 542 MET cc_start: 0.5270 (mmp) cc_final: 0.4166 (ptp) REVERT: b 605 MET cc_start: 0.6205 (mtp) cc_final: 0.5488 (mtp) REVERT: b 613 ARG cc_start: 0.7198 (mtm-85) cc_final: 0.6201 (mtm180) REVERT: C 221 ASN cc_start: 0.9135 (OUTLIER) cc_final: 0.8665 (t0) REVERT: C 285 ASP cc_start: 0.8227 (t0) cc_final: 0.7898 (p0) REVERT: C 313 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8920 (tp) REVERT: C 360 LYS cc_start: 0.8483 (mttt) cc_final: 0.7807 (tppp) REVERT: c 58 TYR cc_start: 0.9292 (t80) cc_final: 0.9088 (t80) REVERT: c 71 GLN cc_start: 0.8183 (mp10) cc_final: 0.7952 (mp10) REVERT: E 157 GLN cc_start: 0.8450 (mp10) cc_final: 0.8105 (mp10) REVERT: E 158 TYR cc_start: 0.9466 (t80) cc_final: 0.9077 (t80) REVERT: e 109 LEU cc_start: 0.9187 (mm) cc_final: 0.8942 (mm) REVERT: F 51 TYR cc_start: 0.9547 (m-10) cc_final: 0.9164 (m-80) REVERT: F 64 GLN cc_start: 0.8696 (tp40) cc_final: 0.7686 (tp40) REVERT: F 68 ASP cc_start: 0.8307 (m-30) cc_final: 0.7752 (m-30) REVERT: F 125 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8053 (mm-30) REVERT: f 14 LEU cc_start: 0.9198 (mm) cc_final: 0.8788 (mt) REVERT: f 24 ASN cc_start: 0.9195 (t0) cc_final: 0.8990 (t0) REVERT: f 78 SER cc_start: 0.9054 (m) cc_final: 0.8850 (m) REVERT: f 93 THR cc_start: 0.9389 (p) cc_final: 0.9150 (p) REVERT: G 112 GLU cc_start: 0.8226 (mt-10) cc_final: 0.8025 (tm-30) REVERT: G 134 TYR cc_start: 0.8829 (p90) cc_final: 0.8413 (p90) REVERT: G 228 GLU cc_start: 0.8106 (pp20) cc_final: 0.7459 (tm-30) REVERT: G 232 HIS cc_start: 0.6605 (p90) cc_final: 0.6383 (p90) REVERT: g 11 ASN cc_start: 0.9235 (t0) cc_final: 0.8799 (t0) REVERT: g 18 ASN cc_start: 0.9145 (t0) cc_final: 0.8663 (t0) REVERT: g 31 ARG cc_start: 0.8456 (mtt-85) cc_final: 0.8106 (mmt180) REVERT: g 36 LYS cc_start: 0.8784 (mtmt) cc_final: 0.8405 (mmtt) REVERT: g 95 ILE cc_start: 0.9251 (OUTLIER) cc_final: 0.8976 (mp) REVERT: g 98 GLN cc_start: 0.8762 (tp40) cc_final: 0.8418 (tp-100) REVERT: I 74 LYS cc_start: 0.8545 (mttt) cc_final: 0.8123 (mttp) REVERT: I 78 LYS cc_start: 0.8416 (mttt) cc_final: 0.7294 (pttt) REVERT: H 9 GLN cc_start: 0.8618 (mt0) cc_final: 0.8411 (mt0) REVERT: H 142 ASP cc_start: 0.6798 (t0) cc_final: 0.6545 (t0) REVERT: H 160 ASP cc_start: 0.7669 (m-30) cc_final: 0.7458 (m-30) REVERT: i 43 LEU cc_start: 0.9696 (tm) cc_final: 0.9466 (tt) REVERT: M 113 THR cc_start: 0.8728 (m) cc_final: 0.8481 (p) REVERT: u 27 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8418 (mtpt) REVERT: u 49 LEU cc_start: 0.8803 (mp) cc_final: 0.8596 (mt) REVERT: u 91 LYS cc_start: 0.8892 (mttt) cc_final: 0.8652 (ttpp) REVERT: O 88 VAL cc_start: 0.9060 (t) cc_final: 0.8810 (p) REVERT: O 124 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8764 (mt) REVERT: Q 136 ASN cc_start: 0.8623 (t0) cc_final: 0.8327 (t0) REVERT: Q 151 ARG cc_start: 0.8081 (ttm170) cc_final: 0.7403 (mmp-170) REVERT: R 68 GLN cc_start: 0.9102 (tp40) cc_final: 0.8815 (tp40) REVERT: R 144 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7754 (tp40) REVERT: R 148 ASP cc_start: 0.8772 (m-30) cc_final: 0.8267 (m-30) REVERT: S 110 MET cc_start: 0.9070 (mmm) cc_final: 0.8620 (mmp) REVERT: T 103 GLN cc_start: 0.8276 (tt0) cc_final: 0.8015 (tp40) REVERT: T 115 LYS cc_start: 0.9405 (mttt) cc_final: 0.9204 (mtpp) REVERT: T 129 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8326 (mtmt) REVERT: T 156 TYR cc_start: 0.6219 (t80) cc_final: 0.5272 (t80) REVERT: U 43 VAL cc_start: 0.8705 (t) cc_final: 0.8490 (p) REVERT: U 49 ASN cc_start: 0.9008 (t0) cc_final: 0.8746 (t0) REVERT: U 75 TYR cc_start: 0.8329 (t80) cc_final: 0.8033 (t80) REVERT: U 88 GLN cc_start: 0.8722 (mp10) cc_final: 0.8323 (mp10) REVERT: U 94 ARG cc_start: 0.8620 (ptt180) cc_final: 0.8246 (ptt180) REVERT: V 54 LEU cc_start: 0.9386 (tt) cc_final: 0.9145 (tp) REVERT: V 126 TRP cc_start: 0.9299 (m100) cc_final: 0.8994 (m100) REVERT: W 233 ILE cc_start: 0.0213 (OUTLIER) cc_final: -0.0038 (pp) REVERT: X 67 ILE cc_start: 0.9499 (mt) cc_final: 0.9261 (mt) REVERT: Y 42 GLN cc_start: 0.8415 (tm-30) cc_final: 0.8026 (tm-30) REVERT: Y 43 TYR cc_start: 0.9271 (m-80) cc_final: 0.8904 (m-80) REVERT: Y 53 ASP cc_start: 0.8339 (t0) cc_final: 0.8086 (t0) REVERT: Y 76 LEU cc_start: 0.9547 (OUTLIER) cc_final: 0.9297 (tm) REVERT: Z 103 GLN cc_start: 0.8511 (tm-30) cc_final: 0.8256 (tm-30) REVERT: D 57 ASN cc_start: 0.8733 (m110) cc_final: 0.8458 (m110) REVERT: D 95 TRP cc_start: 0.8988 (OUTLIER) cc_final: 0.8342 (t60) REVERT: D 196 ARG cc_start: 0.8330 (ttt-90) cc_final: 0.6992 (mmt180) REVERT: D 270 LYS cc_start: 0.9176 (mttt) cc_final: 0.8912 (mtmm) REVERT: J 81 GLU cc_start: 0.8793 (tt0) cc_final: 0.8474 (tp30) REVERT: J 89 TYR cc_start: 0.8651 (m-10) cc_final: 0.7769 (m-10) REVERT: J 90 GLN cc_start: 0.8127 (mm-40) cc_final: 0.6895 (tp-100) REVERT: J 132 ASN cc_start: 0.7975 (p0) cc_final: 0.6721 (p0) REVERT: J 167 TYR cc_start: 0.7875 (m-80) cc_final: 0.7272 (m-80) REVERT: J 171 VAL cc_start: 0.7739 (OUTLIER) cc_final: 0.7452 (p) REVERT: J 172 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.6978 (mt) REVERT: q 29 LYS cc_start: 0.7890 (mmtt) cc_final: 0.7458 (mmtt) REVERT: o 23 LYS cc_start: 0.8864 (mmtt) cc_final: 0.8595 (mmmt) outliers start: 227 outliers final: 140 residues processed: 1423 average time/residue: 1.1971 time to fit residues: 2956.9641 Evaluate side-chains 1275 residues out of total 5807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1123 time to evaluate : 6.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain v residue 22 CYS Chi-restraints excluded: chain v residue 26 ILE Chi-restraints excluded: chain v residue 76 LEU Chi-restraints excluded: chain v residue 143 CYS Chi-restraints excluded: chain v residue 159 VAL Chi-restraints excluded: chain v residue 312 VAL Chi-restraints excluded: chain v residue 320 VAL Chi-restraints excluded: chain v residue 357 SER Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 88 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 219 ILE Chi-restraints excluded: chain a residue 72 VAL Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 356 LEU 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 C residue 221 ASN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain e residue 59 SER Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain G residue 195 SER Chi-restraints excluded: chain g residue 86 LYS Chi-restraints excluded: chain g residue 95 ILE Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 49 ASN Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 147 SER Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain H residue 162 GLN Chi-restraints excluded: chain h residue 50 SER Chi-restraints excluded: chain i residue 19 SER Chi-restraints excluded: chain i residue 42 SER Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain i residue 64 SER Chi-restraints excluded: chain j residue 7 SER Chi-restraints excluded: chain j residue 46 SER Chi-restraints excluded: chain j residue 58 THR Chi-restraints excluded: chain j residue 82 SER Chi-restraints excluded: chain k residue 45 VAL Chi-restraints excluded: chain k residue 66 ILE Chi-restraints excluded: chain k residue 72 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 38 ILE Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 103 ILE Chi-restraints excluded: chain p residue 5 THR Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 21 SER Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 171 SER Chi-restraints excluded: chain N residue 196 THR Chi-restraints excluded: chain u residue 9 CYS Chi-restraints excluded: chain u residue 27 LYS Chi-restraints excluded: chain O residue 124 LEU Chi-restraints excluded: chain O residue 188 SER Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 87 SER 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 168 LEU Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 57 ILE Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 59 SER Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain T residue 124 VAL Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain T residue 129 LYS Chi-restraints excluded: chain T residue 139 ARG Chi-restraints excluded: chain T residue 147 VAL Chi-restraints excluded: chain U residue 16 THR Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 57 THR Chi-restraints excluded: chain V residue 9 THR Chi-restraints excluded: chain V residue 13 ILE Chi-restraints excluded: chain V residue 89 ASP Chi-restraints excluded: chain W residue 233 ILE Chi-restraints excluded: chain X residue 29 SER Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain X residue 87 SER Chi-restraints excluded: chain X residue 119 THR Chi-restraints excluded: chain Y residue 76 LEU Chi-restraints excluded: chain Y residue 80 VAL Chi-restraints excluded: chain Y residue 102 SER Chi-restraints excluded: chain y residue 5 THR Chi-restraints excluded: chain y residue 169 ASP Chi-restraints excluded: chain y residue 179 VAL Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain Z residue 98 THR Chi-restraints excluded: chain D residue 16 PHE Chi-restraints excluded: chain D residue 95 TRP Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 14 ILE Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 173 ASP Chi-restraints excluded: chain q residue 7 THR Chi-restraints excluded: chain q residue 34 SER Chi-restraints excluded: chain o residue 8 THR Chi-restraints excluded: chain o residue 13 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1037 random chunks: chunk 523 optimal weight: 9.9990 chunk 292 optimal weight: 5.9990 chunk 783 optimal weight: 10.0000 chunk 641 optimal weight: 6.9990 chunk 259 optimal weight: 3.9990 chunk 943 optimal weight: 10.0000 chunk 1019 optimal weight: 10.0000 chunk 840 optimal weight: 10.0000 chunk 935 optimal weight: 10.0000 chunk 321 optimal weight: 6.9990 chunk 756 optimal weight: 10.0000 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 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 HIS a 120 ASN b 633 HIS ** C 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 ASN d 57 GLN G 28 HIS H 9 GLN k 67 GLN l 20 ASN M 27 GLN ** u 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 121 HIS V 81 GLN V 132 ASN ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 223 ASN Y 120 GLN ** y 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 178 GLN ** Z 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 101 ASN ** J 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 11 ASN o 45 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 139723 Z= 0.401 Angle : 0.712 22.871 205723 Z= 0.364 Chirality : 0.041 0.360 25901 Planarity : 0.006 0.124 13168 Dihedral : 23.075 179.832 61671 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.90 % Favored : 91.79 % Rotamer: Outliers : 5.78 % Allowed : 14.70 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.21 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.21 % 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: -2.46 (0.09), residues: 6774 helix: -1.21 (0.10), residues: 2240 sheet: -1.20 (0.16), residues: 928 loop : -2.04 (0.09), residues: 3606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP M 85 HIS 0.010 0.002 HIS C 311 PHE 0.028 0.002 PHE D 16 TYR 0.028 0.002 TYR y 113 ARG 0.018 0.001 ARG q 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13548 Ramachandran restraints generated. 6774 Oldfield, 0 Emsley, 6774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13548 Ramachandran restraints generated. 6774 Oldfield, 0 Emsley, 6774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1542 residues out of total 5807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 333 poor density : 1209 time to evaluate : 6.862 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: v 135 GLU cc_start: 0.7487 (tt0) cc_final: 0.7026 (tp30) REVERT: v 197 LEU cc_start: 0.8886 (pt) cc_final: 0.8572 (mp) REVERT: v 210 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.8465 (tpp) REVERT: v 215 ASN cc_start: 0.9095 (t0) cc_final: 0.8637 (t0) REVERT: v 226 GLU cc_start: 0.8732 (pm20) cc_final: 0.8406 (pm20) REVERT: v 240 TYR cc_start: 0.7171 (m-80) cc_final: 0.6362 (m-80) REVERT: v 281 ASN cc_start: 0.7934 (t0) cc_final: 0.7686 (t0) REVERT: a 139 ARG cc_start: 0.8679 (mmm-85) cc_final: 0.8276 (mtm180) REVERT: B 72 VAL cc_start: 0.9187 (t) cc_final: 0.8869 (m) REVERT: B 125 SER cc_start: 0.9214 (p) cc_final: 0.8886 (t) REVERT: B 202 THR cc_start: 0.8980 (OUTLIER) cc_final: 0.8687 (p) REVERT: B 214 MET cc_start: 0.8580 (mmm) cc_final: 0.8260 (mtp) REVERT: b 432 MET cc_start: 0.8469 (ttm) cc_final: 0.7947 (ttp) REVERT: b 442 TYR cc_start: 0.8016 (m-80) cc_final: 0.7588 (m-10) REVERT: b 514 LYS cc_start: 0.7761 (pttp) cc_final: 0.7287 (pttt) REVERT: b 542 MET cc_start: 0.5314 (mmp) cc_final: 0.4130 (ptp) REVERT: b 613 ARG cc_start: 0.7497 (mtm-85) cc_final: 0.7263 (mtm110) REVERT: C 5 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.7414 (mt0) REVERT: C 55 LYS cc_start: 0.8906 (pttm) cc_final: 0.8519 (tmmt) REVERT: C 147 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7554 (pm20) REVERT: C 285 ASP cc_start: 0.8216 (t0) cc_final: 0.7835 (p0) REVERT: C 313 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8889 (tp) REVERT: c 94 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7869 (mm-30) REVERT: E 157 GLN cc_start: 0.8446 (mp10) cc_final: 0.8085 (mp10) REVERT: F 51 TYR cc_start: 0.9517 (m-10) cc_final: 0.9207 (m-80) REVERT: F 64 GLN cc_start: 0.8641 (tp40) cc_final: 0.7662 (tp40) REVERT: F 68 ASP cc_start: 0.8248 (m-30) cc_final: 0.7636 (m-30) REVERT: F 74 SER cc_start: 0.8511 (m) cc_final: 0.8295 (p) REVERT: F 92 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8114 (tp) REVERT: f 14 LEU cc_start: 0.9301 (mm) cc_final: 0.8857 (mt) REVERT: f 24 ASN cc_start: 0.9219 (t0) cc_final: 0.9010 (t0) REVERT: G 27 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8739 (p) REVERT: G 134 TYR cc_start: 0.9005 (p90) cc_final: 0.8450 (p90) REVERT: g 11 ASN cc_start: 0.9253 (t0) cc_final: 0.8753 (t0) REVERT: g 18 ASN cc_start: 0.9174 (t0) cc_final: 0.8707 (t0) REVERT: g 31 ARG cc_start: 0.8483 (mtt-85) cc_final: 0.8172 (mmt180) REVERT: g 36 LYS cc_start: 0.8819 (mtmt) cc_final: 0.8472 (mmtt) REVERT: g 95 ILE cc_start: 0.9248 (OUTLIER) cc_final: 0.9002 (mp) REVERT: g 98 GLN cc_start: 0.8756 (tp40) cc_final: 0.8387 (tp-100) REVERT: I 78 LYS cc_start: 0.8410 (mttt) cc_final: 0.7328 (pttt) REVERT: H 160 ASP cc_start: 0.7610 (m-30) cc_final: 0.7376 (m-30) REVERT: H 162 GLN cc_start: 0.9326 (OUTLIER) cc_final: 0.9025 (tt0) REVERT: H 163 GLN cc_start: 0.9140 (mm110) cc_final: 0.8651 (mm110) REVERT: i 43 LEU cc_start: 0.9707 (tm) cc_final: 0.9493 (tt) REVERT: i 76 ARG cc_start: 0.8615 (mmm-85) cc_final: 0.8041 (mmm-85) REVERT: L 65 TYR cc_start: 0.9025 (m-80) cc_final: 0.8672 (m-80) REVERT: l 15 LYS cc_start: 0.9196 (tttp) cc_final: 0.8928 (tttp) REVERT: M 113 THR cc_start: 0.8796 (m) cc_final: 0.8522 (p) REVERT: N 4 TYR cc_start: 0.6401 (p90) cc_final: 0.6053 (p90) REVERT: u 20 MET cc_start: 0.8444 (ttp) cc_final: 0.8243 (ttm) REVERT: u 27 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8456 (mtpt) REVERT: O 41 LEU cc_start: 0.9200 (mp) cc_final: 0.8988 (mt) REVERT: O 124 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8751 (mt) REVERT: P 55 GLN cc_start: 0.8877 (mm110) cc_final: 0.8158 (mt0) REVERT: Q 4 ASP cc_start: 0.5611 (OUTLIER) cc_final: 0.4813 (m-30) REVERT: Q 136 ASN cc_start: 0.8815 (t0) cc_final: 0.8512 (t0) REVERT: Q 151 ARG cc_start: 0.8084 (ttm170) cc_final: 0.7338 (mmp-170) REVERT: R 46 LYS cc_start: 0.8881 (tppt) cc_final: 0.8517 (tptp) REVERT: R 68 GLN cc_start: 0.9163 (tp40) cc_final: 0.8792 (tp40) REVERT: R 144 GLN cc_start: 0.8091 (mm-40) cc_final: 0.7770 (tp40) REVERT: R 148 ASP cc_start: 0.8851 (m-30) cc_final: 0.8399 (m-30) REVERT: S 6 GLU cc_start: 0.8134 (tt0) cc_final: 0.7771 (tt0) REVERT: T 128 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7813 (pp) REVERT: U 49 ASN cc_start: 0.9131 (t0) cc_final: 0.8825 (t0) REVERT: U 75 TYR cc_start: 0.8364 (t80) cc_final: 0.8114 (t80) REVERT: U 88 GLN cc_start: 0.8739 (mp10) cc_final: 0.8373 (mp10) REVERT: W 233 ILE cc_start: 0.0452 (OUTLIER) cc_final: 0.0190 (pp) REVERT: X 67 ILE cc_start: 0.9452 (mt) cc_final: 0.9214 (mt) REVERT: X 73 MET cc_start: 0.8384 (mmm) cc_final: 0.8060 (mmm) REVERT: Y 42 GLN cc_start: 0.8417 (tm-30) cc_final: 0.7997 (tm-30) REVERT: Y 43 TYR cc_start: 0.9317 (m-80) cc_final: 0.8758 (m-80) REVERT: Y 53 ASP cc_start: 0.8541 (t0) cc_final: 0.8320 (t0) REVERT: Y 76 LEU cc_start: 0.9583 (OUTLIER) cc_final: 0.9365 (tm) REVERT: y 169 ASP cc_start: 0.9142 (m-30) cc_final: 0.8928 (m-30) REVERT: y 209 ASP cc_start: 0.8616 (m-30) cc_final: 0.8405 (m-30) REVERT: D 48 LYS cc_start: 0.7271 (tppt) cc_final: 0.6830 (mmtm) REVERT: D 95 TRP cc_start: 0.9059 (OUTLIER) cc_final: 0.8338 (t60) REVERT: D 196 ARG cc_start: 0.8337 (ttt-90) cc_final: 0.6877 (mmt180) REVERT: D 218 ARG cc_start: 0.8626 (mmm-85) cc_final: 0.8353 (mtp85) REVERT: D 270 LYS cc_start: 0.9145 (mttt) cc_final: 0.8910 (mtmm) REVERT: J 15 GLU cc_start: 0.7686 (tt0) cc_final: 0.7329 (tt0) REVERT: J 38 GLU cc_start: 0.8420 (tt0) cc_final: 0.7483 (tp30) REVERT: J 81 GLU cc_start: 0.8826 (tt0) cc_final: 0.8189 (tp30) REVERT: J 89 TYR cc_start: 0.8711 (m-10) cc_final: 0.7762 (m-10) REVERT: J 132 ASN cc_start: 0.7995 (p0) cc_final: 0.7618 (p0) REVERT: J 167 TYR cc_start: 0.8127 (m-80) cc_final: 0.7836 (m-80) REVERT: J 171 VAL cc_start: 0.8142 (OUTLIER) cc_final: 0.7879 (p) REVERT: J 172 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.6675 (mt) REVERT: q 29 LYS cc_start: 0.7825 (mmtt) cc_final: 0.7409 (mmtt) REVERT: q 82 GLN cc_start: 0.3749 (OUTLIER) cc_final: 0.2669 (tt0) outliers start: 333 outliers final: 208 residues processed: 1423 average time/residue: 1.1739 time to fit residues: 2933.3105 Evaluate side-chains 1318 residues out of total 5807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 1091 time to evaluate : 6.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain v residue 22 CYS Chi-restraints excluded: chain v residue 26 ILE Chi-restraints excluded: chain v residue 76 LEU Chi-restraints excluded: chain v residue 143 CYS Chi-restraints excluded: chain v residue 177 LEU Chi-restraints excluded: chain v residue 178 ILE Chi-restraints excluded: chain v residue 192 GLU Chi-restraints excluded: chain v residue 210 MET Chi-restraints excluded: chain v residue 312 VAL Chi-restraints excluded: chain v residue 320 VAL Chi-restraints excluded: chain v residue 348 VAL Chi-restraints excluded: chain v residue 357 SER Chi-restraints excluded: chain v residue 374 ILE Chi-restraints excluded: chain v residue 390 ASP Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 88 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 157 VAL Chi-restraints excluded: chain A residue 216 HIS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 169 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 344 THR Chi-restraints excluded: chain b residue 385 LEU Chi-restraints excluded: chain b residue 406 ASN Chi-restraints excluded: chain b residue 418 ASP 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 519 MET Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 18 ILE Chi-restraints excluded: chain c residue 30 THR Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain d residue 46 THR Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain e residue 55 ILE Chi-restraints excluded: chain e residue 59 SER Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 120 THR 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 97 SER Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 195 SER Chi-restraints excluded: chain G residue 246 MET Chi-restraints excluded: chain g residue 15 THR Chi-restraints excluded: chain g residue 35 VAL Chi-restraints excluded: chain g residue 66 SER Chi-restraints excluded: chain g residue 86 LYS Chi-restraints excluded: chain g residue 95 ILE Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 60 THR Chi-restraints excluded: chain I residue 90 SER Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 49 ASN Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 90 MET Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 147 SER Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain H residue 162 GLN Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain h residue 35 LYS Chi-restraints excluded: chain h residue 50 SER Chi-restraints excluded: chain i residue 9 ILE Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 19 SER Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 64 SER Chi-restraints excluded: chain j residue 7 SER Chi-restraints excluded: chain j residue 46 SER Chi-restraints excluded: chain j residue 58 THR Chi-restraints excluded: chain j residue 82 SER Chi-restraints excluded: chain j residue 84 SER Chi-restraints excluded: chain k residue 29 LYS Chi-restraints excluded: chain k residue 45 VAL Chi-restraints excluded: chain k residue 66 ILE Chi-restraints excluded: chain k residue 72 THR Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain M residue 103 ILE Chi-restraints excluded: chain p residue 5 THR Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 21 SER Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 87 GLN Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 171 SER Chi-restraints excluded: chain N residue 174 ILE Chi-restraints excluded: chain N residue 190 THR Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain u residue 9 CYS Chi-restraints excluded: chain u residue 10 SER Chi-restraints excluded: chain u residue 27 LYS Chi-restraints excluded: chain u residue 77 VAL Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 124 LEU Chi-restraints excluded: chain O residue 151 ASP Chi-restraints excluded: chain O residue 188 SER Chi-restraints excluded: chain P residue 10 ASN Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 87 SER 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 168 LEU Chi-restraints excluded: chain Q residue 4 ASP Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 59 SER Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 89 ASN Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain T residue 124 VAL Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain T residue 147 VAL Chi-restraints excluded: chain U residue 16 THR Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 39 ASP Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 72 SER Chi-restraints excluded: chain V residue 13 ILE Chi-restraints excluded: chain V residue 89 ASP Chi-restraints excluded: chain W residue 233 ILE Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 29 SER Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain X residue 87 SER Chi-restraints excluded: chain X residue 106 ASP Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain Y residue 76 LEU Chi-restraints excluded: chain Y residue 80 VAL Chi-restraints excluded: chain Y residue 102 SER Chi-restraints excluded: chain Y residue 106 ILE Chi-restraints excluded: chain Y residue 120 GLN Chi-restraints excluded: chain y residue 5 THR Chi-restraints excluded: chain y residue 90 ASP Chi-restraints excluded: chain y residue 99 GLU Chi-restraints excluded: chain y residue 131 ASP Chi-restraints excluded: chain y residue 135 VAL Chi-restraints excluded: chain y residue 179 VAL Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain Z residue 98 THR Chi-restraints excluded: chain Z residue 132 SER Chi-restraints excluded: chain Z residue 134 LEU Chi-restraints excluded: chain D residue 16 PHE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 95 TRP Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 14 ILE Chi-restraints excluded: chain J residue 20 ASN Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 101 ASN Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 173 ASP Chi-restraints excluded: chain q residue 7 THR Chi-restraints excluded: chain q residue 34 SER Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 82 GLN Chi-restraints excluded: chain o residue 8 THR Chi-restraints excluded: chain o residue 13 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1037 random chunks: chunk 932 optimal weight: 10.0000 chunk 709 optimal weight: 10.0000 chunk 489 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 450 optimal weight: 2.9990 chunk 633 optimal weight: 7.9990 chunk 946 optimal weight: 10.0000 chunk 1002 optimal weight: 10.0000 chunk 494 optimal weight: 0.8980 chunk 897 optimal weight: 10.0000 chunk 270 optimal weight: 4.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** v 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 231 GLN A 47 GLN a 120 ASN ** E 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 52 GLN F 225 GLN f 26 ASN f 106 ASN H 9 GLN k 67 GLN M 27 GLN M 41 GLN ** u 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 122 GLN O 193 GLN P 137 ASN R 39 ASN T 112 ASN ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 11 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 139723 Z= 0.282 Angle : 0.629 18.480 205723 Z= 0.324 Chirality : 0.038 0.349 25901 Planarity : 0.005 0.120 13168 Dihedral : 22.988 179.480 61671 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.56 % Favored : 92.24 % Rotamer: Outliers : 5.33 % Allowed : 16.40 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.21 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.24 % 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: -2.03 (0.10), residues: 6774 helix: -0.64 (0.11), residues: 2253 sheet: -1.09 (0.16), residues: 946 loop : -1.90 (0.10), residues: 3575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP U 92 HIS 0.008 0.001 HIS e 88 PHE 0.026 0.002 PHE D 16 TYR 0.031 0.002 TYR U 83 ARG 0.010 0.001 ARG q 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13548 Ramachandran restraints generated. 6774 Oldfield, 0 Emsley, 6774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13548 Ramachandran restraints generated. 6774 Oldfield, 0 Emsley, 6774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1496 residues out of total 5807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 307 poor density : 1189 time to evaluate : 6.663 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: v 135 GLU cc_start: 0.7377 (tt0) cc_final: 0.6930 (tp30) REVERT: v 197 LEU cc_start: 0.8801 (pt) cc_final: 0.8531 (mp) REVERT: v 215 ASN cc_start: 0.9099 (t0) cc_final: 0.8677 (t0) REVERT: v 226 GLU cc_start: 0.8726 (pm20) cc_final: 0.8394 (pm20) REVERT: v 240 TYR cc_start: 0.7389 (m-80) cc_final: 0.6758 (m-10) REVERT: v 267 MET cc_start: 0.7871 (ptp) cc_final: 0.7626 (ptp) REVERT: a 139 ARG cc_start: 0.8788 (mmm-85) cc_final: 0.8408 (mtm180) REVERT: B 53 MET cc_start: 0.9323 (OUTLIER) cc_final: 0.8941 (mtm) REVERT: B 72 VAL cc_start: 0.9152 (t) cc_final: 0.8843 (m) REVERT: B 125 SER cc_start: 0.9177 (p) cc_final: 0.8869 (t) REVERT: B 213 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7955 (tt0) REVERT: B 214 MET cc_start: 0.8573 (mmm) cc_final: 0.8294 (mtp) REVERT: B 308 MET cc_start: 0.7125 (mtt) cc_final: 0.6841 (mtt) REVERT: b 432 MET cc_start: 0.8477 (ttm) cc_final: 0.7920 (ttp) REVERT: b 437 ASP cc_start: 0.6339 (p0) cc_final: 0.5438 (p0) REVERT: b 499 ARG cc_start: 0.6803 (tpp80) cc_final: 0.5996 (ttp-170) REVERT: b 514 LYS cc_start: 0.7792 (pttp) cc_final: 0.7314 (pttt) REVERT: b 542 MET cc_start: 0.5249 (mmp) cc_final: 0.4053 (ptp) REVERT: b 613 ARG cc_start: 0.7221 (mtm-85) cc_final: 0.6981 (mtm110) REVERT: C 5 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7111 (mt0) REVERT: C 179 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9108 (tp) REVERT: C 285 ASP cc_start: 0.8265 (t0) cc_final: 0.7828 (p0) REVERT: C 313 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8954 (tp) REVERT: c 94 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7852 (mm-30) REVERT: E 157 GLN cc_start: 0.8535 (mp10) cc_final: 0.8184 (mp10) REVERT: e 109 LEU cc_start: 0.9215 (mm) cc_final: 0.8978 (mm) REVERT: F 51 TYR cc_start: 0.9475 (m-10) cc_final: 0.9200 (m-80) REVERT: F 64 GLN cc_start: 0.8645 (tp40) cc_final: 0.7689 (tp40) REVERT: F 68 ASP cc_start: 0.8257 (m-30) cc_final: 0.7755 (m-30) REVERT: F 74 SER cc_start: 0.8615 (m) cc_final: 0.8386 (p) REVERT: G 134 TYR cc_start: 0.8921 (p90) cc_final: 0.8424 (p90) REVERT: g 31 ARG cc_start: 0.8473 (mtt-85) cc_final: 0.8273 (mmt180) REVERT: g 95 ILE cc_start: 0.9248 (OUTLIER) cc_final: 0.9028 (mp) REVERT: g 98 GLN cc_start: 0.8761 (tp40) cc_final: 0.8416 (tp-100) REVERT: H 9 GLN cc_start: 0.8485 (mt0) cc_final: 0.8278 (mt0) REVERT: H 23 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.6540 (mpp80) REVERT: H 68 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9244 (tm) REVERT: H 163 GLN cc_start: 0.9113 (mm110) cc_final: 0.8879 (mm110) REVERT: h 105 ARG cc_start: 0.8101 (ttp80) cc_final: 0.7878 (ttp-170) REVERT: k 3 ARG cc_start: 0.8426 (mtt90) cc_final: 0.8189 (mtt90) REVERT: k 39 ARG cc_start: 0.8061 (mtp180) cc_final: 0.7788 (mtp180) REVERT: L 65 TYR cc_start: 0.8972 (m-80) cc_final: 0.8653 (m-80) REVERT: l 15 LYS cc_start: 0.9200 (tttp) cc_final: 0.8923 (tttp) REVERT: N 4 TYR cc_start: 0.6194 (p90) cc_final: 0.5911 (p90) REVERT: N 31 ARG cc_start: 0.7941 (ttp-170) cc_final: 0.7110 (ttp-170) REVERT: u 20 MET cc_start: 0.8448 (ttp) cc_final: 0.8246 (ttm) REVERT: u 97 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7941 (mt-10) REVERT: O 49 ARG cc_start: 0.7834 (mtp85) cc_final: 0.7489 (mtp85) REVERT: O 113 ASP cc_start: 0.8910 (p0) cc_final: 0.8357 (p0) REVERT: O 124 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8749 (mt) REVERT: P 55 GLN cc_start: 0.8863 (mm110) cc_final: 0.8081 (mt0) REVERT: P 64 ASN cc_start: 0.8676 (p0) cc_final: 0.8468 (p0) REVERT: P 101 ASN cc_start: 0.8707 (m-40) cc_final: 0.8419 (m-40) REVERT: P 138 LYS cc_start: 0.9075 (pttp) cc_final: 0.8870 (pttt) REVERT: Q 136 ASN cc_start: 0.8787 (t0) cc_final: 0.8473 (t0) REVERT: Q 151 ARG cc_start: 0.8058 (ttm170) cc_final: 0.7390 (mmp-170) REVERT: R 46 LYS cc_start: 0.8896 (tppt) cc_final: 0.8571 (tptp) REVERT: R 68 GLN cc_start: 0.9144 (tp40) cc_final: 0.8773 (tp40) REVERT: R 144 GLN cc_start: 0.8159 (mm-40) cc_final: 0.7843 (tp40) REVERT: R 148 ASP cc_start: 0.8806 (m-30) cc_final: 0.8351 (m-30) REVERT: S 6 GLU cc_start: 0.8029 (tt0) cc_final: 0.7641 (tt0) REVERT: T 104 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8466 (mp0) REVERT: T 129 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8104 (mtmm) REVERT: T 136 ARG cc_start: 0.8840 (pmm-80) cc_final: 0.8381 (mtm110) REVERT: U 33 TYR cc_start: 0.8381 (t80) cc_final: 0.7947 (t80) REVERT: U 49 ASN cc_start: 0.9134 (t0) cc_final: 0.8773 (t0) REVERT: U 75 TYR cc_start: 0.8229 (t80) cc_final: 0.7984 (t80) REVERT: U 88 GLN cc_start: 0.8610 (mp10) cc_final: 0.8238 (mp10) REVERT: W 21 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7073 (mm-30) REVERT: W 114 GLU cc_start: 0.7900 (pt0) cc_final: 0.7578 (tp30) REVERT: W 233 ILE cc_start: 0.0671 (OUTLIER) cc_final: 0.0417 (pp) REVERT: X 67 ILE cc_start: 0.9470 (mt) cc_final: 0.9221 (mt) REVERT: Y 42 GLN cc_start: 0.8497 (tm-30) cc_final: 0.8052 (tm-30) REVERT: Y 43 TYR cc_start: 0.9281 (m-80) cc_final: 0.8712 (m-80) REVERT: Y 53 ASP cc_start: 0.8508 (t0) cc_final: 0.8197 (t0) REVERT: y 18 LYS cc_start: 0.8710 (tppt) cc_final: 0.8494 (tppt) REVERT: y 209 ASP cc_start: 0.8613 (m-30) cc_final: 0.8283 (m-30) REVERT: y 215 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8096 (tt) REVERT: Z 46 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8851 (pt) REVERT: Z 101 PHE cc_start: 0.9223 (m-80) cc_final: 0.8960 (m-80) REVERT: D 95 TRP cc_start: 0.8949 (OUTLIER) cc_final: 0.8346 (t60) REVERT: D 196 ARG cc_start: 0.8334 (ttt-90) cc_final: 0.6843 (mmt180) REVERT: D 218 ARG cc_start: 0.8643 (mmm-85) cc_final: 0.8385 (mtp85) REVERT: D 270 LYS cc_start: 0.9131 (mttt) cc_final: 0.8893 (mtmm) REVERT: J 15 GLU cc_start: 0.7527 (tt0) cc_final: 0.7203 (tt0) REVERT: J 38 GLU cc_start: 0.8096 (tt0) cc_final: 0.7329 (tp30) REVERT: J 171 VAL cc_start: 0.8059 (OUTLIER) cc_final: 0.7823 (p) REVERT: J 172 LEU cc_start: 0.7112 (OUTLIER) cc_final: 0.6618 (mt) REVERT: q 29 LYS cc_start: 0.7742 (mmtt) cc_final: 0.7352 (mmtt) REVERT: q 82 GLN cc_start: 0.3437 (OUTLIER) cc_final: 0.2548 (tp40) outliers start: 307 outliers final: 211 residues processed: 1383 average time/residue: 1.1125 time to fit residues: 2693.3730 Evaluate side-chains 1334 residues out of total 5807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 1104 time to evaluate : 6.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain v residue 22 CYS Chi-restraints excluded: chain v residue 26 ILE Chi-restraints excluded: chain v residue 38 CYS Chi-restraints excluded: chain v residue 143 CYS Chi-restraints excluded: chain v residue 312 VAL Chi-restraints excluded: chain v residue 320 VAL Chi-restraints excluded: chain v residue 345 ASP Chi-restraints excluded: chain v residue 348 VAL Chi-restraints excluded: chain v residue 357 SER Chi-restraints excluded: chain v residue 378 ASN Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 88 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 157 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 216 HIS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain a residue 75 LEU Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 213 GLU 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 344 THR Chi-restraints excluded: chain b residue 361 ILE Chi-restraints excluded: chain b residue 406 ASN Chi-restraints excluded: chain b residue 418 ASP 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 519 MET Chi-restraints excluded: chain b residue 595 ASP Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 18 ILE Chi-restraints excluded: chain c residue 30 THR Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain d residue 46 THR Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain e residue 59 SER Chi-restraints excluded: chain e residue 86 THR Chi-restraints excluded: chain e residue 87 MET Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 126 LEU Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 97 SER Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 104 GLU Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 195 SER Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 246 MET Chi-restraints excluded: chain g residue 6 THR Chi-restraints excluded: chain g residue 15 THR Chi-restraints excluded: chain g residue 35 VAL Chi-restraints excluded: chain g residue 55 SER Chi-restraints excluded: chain g residue 66 SER Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 86 LYS Chi-restraints excluded: chain g residue 95 ILE Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 60 THR Chi-restraints excluded: chain I residue 90 SER Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 90 MET Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain h residue 50 SER Chi-restraints excluded: chain i residue 19 SER Chi-restraints excluded: chain i residue 42 SER Chi-restraints excluded: chain i residue 59 ASP Chi-restraints excluded: chain i residue 64 SER Chi-restraints excluded: chain j residue 7 SER Chi-restraints excluded: chain j residue 46 SER Chi-restraints excluded: chain j residue 82 SER Chi-restraints excluded: chain j residue 84 SER Chi-restraints excluded: chain k residue 29 LYS Chi-restraints excluded: chain k residue 45 VAL Chi-restraints excluded: chain k residue 66 ILE Chi-restraints excluded: chain k residue 72 THR Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain M residue 103 ILE Chi-restraints excluded: chain p residue 5 THR Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 21 SER Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain N residue 16 SER Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 171 SER Chi-restraints excluded: chain N residue 190 THR Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain u residue 9 CYS Chi-restraints excluded: chain u residue 10 SER Chi-restraints excluded: chain u residue 77 VAL Chi-restraints excluded: chain u residue 97 GLU Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 124 LEU Chi-restraints excluded: chain O residue 151 ASP Chi-restraints excluded: chain O residue 188 SER Chi-restraints excluded: chain P residue 10 ASN Chi-restraints excluded: chain P residue 79 THR 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 Q residue 6 THR Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 146 SER Chi-restraints excluded: chain R residue 59 SER Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 104 ARG Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain T residue 98 HIS Chi-restraints excluded: chain T residue 104 GLU Chi-restraints excluded: chain T residue 124 VAL Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain T residue 129 LYS Chi-restraints excluded: chain T residue 147 VAL Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 72 SER Chi-restraints excluded: chain U residue 110 VAL Chi-restraints excluded: chain V residue 13 ILE Chi-restraints excluded: chain V residue 89 ASP Chi-restraints excluded: chain W residue 45 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 224 ASP Chi-restraints excluded: chain W residue 233 ILE Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 29 SER Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain X residue 87 SER Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Y residue 80 VAL Chi-restraints excluded: chain Y residue 102 SER Chi-restraints excluded: chain y residue 5 THR Chi-restraints excluded: chain y residue 90 ASP Chi-restraints excluded: chain y residue 99 GLU Chi-restraints excluded: chain y residue 101 LEU Chi-restraints excluded: chain y residue 112 ASP Chi-restraints excluded: chain y residue 131 ASP Chi-restraints excluded: chain y residue 179 VAL Chi-restraints excluded: chain y residue 215 LEU Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 46 ILE Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain Z residue 132 SER Chi-restraints excluded: chain Z residue 134 LEU Chi-restraints excluded: chain D residue 16 PHE Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 95 TRP Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 14 ILE Chi-restraints excluded: chain J residue 20 ASN Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 173 ASP Chi-restraints excluded: chain q residue 7 THR Chi-restraints excluded: chain q residue 34 SER Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 82 GLN Chi-restraints excluded: chain o residue 8 THR Chi-restraints excluded: chain o residue 13 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1037 random chunks: chunk 834 optimal weight: 10.0000 chunk 569 optimal weight: 40.0000 chunk 14 optimal weight: 7.9990 chunk 746 optimal weight: 10.0000 chunk 413 optimal weight: 2.9990 chunk 855 optimal weight: 10.0000 chunk 692 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 511 optimal weight: 5.9990 chunk 899 optimal weight: 10.0000 chunk 252 optimal weight: 9.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: v 281 ASN ** v 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 GLN ** E 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 26 ASN ** f 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 GLN G 95 ASN ** G 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 18 ASN k 67 GLN M 27 GLN M 119 GLN u 5 GLN u 37 HIS O 182 ASN O 193 GLN P 137 ASN ** U 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 85 GLN Y 120 GLN y 83 HIS ** y 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 11 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 139723 Z= 0.335 Angle : 0.656 16.132 205723 Z= 0.336 Chirality : 0.039 0.341 25901 Planarity : 0.005 0.118 13168 Dihedral : 22.965 179.789 61665 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.56 % Favored : 91.25 % Rotamer: Outliers : 6.23 % Allowed : 16.81 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.21 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.21 % 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: -1.84 (0.10), residues: 6774 helix: -0.34 (0.11), residues: 2252 sheet: -1.06 (0.16), residues: 920 loop : -1.87 (0.10), residues: 3602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP U 92 HIS 0.010 0.001 HIS q 90 PHE 0.027 0.002 PHE D 16 TYR 0.042 0.002 TYR B 137 ARG 0.013 0.001 ARG q 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13548 Ramachandran restraints generated. 6774 Oldfield, 0 Emsley, 6774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13548 Ramachandran restraints generated. 6774 Oldfield, 0 Emsley, 6774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1501 residues out of total 5807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 359 poor density : 1142 time to evaluate : 6.833 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 135 GLU cc_start: 0.7185 (tt0) cc_final: 0.6695 (tp30) REVERT: v 210 MET cc_start: 0.9037 (tpp) cc_final: 0.8792 (tpp) REVERT: v 215 ASN cc_start: 0.9280 (t0) cc_final: 0.9072 (t0) REVERT: v 226 GLU cc_start: 0.8753 (pm20) cc_final: 0.8425 (pm20) REVERT: v 240 TYR cc_start: 0.7425 (m-80) cc_final: 0.6643 (m-10) REVERT: v 267 MET cc_start: 0.7942 (ptp) cc_final: 0.7692 (ptp) REVERT: a 139 ARG cc_start: 0.8676 (mmm-85) cc_final: 0.8366 (mtm180) REVERT: B 53 MET cc_start: 0.9322 (OUTLIER) cc_final: 0.8909 (mtm) REVERT: B 72 VAL cc_start: 0.9078 (t) cc_final: 0.8835 (m) REVERT: B 125 SER cc_start: 0.9198 (p) cc_final: 0.8906 (t) REVERT: B 213 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8093 (tt0) REVERT: b 432 MET cc_start: 0.8503 (ttm) cc_final: 0.7918 (ttp) REVERT: b 437 ASP cc_start: 0.6584 (p0) cc_final: 0.6047 (p0) REVERT: b 499 ARG cc_start: 0.6788 (tpp80) cc_final: 0.6116 (ttp-170) REVERT: b 514 LYS cc_start: 0.7683 (pttp) cc_final: 0.7205 (pttt) REVERT: b 542 MET cc_start: 0.5300 (mmp) cc_final: 0.4051 (ptp) REVERT: b 588 ARG cc_start: 0.6825 (OUTLIER) cc_final: 0.5963 (mtt180) REVERT: C 5 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7339 (mp10) REVERT: C 179 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9117 (tp) REVERT: C 221 ASN cc_start: 0.8935 (t0) cc_final: 0.8587 (t0) REVERT: C 285 ASP cc_start: 0.8195 (t0) cc_final: 0.7774 (p0) REVERT: C 313 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8951 (tp) REVERT: c 23 TYR cc_start: 0.8692 (p90) cc_final: 0.8302 (p90) REVERT: c 94 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7915 (mm-30) REVERT: E 157 GLN cc_start: 0.8474 (mp10) cc_final: 0.8131 (mp10) REVERT: e 19 ARG cc_start: 0.9148 (OUTLIER) cc_final: 0.8795 (ttt180) REVERT: e 109 LEU cc_start: 0.9206 (mm) cc_final: 0.8948 (mm) REVERT: F 40 LYS cc_start: 0.9336 (tppt) cc_final: 0.9120 (ttpt) REVERT: F 51 TYR cc_start: 0.9488 (m-10) cc_final: 0.9210 (m-80) REVERT: F 64 GLN cc_start: 0.8613 (tp40) cc_final: 0.7967 (tp40) REVERT: F 68 ASP cc_start: 0.8221 (m-30) cc_final: 0.7839 (m-30) REVERT: F 74 SER cc_start: 0.8706 (m) cc_final: 0.8488 (p) REVERT: f 26 ASN cc_start: 0.9221 (m-40) cc_final: 0.8920 (m-40) REVERT: G 27 THR cc_start: 0.8904 (OUTLIER) cc_final: 0.8700 (p) REVERT: G 134 TYR cc_start: 0.8919 (p90) cc_final: 0.8439 (p90) REVERT: G 146 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7803 (mtpt) REVERT: g 11 ASN cc_start: 0.9260 (t0) cc_final: 0.8405 (t0) REVERT: g 18 ASN cc_start: 0.9140 (t0) cc_final: 0.8903 (t0) REVERT: g 95 ILE cc_start: 0.9248 (OUTLIER) cc_final: 0.9016 (mp) REVERT: g 98 GLN cc_start: 0.8794 (tp40) cc_final: 0.8455 (tp-100) REVERT: H 9 GLN cc_start: 0.8556 (mt0) cc_final: 0.8352 (mt0) REVERT: H 23 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.6672 (mpp80) REVERT: h 15 GLU cc_start: 0.7797 (tp30) cc_final: 0.7581 (tp30) REVERT: L 65 TYR cc_start: 0.8967 (m-80) cc_final: 0.8664 (m-80) REVERT: L 118 GLU cc_start: 0.8031 (tp30) cc_final: 0.7756 (tp30) REVERT: l 15 LYS cc_start: 0.9239 (tttp) cc_final: 0.8961 (tttp) REVERT: N 4 TYR cc_start: 0.6289 (p90) cc_final: 0.5948 (p90) REVERT: u 20 MET cc_start: 0.8428 (ttp) cc_final: 0.8197 (ttm) REVERT: u 97 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7990 (mt-10) REVERT: O 113 ASP cc_start: 0.8917 (p0) cc_final: 0.8361 (p0) REVERT: O 124 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8770 (mt) REVERT: P 55 GLN cc_start: 0.8807 (mm110) cc_final: 0.8095 (mt0) REVERT: Q 136 ASN cc_start: 0.8826 (t0) cc_final: 0.8497 (t0) REVERT: Q 151 ARG cc_start: 0.8017 (ttm170) cc_final: 0.7391 (mmp-170) REVERT: R 46 LYS cc_start: 0.8920 (tppt) cc_final: 0.8617 (tptp) REVERT: R 68 GLN cc_start: 0.9136 (tp40) cc_final: 0.8729 (tp40) REVERT: R 144 GLN cc_start: 0.8197 (mm-40) cc_final: 0.7828 (tp40) REVERT: R 148 ASP cc_start: 0.8806 (m-30) cc_final: 0.8364 (m-30) REVERT: S 6 GLU cc_start: 0.8019 (tt0) cc_final: 0.7659 (tt0) REVERT: S 108 GLN cc_start: 0.8840 (mm-40) cc_final: 0.8519 (mm110) REVERT: T 129 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8033 (mtmm) REVERT: T 136 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8313 (mtm110) REVERT: U 33 TYR cc_start: 0.8471 (t80) cc_final: 0.8109 (t80) REVERT: U 49 ASN cc_start: 0.9163 (t0) cc_final: 0.8724 (t0) REVERT: U 75 TYR cc_start: 0.8318 (t80) cc_final: 0.8103 (t80) REVERT: U 88 GLN cc_start: 0.8672 (mp10) cc_final: 0.8297 (mp10) REVERT: V 102 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8883 (tt) REVERT: W 21 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7121 (mm-30) REVERT: W 114 GLU cc_start: 0.7936 (pt0) cc_final: 0.7523 (tp30) REVERT: W 233 ILE cc_start: 0.0576 (OUTLIER) cc_final: 0.0306 (pp) REVERT: X 67 ILE cc_start: 0.9508 (mt) cc_final: 0.9253 (mt) REVERT: Y 42 GLN cc_start: 0.8553 (tm-30) cc_final: 0.8010 (tm-30) REVERT: Y 43 TYR cc_start: 0.9306 (m-80) cc_final: 0.8741 (m-80) REVERT: Y 53 ASP cc_start: 0.8552 (t0) cc_final: 0.8237 (t0) REVERT: y 209 ASP cc_start: 0.8661 (m-30) cc_final: 0.8239 (m-30) REVERT: Z 9 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8868 (tptp) REVERT: D 95 TRP cc_start: 0.9042 (OUTLIER) cc_final: 0.8317 (t60) REVERT: D 196 ARG cc_start: 0.8361 (ttt-90) cc_final: 0.6829 (mmt180) REVERT: D 218 ARG cc_start: 0.8675 (mmm-85) cc_final: 0.8440 (mmm-85) REVERT: J 35 LYS cc_start: 0.9307 (mtmm) cc_final: 0.8898 (tptt) REVERT: J 60 ARG cc_start: 0.7227 (mtp-110) cc_final: 0.7024 (mtm110) REVERT: J 90 GLN cc_start: 0.8322 (tp-100) cc_final: 0.7957 (tp-100) REVERT: J 172 LEU cc_start: 0.6982 (OUTLIER) cc_final: 0.6304 (mt) REVERT: q 29 LYS cc_start: 0.7694 (mmtt) cc_final: 0.7348 (mmtt) REVERT: q 82 GLN cc_start: 0.3104 (OUTLIER) cc_final: 0.2540 (tp40) outliers start: 359 outliers final: 265 residues processed: 1365 average time/residue: 1.1441 time to fit residues: 2738.4454 Evaluate side-chains 1381 residues out of total 5807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 1095 time to evaluate : 6.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain v residue 22 CYS Chi-restraints excluded: chain v residue 26 ILE Chi-restraints excluded: chain v residue 38 CYS Chi-restraints excluded: chain v residue 76 LEU Chi-restraints excluded: chain v residue 177 LEU Chi-restraints excluded: chain v residue 218 VAL Chi-restraints excluded: chain v residue 281 ASN Chi-restraints excluded: chain v residue 312 VAL Chi-restraints excluded: chain v residue 320 VAL Chi-restraints excluded: chain v residue 345 ASP Chi-restraints excluded: chain v residue 348 VAL Chi-restraints excluded: chain v residue 357 SER Chi-restraints excluded: chain v residue 378 ASN Chi-restraints excluded: chain v residue 390 ASP Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 88 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 157 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 216 HIS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain a residue 75 LEU Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 121 VAL Chi-restraints excluded: chain a residue 123 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 213 GLU 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 255 TRP Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain b residue 361 ILE Chi-restraints excluded: chain b residue 371 ASP Chi-restraints excluded: chain b residue 385 LEU Chi-restraints excluded: chain b residue 406 ASN Chi-restraints excluded: chain b residue 418 ASP 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 519 MET Chi-restraints excluded: chain b residue 588 ARG Chi-restraints excluded: chain b residue 595 ASP Chi-restraints excluded: chain b residue 634 LEU Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 316 ASN Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 18 ILE Chi-restraints excluded: chain c residue 30 THR Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain d residue 46 THR Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain e residue 19 ARG Chi-restraints excluded: chain e residue 55 ILE Chi-restraints excluded: chain e residue 59 SER Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 117 ILE Chi-restraints excluded: chain e residue 126 LEU Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 97 SER Chi-restraints excluded: chain f residue 98 VAL Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 104 GLU Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 146 LYS Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 195 SER Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 246 MET Chi-restraints excluded: chain g residue 6 THR Chi-restraints excluded: chain g residue 15 THR Chi-restraints excluded: chain g residue 35 VAL Chi-restraints excluded: chain g residue 55 SER Chi-restraints excluded: chain g residue 66 SER Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 95 ILE Chi-restraints excluded: chain I residue 17 ASP Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 60 THR Chi-restraints excluded: chain I residue 90 SER Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 90 MET Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain h residue 50 SER Chi-restraints excluded: chain i residue 19 SER Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 64 SER Chi-restraints excluded: chain i residue 70 ARG Chi-restraints excluded: chain j residue 7 SER Chi-restraints excluded: chain j residue 46 SER Chi-restraints excluded: chain j residue 82 SER Chi-restraints excluded: chain j residue 84 SER Chi-restraints excluded: chain k residue 27 ILE Chi-restraints excluded: chain k residue 29 LYS Chi-restraints excluded: chain k residue 45 VAL Chi-restraints excluded: chain k residue 66 ILE Chi-restraints excluded: chain k residue 72 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain M residue 12 TRP Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain M residue 103 ILE Chi-restraints excluded: chain p residue 5 THR Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 21 SER Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain N residue 16 SER Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 87 GLN Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 165 THR Chi-restraints excluded: chain N residue 171 SER Chi-restraints excluded: chain N residue 174 ILE Chi-restraints excluded: chain N residue 190 THR Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 9 CYS Chi-restraints excluded: chain u residue 10 SER Chi-restraints excluded: chain u residue 77 VAL Chi-restraints excluded: chain u residue 97 GLU Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 55 HIS Chi-restraints excluded: chain O residue 124 LEU Chi-restraints excluded: chain O residue 151 ASP Chi-restraints excluded: chain O residue 188 SER Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 10 ASN Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 87 SER 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 168 LEU Chi-restraints excluded: chain P residue 172 GLN Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 41 ASP 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 123 THR Chi-restraints excluded: chain R residue 59 SER Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 82 ASP Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 171 PHE Chi-restraints excluded: chain T residue 98 HIS Chi-restraints excluded: chain T residue 124 VAL Chi-restraints excluded: chain T residue 129 LYS Chi-restraints excluded: chain T residue 136 ARG Chi-restraints excluded: chain T residue 147 VAL Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 16 THR Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 72 SER Chi-restraints excluded: chain U residue 76 LEU Chi-restraints excluded: chain U residue 80 THR Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain U residue 110 VAL Chi-restraints excluded: chain V residue 13 ILE Chi-restraints excluded: chain V residue 89 ASP Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain W residue 45 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 224 ASP Chi-restraints excluded: chain W residue 233 ILE Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 29 SER Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain X residue 87 SER Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain X residue 135 ILE Chi-restraints excluded: chain Y residue 80 VAL Chi-restraints excluded: chain Y residue 95 VAL Chi-restraints excluded: chain Y residue 102 SER Chi-restraints excluded: chain y residue 5 THR Chi-restraints excluded: chain y residue 90 ASP Chi-restraints excluded: chain y residue 99 GLU Chi-restraints excluded: chain y residue 101 LEU Chi-restraints excluded: chain y residue 112 ASP Chi-restraints excluded: chain y residue 127 GLU Chi-restraints excluded: chain y residue 135 VAL Chi-restraints excluded: chain y residue 179 VAL Chi-restraints excluded: chain Z residue 9 LYS Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain Z residue 132 SER Chi-restraints excluded: chain Z residue 134 LEU Chi-restraints excluded: chain D residue 16 PHE Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 95 TRP Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 260 PHE Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 20 ASN Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 173 ASP Chi-restraints excluded: chain q residue 2 VAL Chi-restraints excluded: chain q residue 7 THR Chi-restraints excluded: chain q residue 34 SER Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 70 LEU Chi-restraints excluded: chain q residue 82 GLN Chi-restraints excluded: chain o residue 8 THR Chi-restraints excluded: chain o residue 13 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1037 random chunks: chunk 337 optimal weight: 0.9980 chunk 902 optimal weight: 10.0000 chunk 198 optimal weight: 10.0000 chunk 588 optimal weight: 6.9990 chunk 247 optimal weight: 0.9980 chunk 1003 optimal weight: 10.0000 chunk 832 optimal weight: 10.0000 chunk 464 optimal weight: 10.0000 chunk 83 optimal weight: 0.0970 chunk 331 optimal weight: 10.0000 chunk 526 optimal weight: 8.9990 overall best weight: 3.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: v 281 ASN ** v 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 GLN f 106 ASN G 232 HIS H 162 GLN k 67 GLN M 27 GLN M 119 GLN N 182 ASN Q 45 ASN U 87 ASN ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 85 GLN ** y 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 40 HIS ** Z 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 11 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 139723 Z= 0.233 Angle : 0.598 15.001 205723 Z= 0.308 Chirality : 0.036 0.331 25901 Planarity : 0.005 0.116 13168 Dihedral : 22.912 179.989 61662 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.54 % Favored : 92.31 % Rotamer: Outliers : 5.43 % Allowed : 18.50 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.21 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.21 % 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: -1.59 (0.10), residues: 6774 helix: -0.05 (0.11), residues: 2258 sheet: -0.94 (0.16), residues: 942 loop : -1.77 (0.10), residues: 3574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP U 92 HIS 0.008 0.001 HIS y 118 PHE 0.025 0.001 PHE D 16 TYR 0.030 0.002 TYR O 167 ARG 0.008 0.000 ARG q 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13548 Ramachandran restraints generated. 6774 Oldfield, 0 Emsley, 6774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13548 Ramachandran restraints generated. 6774 Oldfield, 0 Emsley, 6774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1493 residues out of total 5807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 313 poor density : 1180 time to evaluate : 6.717 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 135 GLU cc_start: 0.7169 (tt0) cc_final: 0.6689 (tp30) REVERT: v 155 TRP cc_start: 0.8703 (OUTLIER) cc_final: 0.8375 (p-90) REVERT: v 210 MET cc_start: 0.8970 (tpp) cc_final: 0.8754 (tpp) REVERT: v 226 GLU cc_start: 0.8713 (pm20) cc_final: 0.8376 (pm20) REVERT: v 240 TYR cc_start: 0.7307 (m-80) cc_final: 0.6556 (m-10) REVERT: v 267 MET cc_start: 0.7808 (ptp) cc_final: 0.7578 (ptp) REVERT: A 52 SER cc_start: 0.9147 (m) cc_final: 0.8880 (p) REVERT: a 139 ARG cc_start: 0.8771 (mmm-85) cc_final: 0.8371 (mtm180) REVERT: B 53 MET cc_start: 0.9299 (OUTLIER) cc_final: 0.8951 (mtm) REVERT: B 56 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8656 (mm) REVERT: B 72 VAL cc_start: 0.9050 (t) cc_final: 0.8826 (m) REVERT: B 125 SER cc_start: 0.9187 (p) cc_final: 0.8925 (t) REVERT: b 432 MET cc_start: 0.8480 (ttm) cc_final: 0.7916 (ttp) REVERT: b 462 LYS cc_start: 0.8517 (pptt) cc_final: 0.8246 (ptpt) REVERT: b 468 PHE cc_start: 0.8123 (t80) cc_final: 0.7738 (t80) REVERT: b 499 ARG cc_start: 0.6802 (tpp80) cc_final: 0.6082 (ttp-170) REVERT: b 514 LYS cc_start: 0.7647 (pttp) cc_final: 0.7156 (pttt) REVERT: b 542 MET cc_start: 0.5204 (mmp) cc_final: 0.4046 (ptp) REVERT: b 588 ARG cc_start: 0.6871 (OUTLIER) cc_final: 0.6001 (mtt180) REVERT: b 605 MET cc_start: 0.6046 (mtp) cc_final: 0.5199 (mtp) REVERT: C 5 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7428 (mp10) REVERT: C 55 LYS cc_start: 0.8980 (ttpt) cc_final: 0.8603 (ttpt) REVERT: C 179 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9089 (tp) REVERT: C 221 ASN cc_start: 0.8723 (t0) cc_final: 0.8474 (t0) REVERT: C 252 GLU cc_start: 0.7662 (tm-30) cc_final: 0.7451 (tm-30) REVERT: C 285 ASP cc_start: 0.8192 (t0) cc_final: 0.7746 (p0) REVERT: C 304 GLN cc_start: 0.8115 (tt0) cc_final: 0.7824 (tt0) REVERT: c 23 TYR cc_start: 0.8642 (p90) cc_final: 0.8286 (p90) REVERT: c 94 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7894 (mm-30) REVERT: E 157 GLN cc_start: 0.8539 (mp10) cc_final: 0.8184 (mp10) REVERT: e 19 ARG cc_start: 0.9079 (OUTLIER) cc_final: 0.8777 (ttt180) REVERT: e 109 LEU cc_start: 0.9220 (mm) cc_final: 0.8952 (mm) REVERT: F 51 TYR cc_start: 0.9466 (m-10) cc_final: 0.9193 (m-80) REVERT: F 64 GLN cc_start: 0.8607 (tp40) cc_final: 0.8016 (tp40) REVERT: F 68 ASP cc_start: 0.8268 (m-30) cc_final: 0.7979 (m-30) REVERT: F 74 SER cc_start: 0.8712 (m) cc_final: 0.8510 (p) REVERT: f 10 LYS cc_start: 0.9182 (ptpt) cc_final: 0.8795 (ptpp) REVERT: f 26 ASN cc_start: 0.9224 (m-40) cc_final: 0.8917 (m-40) REVERT: G 134 TYR cc_start: 0.8798 (p90) cc_final: 0.8336 (p90) REVERT: G 146 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7697 (mtpt) REVERT: g 95 ILE cc_start: 0.9247 (OUTLIER) cc_final: 0.9027 (mp) REVERT: g 98 GLN cc_start: 0.8758 (tp40) cc_final: 0.8460 (tp-100) REVERT: H 23 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.6552 (mpp80) REVERT: H 42 ASP cc_start: 0.8183 (t0) cc_final: 0.7865 (t0) REVERT: h 15 GLU cc_start: 0.7757 (tp30) cc_final: 0.7470 (tp30) REVERT: L 65 TYR cc_start: 0.8927 (m-80) cc_final: 0.8638 (m-80) REVERT: L 93 ILE cc_start: 0.9377 (tt) cc_final: 0.9112 (tt) REVERT: L 192 GLU cc_start: 0.7796 (pp20) cc_final: 0.7018 (pp20) REVERT: l 25 GLN cc_start: 0.8300 (mm-40) cc_final: 0.7931 (mm-40) REVERT: p 37 TYR cc_start: 0.8845 (m-80) cc_final: 0.8526 (m-80) REVERT: N 4 TYR cc_start: 0.6360 (p90) cc_final: 0.5861 (p90) REVERT: N 20 ARG cc_start: 0.8840 (ptm160) cc_final: 0.8577 (ttm170) REVERT: O 49 ARG cc_start: 0.7903 (mtp85) cc_final: 0.7581 (mtp85) REVERT: O 113 ASP cc_start: 0.8855 (p0) cc_final: 0.8327 (p0) REVERT: O 124 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8759 (mt) REVERT: P 55 GLN cc_start: 0.8842 (mm110) cc_final: 0.8073 (mt0) REVERT: P 101 ASN cc_start: 0.8695 (m-40) cc_final: 0.8417 (m-40) REVERT: P 138 LYS cc_start: 0.9045 (pttp) cc_final: 0.8812 (pttt) REVERT: Q 136 ASN cc_start: 0.8757 (t0) cc_final: 0.8426 (t0) REVERT: Q 151 ARG cc_start: 0.7960 (ttm170) cc_final: 0.7511 (mmp-170) REVERT: R 46 LYS cc_start: 0.8916 (tppt) cc_final: 0.8626 (tptp) REVERT: R 68 GLN cc_start: 0.9063 (tp40) cc_final: 0.8726 (tp40) REVERT: R 144 GLN cc_start: 0.8214 (mm-40) cc_final: 0.7876 (tp40) REVERT: R 148 ASP cc_start: 0.8783 (m-30) cc_final: 0.8138 (m-30) REVERT: S 6 GLU cc_start: 0.7942 (tt0) cc_final: 0.7695 (tt0) REVERT: T 108 ARG cc_start: 0.8693 (ttp80) cc_final: 0.8417 (ttp80) REVERT: T 129 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.7829 (mtmm) REVERT: U 33 TYR cc_start: 0.8369 (t80) cc_final: 0.8011 (t80) REVERT: U 49 ASN cc_start: 0.9177 (t0) cc_final: 0.8677 (t0) REVERT: U 75 TYR cc_start: 0.8182 (t80) cc_final: 0.7941 (t80) REVERT: U 88 GLN cc_start: 0.8606 (mp10) cc_final: 0.8289 (mp10) REVERT: W 21 GLU cc_start: 0.7360 (mm-30) cc_final: 0.7148 (mm-30) REVERT: W 114 GLU cc_start: 0.7755 (pt0) cc_final: 0.7368 (tp30) REVERT: W 233 ILE cc_start: 0.0830 (OUTLIER) cc_final: 0.0573 (pp) REVERT: X 67 ILE cc_start: 0.9471 (mt) cc_final: 0.9246 (mt) REVERT: Y 42 GLN cc_start: 0.8573 (tm-30) cc_final: 0.8047 (tm-30) REVERT: Y 43 TYR cc_start: 0.9263 (m-80) cc_final: 0.8703 (m-80) REVERT: Y 53 ASP cc_start: 0.8506 (t0) cc_final: 0.8174 (t0) REVERT: y 169 ASP cc_start: 0.8976 (m-30) cc_final: 0.8741 (m-30) REVERT: y 173 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9080 (tt) REVERT: y 201 ASP cc_start: 0.7636 (m-30) cc_final: 0.7417 (m-30) REVERT: Z 9 LYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8875 (tptp) REVERT: D 95 TRP cc_start: 0.8946 (OUTLIER) cc_final: 0.8292 (t60) REVERT: D 196 ARG cc_start: 0.8299 (ttt-90) cc_final: 0.6821 (mmt180) REVERT: D 218 ARG cc_start: 0.8684 (mmm-85) cc_final: 0.8379 (mtp85) REVERT: J 35 LYS cc_start: 0.9286 (mtmm) cc_final: 0.8654 (tptt) REVERT: J 172 LEU cc_start: 0.6804 (mt) cc_final: 0.6414 (mt) REVERT: q 29 LYS cc_start: 0.7649 (mmtt) cc_final: 0.7263 (mmtt) REVERT: q 82 GLN cc_start: 0.2593 (OUTLIER) cc_final: 0.2332 (tp40) outliers start: 313 outliers final: 236 residues processed: 1380 average time/residue: 1.1709 time to fit residues: 2828.4979 Evaluate side-chains 1361 residues out of total 5807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 1108 time to evaluate : 6.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain v residue 22 CYS Chi-restraints excluded: chain v residue 26 ILE Chi-restraints excluded: chain v residue 38 CYS Chi-restraints excluded: chain v residue 76 LEU Chi-restraints excluded: chain v residue 155 TRP Chi-restraints excluded: chain v residue 177 LEU Chi-restraints excluded: chain v residue 197 LEU Chi-restraints excluded: chain v residue 218 VAL Chi-restraints excluded: chain v residue 271 SER Chi-restraints excluded: chain v residue 312 VAL Chi-restraints excluded: chain v residue 320 VAL Chi-restraints excluded: chain v residue 345 ASP Chi-restraints excluded: chain v residue 348 VAL Chi-restraints excluded: chain v residue 357 SER Chi-restraints excluded: chain v residue 378 ASN Chi-restraints excluded: chain v residue 390 ASP Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 45 VAL 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 157 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 216 HIS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 121 VAL Chi-restraints excluded: chain a residue 123 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 102 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 344 THR Chi-restraints excluded: chain b residue 361 ILE Chi-restraints excluded: chain b residue 371 ASP Chi-restraints excluded: chain b residue 385 LEU Chi-restraints excluded: chain b residue 418 ASP 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 519 MET Chi-restraints excluded: chain b residue 588 ARG Chi-restraints excluded: chain b residue 634 LEU Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 316 ASN Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 18 ILE Chi-restraints excluded: chain c residue 30 THR Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain d residue 48 ASP Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain e residue 19 ARG Chi-restraints excluded: chain e residue 55 ILE Chi-restraints excluded: chain e residue 86 THR Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 117 ILE Chi-restraints excluded: chain e residue 126 LEU Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 97 SER Chi-restraints excluded: chain f residue 98 VAL Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 104 GLU Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 146 LYS Chi-restraints excluded: chain G residue 195 SER Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 232 HIS Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 246 MET Chi-restraints excluded: chain g residue 15 THR Chi-restraints excluded: chain g residue 35 VAL Chi-restraints excluded: chain g residue 55 SER Chi-restraints excluded: chain g residue 66 SER Chi-restraints excluded: chain g residue 95 ILE Chi-restraints excluded: chain I residue 17 ASP Chi-restraints excluded: chain I residue 60 THR Chi-restraints excluded: chain I residue 90 SER Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 90 MET Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain h residue 50 SER Chi-restraints excluded: chain i residue 19 SER Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 64 SER Chi-restraints excluded: chain i residue 70 ARG Chi-restraints excluded: chain j residue 7 SER Chi-restraints excluded: chain j residue 46 SER Chi-restraints excluded: chain j residue 82 SER Chi-restraints excluded: chain j residue 84 SER Chi-restraints excluded: chain k residue 27 ILE Chi-restraints excluded: chain k residue 29 LYS Chi-restraints excluded: chain k residue 45 VAL Chi-restraints excluded: chain k residue 66 ILE Chi-restraints excluded: chain k residue 72 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain p residue 5 THR Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 21 SER Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain N residue 16 SER Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 171 SER Chi-restraints excluded: chain N residue 190 THR Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 9 CYS Chi-restraints excluded: chain u residue 10 SER Chi-restraints excluded: chain u residue 97 GLU Chi-restraints excluded: chain u residue 134 LEU Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 55 HIS Chi-restraints excluded: chain O residue 124 LEU Chi-restraints excluded: chain O residue 151 ASP Chi-restraints excluded: chain O residue 188 SER Chi-restraints excluded: chain P residue 10 ASN Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 87 SER 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 168 LEU Chi-restraints excluded: chain P residue 172 GLN Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 41 ASP 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 123 THR Chi-restraints excluded: chain R residue 59 SER Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 82 ASP Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 144 LEU Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 171 PHE Chi-restraints excluded: chain T residue 98 HIS Chi-restraints excluded: chain T residue 124 VAL Chi-restraints excluded: chain T residue 129 LYS Chi-restraints excluded: chain T residue 147 VAL Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 16 THR Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 72 SER Chi-restraints excluded: chain U residue 76 LEU Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain U residue 110 VAL Chi-restraints excluded: chain V residue 13 ILE Chi-restraints excluded: chain V residue 89 ASP Chi-restraints excluded: chain W residue 45 LEU Chi-restraints excluded: chain W residue 55 GLU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 224 ASP Chi-restraints excluded: chain W residue 233 ILE Chi-restraints excluded: chain X residue 87 SER Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 80 VAL Chi-restraints excluded: chain Y residue 95 VAL Chi-restraints excluded: chain Y residue 102 SER Chi-restraints excluded: chain y residue 5 THR Chi-restraints excluded: chain y residue 90 ASP Chi-restraints excluded: chain y residue 99 GLU Chi-restraints excluded: chain y residue 101 LEU Chi-restraints excluded: chain y residue 112 ASP Chi-restraints excluded: chain y residue 131 ASP Chi-restraints excluded: chain y residue 135 VAL Chi-restraints excluded: chain y residue 173 LEU Chi-restraints excluded: chain y residue 179 VAL Chi-restraints excluded: chain y residue 215 LEU Chi-restraints excluded: chain Z residue 9 LYS Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain Z residue 132 SER Chi-restraints excluded: chain Z residue 134 LEU Chi-restraints excluded: chain D residue 16 PHE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 95 TRP Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 260 PHE Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 20 ASN Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 173 ASP Chi-restraints excluded: chain q residue 2 VAL Chi-restraints excluded: chain q residue 7 THR Chi-restraints excluded: chain q residue 34 SER Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 71 ARG Chi-restraints excluded: chain q residue 79 THR Chi-restraints excluded: chain q residue 82 GLN Chi-restraints excluded: chain q residue 90 HIS Chi-restraints excluded: chain o residue 8 THR Chi-restraints excluded: chain o residue 13 THR Chi-restraints excluded: chain o residue 25 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1037 random chunks: chunk 967 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 571 optimal weight: 10.0000 chunk 732 optimal weight: 10.0000 chunk 567 optimal weight: 9.9990 chunk 844 optimal weight: 10.0000 chunk 560 optimal weight: 8.9990 chunk 999 optimal weight: 20.0000 chunk 625 optimal weight: 0.8980 chunk 609 optimal weight: 6.9990 chunk 461 optimal weight: 3.9990 overall best weight: 6.1788 ------------------------------------------------------------------------------- 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 47 GLN C 322 GLN F 225 GLN f 106 ASN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 9 GLN k 67 GLN L 12 ASN ** l 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 119 GLN R 27 ASN ** U 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 47 ASN V 132 ASN ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 11 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 139723 Z= 0.365 Angle : 0.666 14.107 205723 Z= 0.339 Chirality : 0.039 0.325 25901 Planarity : 0.005 0.116 13168 Dihedral : 22.910 179.743 61662 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.75 % Favored : 91.05 % Rotamer: Outliers : 5.87 % Allowed : 18.81 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.21 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.20 % 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: -1.65 (0.10), residues: 6774 helix: -0.08 (0.11), residues: 2277 sheet: -1.00 (0.16), residues: 932 loop : -1.83 (0.10), residues: 3565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP U 92 HIS 0.022 0.001 HIS q 23 PHE 0.027 0.002 PHE D 16 TYR 0.047 0.002 TYR y 113 ARG 0.014 0.001 ARG q 71 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13548 Ramachandran restraints generated. 6774 Oldfield, 0 Emsley, 6774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13548 Ramachandran restraints generated. 6774 Oldfield, 0 Emsley, 6774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1450 residues out of total 5807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 338 poor density : 1112 time to evaluate : 6.689 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 135 GLU cc_start: 0.7177 (tt0) cc_final: 0.6692 (tp30) REVERT: v 155 TRP cc_start: 0.8672 (OUTLIER) cc_final: 0.8338 (p-90) REVERT: v 197 LEU cc_start: 0.8759 (pt) cc_final: 0.8501 (mp) REVERT: v 226 GLU cc_start: 0.8741 (pm20) cc_final: 0.8394 (pm20) REVERT: v 240 TYR cc_start: 0.7354 (m-80) cc_final: 0.6639 (m-10) REVERT: v 267 MET cc_start: 0.7919 (ptp) cc_final: 0.7645 (ptp) REVERT: a 139 ARG cc_start: 0.8694 (mmm-85) cc_final: 0.8329 (mtm180) REVERT: B 72 VAL cc_start: 0.9095 (t) cc_final: 0.8862 (m) REVERT: B 125 SER cc_start: 0.9216 (p) cc_final: 0.8961 (t) REVERT: B 308 MET cc_start: 0.8418 (mmm) cc_final: 0.7974 (mtt) REVERT: b 432 MET cc_start: 0.8529 (ttm) cc_final: 0.7970 (ttp) REVERT: b 462 LYS cc_start: 0.8535 (pptt) cc_final: 0.8269 (ptpt) REVERT: b 468 PHE cc_start: 0.8276 (t80) cc_final: 0.7919 (t80) REVERT: b 479 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.8054 (p0) REVERT: b 499 ARG cc_start: 0.6771 (tpp80) cc_final: 0.6033 (ttp-170) REVERT: b 514 LYS cc_start: 0.7656 (pttp) cc_final: 0.7168 (pttt) REVERT: b 542 MET cc_start: 0.5162 (mmp) cc_final: 0.4103 (ptp) REVERT: b 588 ARG cc_start: 0.7034 (OUTLIER) cc_final: 0.6147 (mtt180) REVERT: b 605 MET cc_start: 0.6085 (mtp) cc_final: 0.5202 (mtp) REVERT: b 608 MET cc_start: 0.3800 (mmt) cc_final: 0.3592 (mmt) REVERT: C 5 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7307 (mp10) REVERT: C 179 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9080 (tp) REVERT: C 221 ASN cc_start: 0.8913 (t0) cc_final: 0.8581 (t0) REVERT: C 285 ASP cc_start: 0.8211 (t0) cc_final: 0.7773 (p0) REVERT: c 23 TYR cc_start: 0.8713 (p90) cc_final: 0.8476 (p90) REVERT: c 94 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7920 (mm-30) REVERT: E 157 GLN cc_start: 0.8505 (mp10) cc_final: 0.8150 (mp10) REVERT: e 19 ARG cc_start: 0.9157 (OUTLIER) cc_final: 0.8773 (ttt180) REVERT: e 109 LEU cc_start: 0.9307 (mm) cc_final: 0.9056 (mm) REVERT: F 40 LYS cc_start: 0.9340 (tppt) cc_final: 0.9072 (ttpt) REVERT: F 51 TYR cc_start: 0.9480 (m-10) cc_final: 0.9205 (m-80) REVERT: F 64 GLN cc_start: 0.8605 (tp40) cc_final: 0.8016 (tp40) REVERT: F 68 ASP cc_start: 0.8273 (m-30) cc_final: 0.8013 (m-30) REVERT: f 26 ASN cc_start: 0.9221 (m-40) cc_final: 0.8926 (m-40) REVERT: G 146 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7746 (mtpt) REVERT: g 95 ILE cc_start: 0.9250 (OUTLIER) cc_final: 0.9015 (mp) REVERT: g 98 GLN cc_start: 0.8842 (tp40) cc_final: 0.8507 (tp-100) REVERT: H 9 GLN cc_start: 0.8627 (mt0) cc_final: 0.8300 (mt0) REVERT: H 23 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.6664 (mpp80) REVERT: H 52 LEU cc_start: 0.8879 (tp) cc_final: 0.8554 (tp) REVERT: h 15 GLU cc_start: 0.7819 (tp30) cc_final: 0.7606 (tp30) REVERT: L 65 TYR cc_start: 0.8980 (m-80) cc_final: 0.8683 (m-80) REVERT: L 89 TYR cc_start: 0.8828 (t80) cc_final: 0.8584 (t80) REVERT: L 93 ILE cc_start: 0.9473 (tt) cc_final: 0.9194 (tt) REVERT: l 25 GLN cc_start: 0.8284 (mm-40) cc_final: 0.7777 (mm-40) REVERT: N 4 TYR cc_start: 0.6280 (p90) cc_final: 0.5866 (p90) REVERT: N 20 ARG cc_start: 0.8937 (ptm160) cc_final: 0.8703 (ttm170) REVERT: N 91 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.6820 (mm-30) REVERT: O 113 ASP cc_start: 0.8903 (p0) cc_final: 0.8347 (p0) REVERT: O 124 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8833 (mt) REVERT: P 55 GLN cc_start: 0.8800 (mm110) cc_final: 0.8128 (mt0) REVERT: P 138 LYS cc_start: 0.9000 (pttp) cc_final: 0.8787 (pttt) REVERT: Q 136 ASN cc_start: 0.8843 (t0) cc_final: 0.8540 (t0) REVERT: Q 148 GLU cc_start: 0.7090 (tp30) cc_final: 0.6788 (mm-30) REVERT: Q 151 ARG cc_start: 0.8053 (ttm170) cc_final: 0.7387 (mmp-170) REVERT: R 46 LYS cc_start: 0.9006 (tppt) cc_final: 0.8692 (tptp) REVERT: R 68 GLN cc_start: 0.9079 (tp40) cc_final: 0.8750 (tp40) REVERT: R 144 GLN cc_start: 0.8253 (mm-40) cc_final: 0.7851 (tp40) REVERT: R 148 ASP cc_start: 0.8805 (m-30) cc_final: 0.8154 (m-30) REVERT: S 6 GLU cc_start: 0.7973 (tt0) cc_final: 0.7732 (tt0) REVERT: S 46 GLN cc_start: 0.8796 (mt0) cc_final: 0.8575 (mt0) REVERT: S 108 GLN cc_start: 0.8819 (mm-40) cc_final: 0.8510 (mm110) REVERT: T 108 ARG cc_start: 0.8727 (ttp80) cc_final: 0.8467 (ttp80) REVERT: T 129 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.7864 (mtmm) REVERT: T 136 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.7934 (pmm-80) REVERT: U 33 TYR cc_start: 0.8427 (t80) cc_final: 0.8034 (t80) REVERT: U 49 ASN cc_start: 0.9211 (t0) cc_final: 0.8714 (t0) REVERT: U 75 TYR cc_start: 0.8317 (t80) cc_final: 0.8096 (t80) REVERT: W 21 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7179 (mm-30) REVERT: W 67 MET cc_start: 0.6048 (ptm) cc_final: 0.5573 (ppp) REVERT: W 75 LYS cc_start: 0.6141 (mptt) cc_final: 0.5843 (mttp) REVERT: W 114 GLU cc_start: 0.7913 (pt0) cc_final: 0.7354 (tp30) REVERT: W 233 ILE cc_start: 0.0802 (OUTLIER) cc_final: 0.0533 (pp) REVERT: X 67 ILE cc_start: 0.9484 (mt) cc_final: 0.9261 (mt) REVERT: Y 42 GLN cc_start: 0.8555 (tm-30) cc_final: 0.7971 (tm-30) REVERT: Y 43 TYR cc_start: 0.9275 (m-80) cc_final: 0.8699 (m-80) REVERT: Y 53 ASP cc_start: 0.8584 (t0) cc_final: 0.8320 (t0) REVERT: y 173 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9101 (tt) REVERT: Z 9 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8844 (tptp) REVERT: D 95 TRP cc_start: 0.9046 (OUTLIER) cc_final: 0.8321 (t60) REVERT: D 196 ARG cc_start: 0.8345 (ttt-90) cc_final: 0.6906 (mmt180) REVERT: D 218 ARG cc_start: 0.8733 (mmm-85) cc_final: 0.8406 (mtp85) REVERT: J 35 LYS cc_start: 0.9250 (mtmm) cc_final: 0.8803 (tptt) REVERT: q 29 LYS cc_start: 0.7665 (mmtt) cc_final: 0.7306 (mmtt) outliers start: 338 outliers final: 273 residues processed: 1322 average time/residue: 1.0686 time to fit residues: 2473.6990 Evaluate side-chains 1373 residues out of total 5807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 290 poor density : 1083 time to evaluate : 6.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain v residue 22 CYS Chi-restraints excluded: chain v residue 26 ILE Chi-restraints excluded: chain v residue 38 CYS Chi-restraints excluded: chain v residue 76 LEU Chi-restraints excluded: chain v residue 155 TRP Chi-restraints excluded: chain v residue 177 LEU Chi-restraints excluded: chain v residue 178 ILE Chi-restraints excluded: chain v residue 192 GLU Chi-restraints excluded: chain v residue 218 VAL Chi-restraints excluded: chain v residue 271 SER Chi-restraints excluded: chain v residue 312 VAL Chi-restraints excluded: chain v residue 320 VAL Chi-restraints excluded: chain v residue 345 ASP Chi-restraints excluded: chain v residue 348 VAL Chi-restraints excluded: chain v residue 357 SER Chi-restraints excluded: chain v residue 378 ASN Chi-restraints excluded: chain v residue 390 ASP Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 88 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 157 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 216 HIS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 121 VAL Chi-restraints excluded: chain a residue 123 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 164 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 344 THR Chi-restraints excluded: chain b residue 361 ILE Chi-restraints excluded: chain b residue 385 LEU Chi-restraints excluded: chain b residue 406 ASN Chi-restraints excluded: chain b residue 418 ASP 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 519 MET Chi-restraints excluded: chain b residue 588 ARG Chi-restraints excluded: chain b residue 634 LEU Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 316 ASN Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 18 ILE Chi-restraints excluded: chain c residue 30 THR Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain d residue 46 THR Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain e residue 19 ARG Chi-restraints excluded: chain e residue 55 ILE Chi-restraints excluded: chain e residue 59 SER Chi-restraints excluded: chain e residue 86 THR Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 117 ILE Chi-restraints excluded: chain e residue 126 LEU Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 62 SER Chi-restraints excluded: chain f residue 97 SER Chi-restraints excluded: chain f residue 98 VAL Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 104 GLU Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 146 LYS Chi-restraints excluded: chain G residue 195 SER Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 246 MET Chi-restraints excluded: chain G residue 252 ASN Chi-restraints excluded: chain g residue 6 THR Chi-restraints excluded: chain g residue 15 THR Chi-restraints excluded: chain g residue 35 VAL Chi-restraints excluded: chain g residue 55 SER Chi-restraints excluded: chain g residue 66 SER Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 95 ILE Chi-restraints excluded: chain I residue 17 ASP Chi-restraints excluded: chain I residue 60 THR Chi-restraints excluded: chain I residue 90 SER Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 90 MET Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain h residue 50 SER Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 19 SER Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 46 GLU Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 61 ILE Chi-restraints excluded: chain i residue 64 SER Chi-restraints excluded: chain i residue 70 ARG Chi-restraints excluded: chain j residue 7 SER Chi-restraints excluded: chain j residue 46 SER Chi-restraints excluded: chain j residue 82 SER Chi-restraints excluded: chain j residue 84 SER Chi-restraints excluded: chain k residue 27 ILE Chi-restraints excluded: chain k residue 29 LYS Chi-restraints excluded: chain k residue 45 VAL Chi-restraints excluded: chain k residue 55 VAL Chi-restraints excluded: chain k residue 66 ILE Chi-restraints excluded: chain k residue 72 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain M residue 12 TRP Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 40 ASP Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain p residue 5 THR Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 21 SER Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain N residue 16 SER Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 87 GLN Chi-restraints excluded: chain N residue 91 GLU Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 171 SER Chi-restraints excluded: chain N residue 190 THR Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 9 CYS Chi-restraints excluded: chain u residue 10 SER Chi-restraints excluded: chain u residue 134 LEU Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 55 HIS Chi-restraints excluded: chain O residue 124 LEU Chi-restraints excluded: chain O residue 151 ASP Chi-restraints excluded: chain O residue 188 SER Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 10 ASN Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 87 SER 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 168 LEU Chi-restraints excluded: chain P residue 172 GLN Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 57 ILE Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain R residue 59 SER Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 82 ASP Chi-restraints excluded: chain S residue 89 ASN Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 144 LEU Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 171 PHE Chi-restraints excluded: chain T residue 98 HIS Chi-restraints excluded: chain T residue 124 VAL Chi-restraints excluded: chain T residue 129 LYS Chi-restraints excluded: chain T residue 136 ARG Chi-restraints excluded: chain T residue 147 VAL Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 16 THR Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 72 SER Chi-restraints excluded: chain U residue 76 LEU Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain U residue 110 VAL Chi-restraints excluded: chain V residue 13 ILE Chi-restraints excluded: chain V residue 89 ASP Chi-restraints excluded: chain W residue 45 LEU Chi-restraints excluded: chain W residue 55 GLU Chi-restraints excluded: chain W residue 77 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 224 ASP Chi-restraints excluded: chain W residue 233 ILE Chi-restraints excluded: chain X residue 29 SER Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain X residue 87 SER Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 50 ILE Chi-restraints excluded: chain Y residue 80 VAL Chi-restraints excluded: chain Y residue 95 VAL Chi-restraints excluded: chain Y residue 102 SER Chi-restraints excluded: chain y residue 5 THR Chi-restraints excluded: chain y residue 90 ASP Chi-restraints excluded: chain y residue 99 GLU Chi-restraints excluded: chain y residue 101 LEU Chi-restraints excluded: chain y residue 112 ASP Chi-restraints excluded: chain y residue 135 VAL Chi-restraints excluded: chain y residue 173 LEU Chi-restraints excluded: chain y residue 179 VAL Chi-restraints excluded: chain Z residue 9 LYS Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain Z residue 132 SER Chi-restraints excluded: chain Z residue 134 LEU Chi-restraints excluded: chain D residue 16 PHE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 95 TRP Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 260 PHE Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 20 ASN Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 150 ASN Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 173 ASP Chi-restraints excluded: chain q residue 2 VAL Chi-restraints excluded: chain q residue 7 THR Chi-restraints excluded: chain q residue 34 SER Chi-restraints excluded: chain q residue 41 ARG Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 65 THR Chi-restraints excluded: chain q residue 70 LEU Chi-restraints excluded: chain q residue 71 ARG Chi-restraints excluded: chain q residue 79 THR Chi-restraints excluded: chain q residue 90 HIS Chi-restraints excluded: chain o residue 8 THR Chi-restraints excluded: chain o residue 13 THR Chi-restraints excluded: chain o residue 25 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1037 random chunks: chunk 618 optimal weight: 0.9980 chunk 399 optimal weight: 5.9990 chunk 596 optimal weight: 8.9990 chunk 301 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 chunk 193 optimal weight: 10.0000 chunk 635 optimal weight: 5.9990 chunk 680 optimal weight: 5.9990 chunk 494 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 785 optimal weight: 50.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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 47 GLN f 106 ASN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 67 GLN M 27 GLN M 119 GLN R 27 ASN S 63 GLN ** U 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 132 ASN ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 11 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.153 139723 Z= 0.260 Angle : 0.611 13.885 205723 Z= 0.314 Chirality : 0.037 0.314 25901 Planarity : 0.005 0.115 13168 Dihedral : 22.873 179.910 61662 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.66 % Favored : 92.13 % Rotamer: Outliers : 5.64 % Allowed : 19.52 % Favored : 74.84 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.21 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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: -1.46 (0.10), residues: 6774 helix: 0.10 (0.11), residues: 2274 sheet: -0.92 (0.17), residues: 920 loop : -1.73 (0.10), residues: 3580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP U 92 HIS 0.014 0.001 HIS q 23 PHE 0.025 0.002 PHE D 16 TYR 0.037 0.002 TYR O 167 ARG 0.012 0.000 ARG q 71 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13548 Ramachandran restraints generated. 6774 Oldfield, 0 Emsley, 6774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13548 Ramachandran restraints generated. 6774 Oldfield, 0 Emsley, 6774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1460 residues out of total 5807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 325 poor density : 1135 time to evaluate : 6.867 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 135 GLU cc_start: 0.7165 (tt0) cc_final: 0.6691 (tp30) REVERT: v 155 TRP cc_start: 0.8661 (OUTLIER) cc_final: 0.8341 (p-90) REVERT: v 226 GLU cc_start: 0.8710 (pm20) cc_final: 0.8357 (pm20) REVERT: v 240 TYR cc_start: 0.7382 (m-80) cc_final: 0.6630 (m-10) REVERT: v 267 MET cc_start: 0.7817 (ptp) cc_final: 0.7585 (ptp) REVERT: A 52 SER cc_start: 0.9137 (m) cc_final: 0.8885 (p) REVERT: a 90 TYR cc_start: 0.8687 (m-80) cc_final: 0.8430 (m-80) REVERT: a 139 ARG cc_start: 0.8758 (mmm-85) cc_final: 0.8372 (mtm180) REVERT: B 72 VAL cc_start: 0.9117 (t) cc_final: 0.8884 (m) REVERT: B 125 SER cc_start: 0.9195 (p) cc_final: 0.8943 (t) REVERT: B 308 MET cc_start: 0.8326 (mmm) cc_final: 0.7878 (mtt) REVERT: b 432 MET cc_start: 0.8502 (ttm) cc_final: 0.7933 (ttp) REVERT: b 459 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7405 (tt0) REVERT: b 462 LYS cc_start: 0.8476 (pptt) cc_final: 0.8209 (ptpt) REVERT: b 468 PHE cc_start: 0.8190 (t80) cc_final: 0.7829 (t80) REVERT: b 479 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.8085 (p0) REVERT: b 499 ARG cc_start: 0.6761 (tpp80) cc_final: 0.6037 (ttp-170) REVERT: b 514 LYS cc_start: 0.7776 (pttp) cc_final: 0.7201 (pttt) REVERT: b 542 MET cc_start: 0.5288 (mmp) cc_final: 0.4165 (ptp) REVERT: b 588 ARG cc_start: 0.6970 (OUTLIER) cc_final: 0.6094 (mtt180) REVERT: b 605 MET cc_start: 0.6115 (mtp) cc_final: 0.5200 (mtp) REVERT: C 5 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7426 (mp10) REVERT: C 179 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.9089 (tp) REVERT: C 221 ASN cc_start: 0.8776 (t0) cc_final: 0.8424 (t0) REVERT: C 285 ASP cc_start: 0.8189 (t0) cc_final: 0.7735 (p0) REVERT: c 23 TYR cc_start: 0.8656 (p90) cc_final: 0.8343 (p90) REVERT: c 94 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7898 (mm-30) REVERT: E 157 GLN cc_start: 0.8563 (mp10) cc_final: 0.8294 (mp10) REVERT: e 19 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.8759 (ttt180) REVERT: e 30 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8359 (mm-30) REVERT: e 109 LEU cc_start: 0.9247 (mm) cc_final: 0.8974 (mm) REVERT: F 51 TYR cc_start: 0.9438 (m-10) cc_final: 0.9162 (m-80) REVERT: F 64 GLN cc_start: 0.8545 (tp40) cc_final: 0.7431 (tp40) REVERT: F 68 ASP cc_start: 0.8324 (m-30) cc_final: 0.7571 (m-30) REVERT: f 26 ASN cc_start: 0.9208 (m-40) cc_final: 0.8917 (m-40) REVERT: G 134 TYR cc_start: 0.8821 (p90) cc_final: 0.8388 (p90) REVERT: G 146 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7712 (mtpt) REVERT: g 95 ILE cc_start: 0.9258 (OUTLIER) cc_final: 0.9029 (mp) REVERT: g 96 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8532 (mm-30) REVERT: g 98 GLN cc_start: 0.8838 (tp40) cc_final: 0.8544 (tp-100) REVERT: H 23 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.6632 (mpp80) REVERT: H 42 ASP cc_start: 0.8062 (t0) cc_final: 0.7741 (t0) REVERT: k 67 GLN cc_start: 0.9129 (mm110) cc_final: 0.8760 (mp10) REVERT: L 65 TYR cc_start: 0.8951 (m-80) cc_final: 0.8675 (m-80) REVERT: L 93 ILE cc_start: 0.9440 (tt) cc_final: 0.9228 (tt) REVERT: l 25 GLN cc_start: 0.8264 (mm-40) cc_final: 0.7723 (mm-40) REVERT: p 37 TYR cc_start: 0.8877 (m-80) cc_final: 0.8612 (m-80) REVERT: N 4 TYR cc_start: 0.6395 (p90) cc_final: 0.5898 (p90) REVERT: N 20 ARG cc_start: 0.8887 (ptm160) cc_final: 0.8634 (ttm170) REVERT: N 91 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.6922 (mm-30) REVERT: O 106 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7118 (mt-10) REVERT: O 113 ASP cc_start: 0.8841 (p0) cc_final: 0.8297 (p0) REVERT: O 124 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8771 (mt) REVERT: P 55 GLN cc_start: 0.8851 (mm110) cc_final: 0.8093 (mt0) REVERT: Q 136 ASN cc_start: 0.8799 (t0) cc_final: 0.8478 (t0) REVERT: Q 151 ARG cc_start: 0.8098 (ttm170) cc_final: 0.7476 (mmp-170) REVERT: R 46 LYS cc_start: 0.8987 (tppt) cc_final: 0.8721 (tptp) REVERT: R 68 GLN cc_start: 0.9074 (tp40) cc_final: 0.8762 (tp40) REVERT: R 144 GLN cc_start: 0.8253 (mm-40) cc_final: 0.7795 (tp40) REVERT: R 148 ASP cc_start: 0.8781 (m-30) cc_final: 0.8171 (m-30) REVERT: S 6 GLU cc_start: 0.7939 (tt0) cc_final: 0.7705 (tt0) REVERT: S 46 GLN cc_start: 0.8818 (mt0) cc_final: 0.8596 (mt0) REVERT: S 81 TYR cc_start: 0.9150 (p90) cc_final: 0.8715 (p90) REVERT: S 108 GLN cc_start: 0.8778 (mm-40) cc_final: 0.8520 (mm110) REVERT: T 108 ARG cc_start: 0.8701 (ttp80) cc_final: 0.8434 (ttp80) REVERT: T 129 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7779 (mtmm) REVERT: T 136 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.7910 (pmm-80) REVERT: U 33 TYR cc_start: 0.8335 (t80) cc_final: 0.7961 (t80) REVERT: U 49 ASN cc_start: 0.9171 (t0) cc_final: 0.8663 (t0) REVERT: U 75 TYR cc_start: 0.8229 (t80) cc_final: 0.8023 (t80) REVERT: W 67 MET cc_start: 0.5971 (ptm) cc_final: 0.5721 (ppp) REVERT: W 114 GLU cc_start: 0.7921 (pt0) cc_final: 0.7392 (tp30) REVERT: X 67 ILE cc_start: 0.9470 (mt) cc_final: 0.9236 (mt) REVERT: X 73 MET cc_start: 0.8063 (mmp) cc_final: 0.7675 (mmm) REVERT: Y 42 GLN cc_start: 0.8537 (tm-30) cc_final: 0.7949 (tm-30) REVERT: Y 43 TYR cc_start: 0.9237 (m-80) cc_final: 0.8645 (m-80) REVERT: y 173 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9100 (tt) REVERT: Z 9 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8863 (tptp) REVERT: D 95 TRP cc_start: 0.8998 (OUTLIER) cc_final: 0.8301 (t60) REVERT: D 196 ARG cc_start: 0.8266 (ttt-90) cc_final: 0.6876 (mmt180) REVERT: D 218 ARG cc_start: 0.8735 (mmm-85) cc_final: 0.8338 (mtp85) REVERT: D 230 ASP cc_start: 0.8722 (OUTLIER) cc_final: 0.8492 (m-30) REVERT: J 35 LYS cc_start: 0.9169 (mtmm) cc_final: 0.8820 (tptt) REVERT: J 165 GLN cc_start: 0.9118 (pp30) cc_final: 0.8868 (pp30) REVERT: q 29 LYS cc_start: 0.7601 (mmtt) cc_final: 0.7240 (mmtt) REVERT: o 25 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.7946 (tptt) outliers start: 325 outliers final: 265 residues processed: 1337 average time/residue: 1.2422 time to fit residues: 2942.7977 Evaluate side-chains 1378 residues out of total 5807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 1093 time to evaluate : 5.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain v residue 22 CYS Chi-restraints excluded: chain v residue 26 ILE Chi-restraints excluded: chain v residue 38 CYS Chi-restraints excluded: chain v residue 76 LEU Chi-restraints excluded: chain v residue 155 TRP Chi-restraints excluded: chain v residue 177 LEU Chi-restraints excluded: chain v residue 271 SER Chi-restraints excluded: chain v residue 312 VAL Chi-restraints excluded: chain v residue 320 VAL Chi-restraints excluded: chain v residue 345 ASP Chi-restraints excluded: chain v residue 348 VAL Chi-restraints excluded: chain v residue 357 SER Chi-restraints excluded: chain v residue 378 ASN Chi-restraints excluded: chain v residue 390 ASP Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 88 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 157 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 216 HIS 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 121 VAL Chi-restraints excluded: chain a residue 123 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 169 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 344 THR Chi-restraints excluded: chain b residue 361 ILE Chi-restraints excluded: chain b residue 371 ASP Chi-restraints excluded: chain b residue 385 LEU Chi-restraints excluded: chain b residue 406 ASN Chi-restraints excluded: chain b residue 418 ASP Chi-restraints excluded: chain b residue 435 ILE Chi-restraints excluded: chain b residue 445 LEU Chi-restraints excluded: chain b residue 459 GLU Chi-restraints excluded: chain b residue 479 ASP Chi-restraints excluded: chain b residue 519 MET Chi-restraints excluded: chain b residue 588 ARG Chi-restraints excluded: chain b residue 634 LEU Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 316 ASN Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 18 ILE Chi-restraints excluded: chain c residue 30 THR Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain d residue 46 THR Chi-restraints excluded: chain d residue 48 ASP Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain e residue 19 ARG Chi-restraints excluded: chain e residue 55 ILE Chi-restraints excluded: chain e residue 86 THR Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 117 ILE Chi-restraints excluded: chain e residue 126 LEU Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 97 SER Chi-restraints excluded: chain f residue 98 VAL Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 104 GLU Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 146 LYS Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 195 SER Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 237 ILE Chi-restraints excluded: chain G residue 246 MET Chi-restraints excluded: chain G residue 252 ASN Chi-restraints excluded: chain g residue 6 THR Chi-restraints excluded: chain g residue 15 THR Chi-restraints excluded: chain g residue 35 VAL Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain g residue 55 SER Chi-restraints excluded: chain g residue 66 SER Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 95 ILE Chi-restraints excluded: chain I residue 17 ASP Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 60 THR Chi-restraints excluded: chain I residue 90 SER Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 90 MET Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 147 SER Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain h residue 50 SER Chi-restraints excluded: chain i residue 19 SER Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain i residue 61 ILE Chi-restraints excluded: chain i residue 64 SER Chi-restraints excluded: chain i residue 70 ARG Chi-restraints excluded: chain j residue 7 SER Chi-restraints excluded: chain j residue 46 SER Chi-restraints excluded: chain j residue 82 SER Chi-restraints excluded: chain j residue 84 SER Chi-restraints excluded: chain k residue 27 ILE Chi-restraints excluded: chain k residue 29 LYS Chi-restraints excluded: chain k residue 45 VAL Chi-restraints excluded: chain k residue 55 VAL Chi-restraints excluded: chain k residue 66 ILE Chi-restraints excluded: chain k residue 72 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 27 GLN Chi-restraints excluded: chain M residue 40 ASP Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 113 THR Chi-restraints excluded: chain p residue 5 THR Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 21 SER Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain N residue 16 SER Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 87 GLN Chi-restraints excluded: chain N residue 91 GLU Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 171 SER Chi-restraints excluded: chain N residue 190 THR Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain u residue 9 CYS Chi-restraints excluded: chain u residue 10 SER Chi-restraints excluded: chain u residue 134 LEU Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 55 HIS Chi-restraints excluded: chain O residue 106 GLU Chi-restraints excluded: chain O residue 124 LEU Chi-restraints excluded: chain O residue 151 ASP Chi-restraints excluded: chain O residue 188 SER Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 10 ASN Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 87 SER 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 168 LEU Chi-restraints excluded: chain P residue 172 GLN Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 41 ASP 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 123 THR Chi-restraints excluded: chain R residue 59 SER Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 82 ASP Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 144 LEU Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 171 PHE Chi-restraints excluded: chain T residue 98 HIS Chi-restraints excluded: chain T residue 124 VAL Chi-restraints excluded: chain T residue 129 LYS Chi-restraints excluded: chain T residue 136 ARG Chi-restraints excluded: chain T residue 147 VAL Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 16 THR Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 72 SER Chi-restraints excluded: chain U residue 76 LEU Chi-restraints excluded: chain U residue 80 THR Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain U residue 110 VAL Chi-restraints excluded: chain V residue 13 ILE Chi-restraints excluded: chain V residue 23 MET Chi-restraints excluded: chain V residue 89 ASP Chi-restraints excluded: chain W residue 55 GLU Chi-restraints excluded: chain W residue 77 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 224 ASP Chi-restraints excluded: chain X residue 29 SER Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain X residue 87 SER Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Y residue 80 VAL Chi-restraints excluded: chain Y residue 95 VAL Chi-restraints excluded: chain Y residue 102 SER Chi-restraints excluded: chain y residue 5 THR Chi-restraints excluded: chain y residue 90 ASP Chi-restraints excluded: chain y residue 135 VAL Chi-restraints excluded: chain y residue 173 LEU Chi-restraints excluded: chain y residue 179 VAL Chi-restraints excluded: chain Z residue 9 LYS Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain Z residue 98 THR Chi-restraints excluded: chain Z residue 132 SER Chi-restraints excluded: chain Z residue 134 LEU Chi-restraints excluded: chain D residue 16 PHE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 95 TRP Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 260 PHE Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 20 ASN Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 173 ASP Chi-restraints excluded: chain q residue 2 VAL Chi-restraints excluded: chain q residue 7 THR Chi-restraints excluded: chain q residue 34 SER Chi-restraints excluded: chain q residue 41 ARG Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 65 THR Chi-restraints excluded: chain q residue 71 ARG Chi-restraints excluded: chain q residue 79 THR Chi-restraints excluded: chain q residue 90 HIS Chi-restraints excluded: chain o residue 8 THR Chi-restraints excluded: chain o residue 13 THR Chi-restraints excluded: chain o residue 25 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1037 random chunks: chunk 909 optimal weight: 10.0000 chunk 957 optimal weight: 40.0000 chunk 873 optimal weight: 10.0000 chunk 931 optimal weight: 10.0000 chunk 560 optimal weight: 10.0000 chunk 405 optimal weight: 4.9990 chunk 731 optimal weight: 10.0000 chunk 285 optimal weight: 0.0000 chunk 841 optimal weight: 30.0000 chunk 880 optimal weight: 20.0000 chunk 928 optimal weight: 10.0000 overall best weight: 6.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: v 66 GLN ** v 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 GLN B 3 HIS B 256 HIS ** e 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 42 GLN f 106 ASN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN M 119 GLN R 27 ASN ** U 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 81 GLN ** V 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 44 HIS ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 11 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.141 139723 Z= 0.410 Angle : 0.703 14.184 205723 Z= 0.357 Chirality : 0.041 0.302 25901 Planarity : 0.005 0.116 13168 Dihedral : 22.918 179.651 61662 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.20 % Favored : 90.60 % Rotamer: Outliers : 5.66 % Allowed : 19.69 % Favored : 74.65 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.21 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.10), residues: 6774 helix: -0.05 (0.11), residues: 2278 sheet: -1.08 (0.16), residues: 960 loop : -1.86 (0.10), residues: 3536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP U 92 HIS 0.015 0.001 HIS q 23 PHE 0.028 0.002 PHE D 16 TYR 0.038 0.002 TYR O 167 ARG 0.018 0.001 ARG q 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13548 Ramachandran restraints generated. 6774 Oldfield, 0 Emsley, 6774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13548 Ramachandran restraints generated. 6774 Oldfield, 0 Emsley, 6774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1419 residues out of total 5807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 326 poor density : 1093 time to evaluate : 6.775 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 36 TYR cc_start: 0.7713 (t80) cc_final: 0.7485 (t80) REVERT: v 135 GLU cc_start: 0.7165 (tt0) cc_final: 0.6727 (tp30) REVERT: v 155 TRP cc_start: 0.8610 (OUTLIER) cc_final: 0.8325 (p-90) REVERT: v 226 GLU cc_start: 0.8652 (pm20) cc_final: 0.8361 (pm20) REVERT: v 240 TYR cc_start: 0.7466 (m-80) cc_final: 0.6745 (m-10) REVERT: A 52 SER cc_start: 0.9149 (OUTLIER) cc_final: 0.8891 (p) REVERT: A 237 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8769 (mt) REVERT: a 135 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7579 (tm-30) REVERT: a 139 ARG cc_start: 0.8687 (mmm-85) cc_final: 0.8087 (mtm180) REVERT: B 72 VAL cc_start: 0.9146 (t) cc_final: 0.8895 (m) REVERT: B 125 SER cc_start: 0.9230 (p) cc_final: 0.8985 (t) REVERT: B 255 TRP cc_start: 0.8762 (t-100) cc_final: 0.8511 (t-100) REVERT: B 278 ILE cc_start: 0.8920 (pp) cc_final: 0.8687 (pp) REVERT: B 279 ASN cc_start: 0.8679 (m-40) cc_final: 0.8388 (m-40) REVERT: B 308 MET cc_start: 0.8406 (mmm) cc_final: 0.8046 (mtt) REVERT: b 459 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7473 (tt0) REVERT: b 462 LYS cc_start: 0.8526 (pptt) cc_final: 0.8238 (ptpt) REVERT: b 468 PHE cc_start: 0.8192 (t80) cc_final: 0.7813 (t80) REVERT: b 479 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.8029 (p0) REVERT: b 499 ARG cc_start: 0.6818 (tpp80) cc_final: 0.6136 (ttp-170) REVERT: b 514 LYS cc_start: 0.7813 (pttp) cc_final: 0.7242 (pttt) REVERT: b 588 ARG cc_start: 0.7050 (OUTLIER) cc_final: 0.6179 (mtt180) REVERT: b 605 MET cc_start: 0.6118 (mtp) cc_final: 0.5195 (mtp) REVERT: C 5 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7350 (mp10) REVERT: C 179 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9094 (tp) REVERT: C 221 ASN cc_start: 0.8979 (t0) cc_final: 0.8706 (t0) REVERT: C 285 ASP cc_start: 0.8208 (t0) cc_final: 0.7770 (p0) REVERT: E 5 LYS cc_start: 0.9058 (tppt) cc_final: 0.8820 (tppt) REVERT: E 8 LYS cc_start: 0.8317 (ttpp) cc_final: 0.7611 (tmtt) REVERT: E 148 GLU cc_start: 0.7586 (tm-30) cc_final: 0.7351 (tm-30) REVERT: E 157 GLN cc_start: 0.8510 (mp10) cc_final: 0.8160 (mp10) REVERT: e 19 ARG cc_start: 0.9160 (OUTLIER) cc_final: 0.8725 (ttt180) REVERT: e 109 LEU cc_start: 0.9326 (mm) cc_final: 0.9090 (mm) REVERT: F 51 TYR cc_start: 0.9479 (m-10) cc_final: 0.9233 (m-80) REVERT: F 64 GLN cc_start: 0.8540 (tp40) cc_final: 0.8025 (tp40) REVERT: F 68 ASP cc_start: 0.8275 (m-30) cc_final: 0.8037 (m-30) REVERT: f 26 ASN cc_start: 0.9224 (m-40) cc_final: 0.8932 (m-40) REVERT: g 95 ILE cc_start: 0.9257 (OUTLIER) cc_final: 0.9003 (mp) REVERT: g 96 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8526 (mm-30) REVERT: g 98 GLN cc_start: 0.8878 (tp40) cc_final: 0.8553 (tp-100) REVERT: H 23 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.6650 (mpp80) REVERT: H 160 ASP cc_start: 0.7687 (m-30) cc_final: 0.7442 (m-30) REVERT: i 76 ARG cc_start: 0.8610 (mmm-85) cc_final: 0.7665 (mmm-85) REVERT: L 65 TYR cc_start: 0.9030 (m-80) cc_final: 0.8733 (m-80) REVERT: L 192 GLU cc_start: 0.7886 (pp20) cc_final: 0.7444 (pp20) REVERT: l 25 GLN cc_start: 0.8280 (mm-40) cc_final: 0.7701 (mm-40) REVERT: N 4 TYR cc_start: 0.6331 (p90) cc_final: 0.5920 (p90) REVERT: N 20 ARG cc_start: 0.9018 (ptm160) cc_final: 0.8782 (ttm170) REVERT: N 91 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6799 (mm-30) REVERT: O 106 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7101 (mt-10) REVERT: O 113 ASP cc_start: 0.8909 (p0) cc_final: 0.8337 (p0) REVERT: O 124 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8850 (mt) REVERT: P 55 GLN cc_start: 0.8813 (mm110) cc_final: 0.8143 (mt0) REVERT: Q 136 ASN cc_start: 0.8894 (t0) cc_final: 0.8582 (t0) REVERT: Q 151 ARG cc_start: 0.7922 (ttm170) cc_final: 0.7196 (mmp-170) REVERT: R 46 LYS cc_start: 0.9082 (tppt) cc_final: 0.8762 (tptp) REVERT: R 68 GLN cc_start: 0.9109 (tp40) cc_final: 0.8810 (tp40) REVERT: R 144 GLN cc_start: 0.8291 (mm-40) cc_final: 0.8050 (tp40) REVERT: S 46 GLN cc_start: 0.8842 (mt0) cc_final: 0.8611 (mt0) REVERT: S 108 GLN cc_start: 0.8848 (mm-40) cc_final: 0.8561 (mm110) REVERT: T 129 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.7929 (mtmm) REVERT: T 136 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8017 (pmm-80) REVERT: U 33 TYR cc_start: 0.8527 (t80) cc_final: 0.8165 (t80) REVERT: U 49 ASN cc_start: 0.9196 (t0) cc_final: 0.8698 (t0) REVERT: U 75 TYR cc_start: 0.8400 (t80) cc_final: 0.8196 (t80) REVERT: W 21 GLU cc_start: 0.7411 (mm-30) cc_final: 0.7198 (mm-30) REVERT: W 67 MET cc_start: 0.5641 (ptm) cc_final: 0.5424 (ppp) REVERT: W 84 GLU cc_start: 0.3151 (OUTLIER) cc_final: 0.2915 (pm20) REVERT: W 114 GLU cc_start: 0.7921 (pt0) cc_final: 0.7296 (tp30) REVERT: X 67 ILE cc_start: 0.9463 (mt) cc_final: 0.9254 (mt) REVERT: Y 42 GLN cc_start: 0.8518 (tm-30) cc_final: 0.7871 (tm-30) REVERT: Y 43 TYR cc_start: 0.9275 (m-80) cc_final: 0.8679 (m-80) REVERT: y 173 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9111 (tt) REVERT: Z 9 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8705 (tptp) REVERT: D 23 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.7989 (tpt170) REVERT: D 95 TRP cc_start: 0.9090 (OUTLIER) cc_final: 0.8394 (t60) REVERT: D 218 ARG cc_start: 0.8770 (mmm-85) cc_final: 0.8370 (mtp85) REVERT: J 35 LYS cc_start: 0.9275 (mtmm) cc_final: 0.8863 (tptt) REVERT: q 29 LYS cc_start: 0.7620 (mmtt) cc_final: 0.7277 (mmtt) outliers start: 326 outliers final: 273 residues processed: 1307 average time/residue: 1.1479 time to fit residues: 2634.6324 Evaluate side-chains 1371 residues out of total 5807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 294 poor density : 1077 time to evaluate : 6.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain v residue 22 CYS Chi-restraints excluded: chain v residue 26 ILE Chi-restraints excluded: chain v residue 38 CYS Chi-restraints excluded: chain v residue 76 LEU Chi-restraints excluded: chain v residue 155 TRP Chi-restraints excluded: chain v residue 177 LEU Chi-restraints excluded: chain v residue 271 SER Chi-restraints excluded: chain v residue 312 VAL Chi-restraints excluded: chain v residue 320 VAL Chi-restraints excluded: chain v residue 345 ASP Chi-restraints excluded: chain v residue 348 VAL Chi-restraints excluded: chain v residue 357 SER Chi-restraints excluded: chain v residue 378 ASN Chi-restraints excluded: chain v residue 390 ASP Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 88 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 157 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 216 HIS 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 121 VAL Chi-restraints excluded: chain a residue 123 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 169 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 344 THR Chi-restraints excluded: chain b residue 361 ILE Chi-restraints excluded: chain b residue 371 ASP Chi-restraints excluded: chain b residue 385 LEU Chi-restraints excluded: chain b residue 406 ASN Chi-restraints excluded: chain b residue 418 ASP Chi-restraints excluded: chain b residue 435 ILE Chi-restraints excluded: chain b residue 445 LEU Chi-restraints excluded: chain b residue 459 GLU Chi-restraints excluded: chain b residue 479 ASP Chi-restraints excluded: chain b residue 519 MET Chi-restraints excluded: chain b residue 588 ARG Chi-restraints excluded: chain b residue 595 ASP Chi-restraints excluded: chain b residue 634 LEU Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 316 ASN Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 18 ILE Chi-restraints excluded: chain c residue 30 THR Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain d residue 46 THR Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain e residue 19 ARG Chi-restraints excluded: chain e residue 55 ILE Chi-restraints excluded: chain e residue 59 SER Chi-restraints excluded: chain e residue 86 THR Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 117 ILE Chi-restraints excluded: chain e residue 126 LEU Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 78 SER Chi-restraints excluded: chain f residue 97 SER Chi-restraints excluded: chain f residue 98 VAL Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 104 GLU Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 146 LYS Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 195 SER Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 246 MET Chi-restraints excluded: chain G residue 252 ASN Chi-restraints excluded: chain g residue 6 THR Chi-restraints excluded: chain g residue 15 THR Chi-restraints excluded: chain g residue 35 VAL Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain g residue 55 SER Chi-restraints excluded: chain g residue 66 SER Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 95 ILE Chi-restraints excluded: chain I residue 17 ASP Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 60 THR Chi-restraints excluded: chain I residue 90 SER Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 90 MET Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 147 SER Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain h residue 50 SER Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 42 SER Chi-restraints excluded: chain i residue 46 GLU Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain i residue 61 ILE Chi-restraints excluded: chain i residue 64 SER Chi-restraints excluded: chain i residue 70 ARG Chi-restraints excluded: chain j residue 7 SER Chi-restraints excluded: chain j residue 46 SER Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain j residue 82 SER Chi-restraints excluded: chain j residue 84 SER Chi-restraints excluded: chain k residue 27 ILE Chi-restraints excluded: chain k residue 29 LYS Chi-restraints excluded: chain k residue 45 VAL Chi-restraints excluded: chain k residue 55 VAL Chi-restraints excluded: chain k residue 66 ILE Chi-restraints excluded: chain k residue 72 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 77 LEU Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 139 LEU Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 27 GLN Chi-restraints excluded: chain M residue 40 ASP Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 113 THR Chi-restraints excluded: chain p residue 5 THR Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 21 SER Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain N residue 16 SER Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 87 GLN Chi-restraints excluded: chain N residue 91 GLU Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 171 SER Chi-restraints excluded: chain N residue 174 ILE Chi-restraints excluded: chain N residue 190 THR Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain u residue 9 CYS Chi-restraints excluded: chain u residue 10 SER Chi-restraints excluded: chain u residue 134 LEU Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 55 HIS Chi-restraints excluded: chain O residue 106 GLU Chi-restraints excluded: chain O residue 124 LEU Chi-restraints excluded: chain O residue 151 ASP Chi-restraints excluded: chain O residue 188 SER Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 10 ASN Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 87 SER 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 168 LEU Chi-restraints excluded: chain P residue 172 GLN Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 57 ILE Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain R residue 59 SER Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 82 ASP Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 103 VAL Chi-restraints excluded: chain S residue 144 LEU Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 171 PHE Chi-restraints excluded: chain T residue 98 HIS Chi-restraints excluded: chain T residue 124 VAL Chi-restraints excluded: chain T residue 129 LYS Chi-restraints excluded: chain T residue 136 ARG Chi-restraints excluded: chain T residue 147 VAL Chi-restraints excluded: chain T residue 151 LEU Chi-restraints excluded: chain U residue 16 THR Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 72 SER Chi-restraints excluded: chain U residue 76 LEU Chi-restraints excluded: chain U residue 80 THR Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain U residue 110 VAL Chi-restraints excluded: chain V residue 13 ILE Chi-restraints excluded: chain V residue 23 MET Chi-restraints excluded: chain V residue 89 ASP Chi-restraints excluded: chain W residue 55 GLU Chi-restraints excluded: chain W residue 84 GLU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 224 ASP Chi-restraints excluded: chain X residue 29 SER Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain X residue 87 SER Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Y residue 80 VAL Chi-restraints excluded: chain Y residue 95 VAL Chi-restraints excluded: chain Y residue 102 SER Chi-restraints excluded: chain Y residue 106 ILE Chi-restraints excluded: chain y residue 5 THR Chi-restraints excluded: chain y residue 90 ASP Chi-restraints excluded: chain y residue 131 ASP Chi-restraints excluded: chain y residue 135 VAL Chi-restraints excluded: chain y residue 173 LEU Chi-restraints excluded: chain y residue 179 VAL Chi-restraints excluded: chain Z residue 9 LYS Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain Z residue 98 THR Chi-restraints excluded: chain Z residue 132 SER Chi-restraints excluded: chain Z residue 134 LEU Chi-restraints excluded: chain D residue 16 PHE Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 95 TRP Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 260 PHE Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 20 ASN Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 150 ASN Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain q residue 2 VAL Chi-restraints excluded: chain q residue 7 THR Chi-restraints excluded: chain q residue 34 SER Chi-restraints excluded: chain q residue 41 ARG Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 71 ARG Chi-restraints excluded: chain q residue 79 THR Chi-restraints excluded: chain q residue 90 HIS Chi-restraints excluded: chain o residue 8 THR Chi-restraints excluded: chain o residue 13 THR Chi-restraints excluded: chain o residue 25 LYS Chi-restraints excluded: chain o residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1037 random chunks: chunk 611 optimal weight: 0.0570 chunk 984 optimal weight: 10.0000 chunk 601 optimal weight: 6.9990 chunk 467 optimal weight: 0.8980 chunk 684 optimal weight: 2.9990 chunk 1033 optimal weight: 10.0000 chunk 950 optimal weight: 10.0000 chunk 822 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 635 optimal weight: 3.9990 chunk 504 optimal weight: 8.9990 overall best weight: 2.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: v 142 GLN A 47 GLN f 106 ASN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 232 HIS j 76 ASN k 10 GLN l 19 GLN M 62 GLN M 119 GLN p 33 GLN R 27 ASN W 44 HIS ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 11 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.183 139723 Z= 0.205 Angle : 0.594 13.851 205723 Z= 0.306 Chirality : 0.036 0.289 25901 Planarity : 0.004 0.115 13168 Dihedral : 22.851 179.599 61662 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.26 % Favored : 92.56 % Rotamer: Outliers : 4.42 % Allowed : 21.33 % Favored : 74.25 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.21 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.15 % 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: -1.32 (0.10), residues: 6774 helix: 0.28 (0.11), residues: 2264 sheet: -0.88 (0.17), residues: 927 loop : -1.66 (0.10), residues: 3583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP U 92 HIS 0.011 0.001 HIS q 23 PHE 0.043 0.001 PHE v 173 TYR 0.038 0.002 TYR O 167 ARG 0.009 0.000 ARG g 16 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13548 Ramachandran restraints generated. 6774 Oldfield, 0 Emsley, 6774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13548 Ramachandran restraints generated. 6774 Oldfield, 0 Emsley, 6774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1406 residues out of total 5807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 1151 time to evaluate : 6.781 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 135 GLU cc_start: 0.7177 (tt0) cc_final: 0.6727 (tp30) REVERT: v 141 MET cc_start: 0.3400 (tpt) cc_final: 0.2658 (tpt) REVERT: v 155 TRP cc_start: 0.8607 (OUTLIER) cc_final: 0.8343 (p-90) REVERT: v 226 GLU cc_start: 0.8618 (pm20) cc_final: 0.8213 (pm20) REVERT: v 240 TYR cc_start: 0.7334 (m-80) cc_final: 0.6597 (m-10) REVERT: a 135 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7555 (tm-30) REVERT: a 139 ARG cc_start: 0.8709 (mmm-85) cc_final: 0.8126 (mtm180) REVERT: B 72 VAL cc_start: 0.9151 (t) cc_final: 0.8911 (m) REVERT: B 125 SER cc_start: 0.9196 (p) cc_final: 0.8945 (t) REVERT: B 308 MET cc_start: 0.8307 (mmm) cc_final: 0.8079 (mtp) REVERT: b 468 PHE cc_start: 0.8250 (t80) cc_final: 0.7819 (t80) REVERT: b 479 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.8045 (p0) REVERT: b 499 ARG cc_start: 0.6790 (tpp80) cc_final: 0.6194 (ttp-170) REVERT: b 514 LYS cc_start: 0.7599 (pttp) cc_final: 0.7206 (pttt) REVERT: b 588 ARG cc_start: 0.6911 (OUTLIER) cc_final: 0.6093 (mtt180) REVERT: b 605 MET cc_start: 0.6161 (mtp) cc_final: 0.5207 (mtp) REVERT: C 5 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7479 (mp10) REVERT: C 55 LYS cc_start: 0.9040 (ttpt) cc_final: 0.8687 (tmmt) REVERT: C 59 GLN cc_start: 0.8273 (mt0) cc_final: 0.8060 (mt0) REVERT: C 179 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.9028 (tp) REVERT: C 285 ASP cc_start: 0.8184 (t0) cc_final: 0.7722 (p0) REVERT: E 5 LYS cc_start: 0.8956 (tppt) cc_final: 0.8742 (tppt) REVERT: E 157 GLN cc_start: 0.8559 (mp10) cc_final: 0.8199 (mp-120) REVERT: e 19 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.8792 (ttt180) REVERT: e 109 LEU cc_start: 0.9255 (mm) cc_final: 0.9034 (mm) REVERT: F 51 TYR cc_start: 0.9396 (m-10) cc_final: 0.9164 (m-80) REVERT: F 64 GLN cc_start: 0.8507 (tp40) cc_final: 0.7381 (tp40) REVERT: F 68 ASP cc_start: 0.8335 (m-30) cc_final: 0.7608 (m-30) REVERT: f 10 LYS cc_start: 0.9122 (ptpt) cc_final: 0.8894 (ptpp) REVERT: f 26 ASN cc_start: 0.9217 (m-40) cc_final: 0.8943 (m-40) REVERT: G 134 TYR cc_start: 0.8743 (p90) cc_final: 0.8281 (p90) REVERT: g 98 GLN cc_start: 0.8843 (tp40) cc_final: 0.8544 (tp-100) REVERT: H 23 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.6601 (mpp80) REVERT: H 177 ASP cc_start: 0.7649 (m-30) cc_final: 0.7349 (m-30) REVERT: L 65 TYR cc_start: 0.8945 (m-80) cc_final: 0.8670 (m-80) REVERT: l 25 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7683 (mm-40) REVERT: p 37 TYR cc_start: 0.8906 (m-80) cc_final: 0.8665 (m-80) REVERT: N 4 TYR cc_start: 0.6135 (p90) cc_final: 0.5552 (p90) REVERT: N 20 ARG cc_start: 0.8841 (ptm160) cc_final: 0.8560 (ttm170) REVERT: N 91 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.6894 (mm-30) REVERT: O 106 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7065 (mt-10) REVERT: O 113 ASP cc_start: 0.8754 (p0) cc_final: 0.8239 (p0) REVERT: P 55 GLN cc_start: 0.8827 (mm110) cc_final: 0.8075 (mt0) REVERT: Q 136 ASN cc_start: 0.8783 (t0) cc_final: 0.8469 (t0) REVERT: Q 151 ARG cc_start: 0.7955 (ttm170) cc_final: 0.7307 (mmp-170) REVERT: R 46 LYS cc_start: 0.8984 (tppt) cc_final: 0.8674 (tptp) REVERT: R 68 GLN cc_start: 0.9070 (tp40) cc_final: 0.8767 (tp40) REVERT: R 144 GLN cc_start: 0.8328 (mm-40) cc_final: 0.8000 (tp40) REVERT: S 46 GLN cc_start: 0.8871 (mt0) cc_final: 0.8664 (mt0) REVERT: S 81 TYR cc_start: 0.9021 (p90) cc_final: 0.8693 (p90) REVERT: S 108 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8518 (mm110) REVERT: T 108 ARG cc_start: 0.8704 (ttp80) cc_final: 0.8465 (ttp80) REVERT: T 129 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7695 (mtmm) REVERT: U 33 TYR cc_start: 0.8339 (t80) cc_final: 0.7953 (t80) REVERT: U 49 ASN cc_start: 0.9156 (t0) cc_final: 0.8588 (t0) REVERT: U 75 TYR cc_start: 0.8173 (t80) cc_final: 0.7955 (t80) REVERT: U 89 LEU cc_start: 0.8224 (mt) cc_final: 0.7995 (mt) REVERT: W 75 LYS cc_start: 0.6508 (mptt) cc_final: 0.6226 (mttp) REVERT: W 114 GLU cc_start: 0.7886 (pt0) cc_final: 0.7365 (tp30) REVERT: X 67 ILE cc_start: 0.9468 (mt) cc_final: 0.9244 (mt) REVERT: Y 42 GLN cc_start: 0.8536 (tm-30) cc_final: 0.7940 (tm-30) REVERT: Y 43 TYR cc_start: 0.9228 (m-80) cc_final: 0.8643 (m-80) REVERT: Y 72 SER cc_start: 0.9360 (p) cc_final: 0.9089 (m) REVERT: y 173 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9082 (tt) REVERT: Z 9 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8790 (tptp) REVERT: D 95 TRP cc_start: 0.8935 (OUTLIER) cc_final: 0.8325 (t60) REVERT: D 196 ARG cc_start: 0.8254 (ttt-90) cc_final: 0.6905 (mmt180) REVERT: D 218 ARG cc_start: 0.8740 (mmm-85) cc_final: 0.8355 (mtp85) REVERT: J 35 LYS cc_start: 0.9214 (mtmm) cc_final: 0.8841 (tptt) REVERT: J 165 GLN cc_start: 0.9134 (pp30) cc_final: 0.8718 (pp30) REVERT: q 29 LYS cc_start: 0.7493 (mmtt) cc_final: 0.7102 (mmtt) REVERT: o 25 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.7802 (tptt) outliers start: 255 outliers final: 216 residues processed: 1312 average time/residue: 1.1471 time to fit residues: 2644.2756 Evaluate side-chains 1336 residues out of total 5807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 1106 time to evaluate : 6.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain v residue 22 CYS Chi-restraints excluded: chain v residue 26 ILE Chi-restraints excluded: chain v residue 38 CYS Chi-restraints excluded: chain v residue 76 LEU Chi-restraints excluded: chain v residue 155 TRP Chi-restraints excluded: chain v residue 177 LEU Chi-restraints excluded: chain v residue 197 LEU Chi-restraints excluded: chain v residue 271 SER Chi-restraints excluded: chain v residue 312 VAL Chi-restraints excluded: chain v residue 320 VAL Chi-restraints excluded: chain v residue 348 VAL Chi-restraints excluded: chain v residue 357 SER Chi-restraints excluded: chain v residue 378 ASN Chi-restraints excluded: chain v residue 390 ASP Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 216 HIS 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 121 VAL Chi-restraints excluded: chain a residue 123 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 169 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 320 ASP Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain b residue 361 ILE Chi-restraints excluded: chain b residue 385 LEU Chi-restraints excluded: chain b residue 406 ASN Chi-restraints excluded: chain b residue 418 ASP Chi-restraints excluded: chain b residue 479 ASP Chi-restraints excluded: chain b residue 519 MET Chi-restraints excluded: chain b residue 542 MET Chi-restraints excluded: chain b residue 588 ARG Chi-restraints excluded: chain b residue 595 ASP Chi-restraints excluded: chain b residue 634 LEU Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 316 ASN Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain c residue 17 VAL 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 46 THR Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain e residue 19 ARG Chi-restraints excluded: chain e residue 55 ILE Chi-restraints excluded: chain e residue 59 SER Chi-restraints excluded: chain e residue 86 THR Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 126 LEU Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 97 SER Chi-restraints excluded: chain f residue 98 VAL Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 104 GLU Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 146 LYS Chi-restraints excluded: chain G residue 195 SER Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 232 HIS Chi-restraints excluded: chain G residue 246 MET Chi-restraints excluded: chain G residue 252 ASN Chi-restraints excluded: chain g residue 6 THR Chi-restraints excluded: chain g residue 35 VAL Chi-restraints excluded: chain g residue 55 SER Chi-restraints excluded: chain g residue 66 SER Chi-restraints excluded: chain I residue 17 ASP Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 90 SER Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 90 MET Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 147 SER Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain h residue 50 SER Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 42 SER Chi-restraints excluded: chain i residue 46 GLU Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 64 SER Chi-restraints excluded: chain i residue 70 ARG Chi-restraints excluded: chain j residue 7 SER Chi-restraints excluded: chain j residue 46 SER Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain j residue 82 SER Chi-restraints excluded: chain j residue 84 SER Chi-restraints excluded: chain k residue 29 LYS Chi-restraints excluded: chain k residue 45 VAL Chi-restraints excluded: chain k residue 55 VAL Chi-restraints excluded: chain k residue 66 ILE Chi-restraints excluded: chain k residue 72 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 113 THR Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 21 SER Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain N residue 16 SER Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 91 GLU Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 171 SER Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain u residue 9 CYS Chi-restraints excluded: chain u residue 10 SER Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 55 HIS Chi-restraints excluded: chain O residue 106 GLU Chi-restraints excluded: chain O residue 151 ASP Chi-restraints excluded: chain O residue 188 SER Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 10 ASN Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 168 LEU Chi-restraints excluded: chain P residue 172 GLN Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 57 ILE Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain R residue 59 SER Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 82 ASP Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 144 LEU Chi-restraints excluded: chain T residue 98 HIS Chi-restraints excluded: chain T residue 124 VAL Chi-restraints excluded: chain T residue 129 LYS Chi-restraints excluded: chain T residue 147 VAL Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 72 SER Chi-restraints excluded: chain U residue 76 LEU Chi-restraints excluded: chain U residue 96 VAL Chi-restraints excluded: chain U residue 110 VAL Chi-restraints excluded: chain V residue 13 ILE Chi-restraints excluded: chain V residue 23 MET Chi-restraints excluded: chain V residue 89 ASP Chi-restraints excluded: chain W residue 55 GLU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 224 ASP Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain X residue 87 SER Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Y residue 102 SER Chi-restraints excluded: chain y residue 5 THR Chi-restraints excluded: chain y residue 72 VAL Chi-restraints excluded: chain y residue 90 ASP Chi-restraints excluded: chain y residue 131 ASP Chi-restraints excluded: chain y residue 173 LEU Chi-restraints excluded: chain y residue 179 VAL Chi-restraints excluded: chain Z residue 9 LYS Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain Z residue 98 THR Chi-restraints excluded: chain Z residue 132 SER Chi-restraints excluded: chain Z residue 134 LEU Chi-restraints excluded: chain D residue 16 PHE Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 95 TRP Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 260 PHE Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 20 ASN Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 150 ASN Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain q residue 2 VAL Chi-restraints excluded: chain q residue 7 THR Chi-restraints excluded: chain q residue 34 SER Chi-restraints excluded: chain q residue 41 ARG Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 71 ARG Chi-restraints excluded: chain q residue 79 THR Chi-restraints excluded: chain q residue 90 HIS Chi-restraints excluded: chain o residue 13 THR Chi-restraints excluded: chain o residue 25 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1037 random chunks: chunk 653 optimal weight: 6.9990 chunk 876 optimal weight: 10.0000 chunk 252 optimal weight: 6.9990 chunk 758 optimal weight: 10.0000 chunk 121 optimal weight: 4.9990 chunk 228 optimal weight: 0.0170 chunk 823 optimal weight: 10.0000 chunk 344 optimal weight: 0.0470 chunk 846 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 151 optimal weight: 20.0000 overall best weight: 3.8122 ------------------------------------------------------------------------------- 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 47 GLN A 140 ASN B 319 ASN F 225 GLN f 106 ASN k 10 GLN L 103 ASN M 119 GLN R 27 ASN S 63 GLN ** W 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 11 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.106966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.081344 restraints weight = 284134.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.083694 restraints weight = 119757.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.085119 restraints weight = 75309.873| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.167 139723 Z= 0.245 Angle : 0.608 13.375 205723 Z= 0.311 Chirality : 0.036 0.278 25901 Planarity : 0.005 0.115 13168 Dihedral : 22.829 179.990 61660 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.18 % Favored : 91.66 % Rotamer: Outliers : 4.25 % Allowed : 21.66 % Favored : 74.09 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.21 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.15 % 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: 6774 helix: 0.31 (0.11), residues: 2273 sheet: -0.85 (0.17), residues: 925 loop : -1.68 (0.10), residues: 3576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP U 92 HIS 0.015 0.001 HIS G 232 PHE 0.042 0.002 PHE v 173 TYR 0.042 0.002 TYR u 81 ARG 0.011 0.000 ARG B 167 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 37258.63 seconds wall clock time: 647 minutes 33.49 seconds (38853.49 seconds total)