Starting phenix.real_space_refine on Sun Apr 14 07:54:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s0x_10076/04_2024/6s0x_10076_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s0x_10076/04_2024/6s0x_10076.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s0x_10076/04_2024/6s0x_10076_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.425 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s0x_10076/04_2024/6s0x_10076_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s0x_10076/04_2024/6s0x_10076_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s0x_10076/04_2024/6s0x_10076.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s0x_10076/04_2024/6s0x_10076.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s0x_10076/04_2024/6s0x_10076_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s0x_10076/04_2024/6s0x_10076_updated.pdb" } resolution = 2.425 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= 0.006 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 4558 5.49 5 S 105 5.16 5 C 70581 2.51 5 N 25966 2.21 5 O 39462 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 13": "NH1" <-> "NH2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C ASP 79": "OD1" <-> "OD2" Residue "C TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 102": "NH1" <-> "NH2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C ARG 238": "NH1" <-> "NH2" Residue "C ARG 243": "NH1" <-> "NH2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "C ARG 274": "NH1" <-> "NH2" Residue "D GLU 54": "OE1" <-> "OE2" Residue "D PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 89": "NH1" <-> "NH2" Residue "D PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 212": "NH1" <-> "NH2" Residue "E ARG 62": "NH1" <-> "NH2" Residue "E TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 106": "NH1" <-> "NH2" Residue "E ARG 107": "NH1" <-> "NH2" Residue "E PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 168": "NH1" <-> "NH2" Residue "F ARG 78": "NH1" <-> "NH2" Residue "F ARG 95": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 40": "NH1" <-> "NH2" Residue "G PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 54": "NH1" <-> "NH2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "G ARG 69": "NH1" <-> "NH2" Residue "G TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 170": "NH1" <-> "NH2" Residue "G ARG 171": "NH1" <-> "NH2" Residue "H ARG 2": "NH1" <-> "NH2" Residue "H ARG 14": "NH1" <-> "NH2" Residue "H ASP 53": "OD1" <-> "OD2" Residue "H TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 94": "NH1" <-> "NH2" Residue "H ARG 95": "NH1" <-> "NH2" Residue "H ARG 100": "NH1" <-> "NH2" Residue "H TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 88": "NH1" <-> "NH2" Residue "I ARG 107": "NH1" <-> "NH2" Residue "I GLU 120": "OE1" <-> "OE2" Residue "J ARG 16": "NH1" <-> "NH2" Residue "J ARG 21": "NH1" <-> "NH2" Residue "K ARG 10": "NH1" <-> "NH2" Residue "K ARG 20": "NH1" <-> "NH2" Residue "K ARG 45": "NH1" <-> "NH2" Residue "K ARG 51": "NH1" <-> "NH2" Residue "K ARG 56": "NH1" <-> "NH2" Residue "K TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 82": "NH1" <-> "NH2" Residue "K ARG 115": "NH1" <-> "NH2" Residue "L ARG 8": "NH1" <-> "NH2" Residue "L GLU 45": "OE1" <-> "OE2" Residue "L ARG 96": "NH1" <-> "NH2" Residue "L ARG 110": "NH1" <-> "NH2" Residue "M ARG 11": "NH1" <-> "NH2" Residue "M ARG 14": "NH1" <-> "NH2" Residue "M ARG 35": "NH1" <-> "NH2" Residue "M TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 47": "OD1" <-> "OD2" Residue "M ARG 96": "NH1" <-> "NH2" Residue "M ARG 104": "NH1" <-> "NH2" Residue "N ARG 16": "NH1" <-> "NH2" Residue "N ARG 23": "NH1" <-> "NH2" Residue "N ARG 33": "NH1" <-> "NH2" Residue "N PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 91": "NH1" <-> "NH2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "P PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 67": "NH1" <-> "NH2" Residue "P ARG 79": "NH1" <-> "NH2" Residue "Q ARG 8": "NH1" <-> "NH2" Residue "Q ARG 11": "NH1" <-> "NH2" Residue "Q ARG 15": "NH1" <-> "NH2" Residue "Q ASP 63": "OD1" <-> "OD2" Residue "R TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 30": "OD1" <-> "OD2" Residue "R TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 64": "NH1" <-> "NH2" Residue "R ARG 76": "NH1" <-> "NH2" Residue "S ASP 31": "OD1" <-> "OD2" Residue "S ARG 32": "NH1" <-> "NH2" Residue "T ARG 9": "NH1" <-> "NH2" Residue "T ARG 22": "NH1" <-> "NH2" Residue "T ARG 53": "NH1" <-> "NH2" Residue "T ARG 57": "NH1" <-> "NH2" Residue "U ARG 22": "NH1" <-> "NH2" Residue "U ARG 33": "NH1" <-> "NH2" Residue "U TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 47": "NH1" <-> "NH2" Residue "U ARG 49": "NH1" <-> "NH2" Residue "U PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 82": "NH1" <-> "NH2" Residue "W ARG 44": "NH1" <-> "NH2" Residue "W ARG 47": "NH1" <-> "NH2" Residue "W ARG 52": "NH1" <-> "NH2" Residue "W ARG 58": "NH1" <-> "NH2" Residue "W ARG 60": "NH1" <-> "NH2" Residue "X ARG 10": "NH1" <-> "NH2" Residue "Y ASP 16": "OD1" <-> "OD2" Residue "Y GLU 38": "OE1" <-> "OE2" Residue "Z ARG 6": "NH1" <-> "NH2" Residue "2 ARG 20": "NH1" <-> "NH2" Residue "2 ARG 22": "NH1" <-> "NH2" Residue "2 ARG 37": "NH1" <-> "NH2" Residue "2 ARG 40": "NH1" <-> "NH2" Residue "3 ARG 24": "NH1" <-> "NH2" Residue "3 ARG 42": "NH1" <-> "NH2" Residue "4 ARG 19": "NH1" <-> "NH2" Residue "b ARG 21": "NH1" <-> "NH2" Residue "b ARG 22": "NH1" <-> "NH2" Residue "b ARG 35": "NH1" <-> "NH2" Residue "b TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 63": "OD1" <-> "OD2" Residue "b GLU 83": "OE1" <-> "OE2" Residue "b ARG 86": "NH1" <-> "NH2" Residue "b TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 95": "NH1" <-> "NH2" Residue "b ARG 110": "NH1" <-> "NH2" Residue "b ARG 113": "NH1" <-> "NH2" Residue "b PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 143": "NH1" <-> "NH2" Residue "b PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 152": "NH1" <-> "NH2" Residue "b PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 167": "NH1" <-> "NH2" Residue "b ARG 170": "NH1" <-> "NH2" Residue "b ARG 177": "NH1" <-> "NH2" Residue "b ASP 205": "OD1" <-> "OD2" Residue "b ARG 208": "NH1" <-> "NH2" Residue "c ARG 113": "NH1" <-> "NH2" Residue "c ARG 121": "NH1" <-> "NH2" Residue "c ARG 126": "NH1" <-> "NH2" Residue "c PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 139": "NH1" <-> "NH2" Residue "c ARG 163": "NH1" <-> "NH2" Residue "c GLU 165": "OE1" <-> "OE2" Residue "c TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 52": "NH1" <-> "NH2" Residue "d ARG 58": "NH1" <-> "NH2" Residue "d TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 69": "NH1" <-> "NH2" Residue "d ASP 73": "OD1" <-> "OD2" Residue "d ARG 93": "NH1" <-> "NH2" Residue "d GLU 163": "OE1" <-> "OE2" Residue "d PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 29": "NH1" <-> "NH2" Residue "e ARG 30": "NH1" <-> "NH2" Residue "e ARG 32": "NH1" <-> "NH2" Residue "e ASP 41": "OD1" <-> "OD2" Residue "e ASP 70": "OD1" <-> "OD2" Residue "e TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 157": "NH1" <-> "NH2" Residue "e GLU 163": "OE1" <-> "OE2" Residue "f ARG 11": "NH1" <-> "NH2" Residue "f GLU 24": "OE1" <-> "OE2" Residue "f ARG 46": "NH1" <-> "NH2" Residue "f ASP 54": "OD1" <-> "OD2" Residue "f ARG 64": "NH1" <-> "NH2" Residue "f PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 78": "NH1" <-> "NH2" Residue "f ASP 85": "OD1" <-> "OD2" Residue "f ARG 88": "NH1" <-> "NH2" Residue "f TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 3": "NH1" <-> "NH2" Residue "g ARG 10": "NH1" <-> "NH2" Residue "g ARG 36": "NH1" <-> "NH2" Residue "g ARG 41": "NH1" <-> "NH2" Residue "g PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 53": "NH1" <-> "NH2" Residue "g ARG 56": "NH1" <-> "NH2" Residue "g ARG 95": "NH1" <-> "NH2" Residue "g ARG 96": "NH1" <-> "NH2" Residue "g ARG 102": "NH1" <-> "NH2" Residue "g ARG 109": "NH1" <-> "NH2" Residue "g ARG 111": "NH1" <-> "NH2" Residue "g ARG 119": "NH1" <-> "NH2" Residue "g ARG 138": "NH1" <-> "NH2" Residue "h GLU 43": "OE1" <-> "OE2" Residue "h PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 54": "OD1" <-> "OD2" Residue "h ARG 61": "NH1" <-> "NH2" Residue "h PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 72": "NH1" <-> "NH2" Residue "h ARG 119": "NH1" <-> "NH2" Residue "i ARG 38": "NH1" <-> "NH2" Residue "i PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 82": "NH1" <-> "NH2" Residue "i ASP 109": "OD1" <-> "OD2" Residue "j TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 16": "NH1" <-> "NH2" Residue "j GLU 45": "OE1" <-> "OE2" Residue "j ARG 53": "NH1" <-> "NH2" Residue "j TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 17": "OE1" <-> "OE2" Residue "k ARG 24": "NH1" <-> "NH2" Residue "k ARG 111": "NH1" <-> "NH2" Residue "l ARG 9": "NH1" <-> "NH2" Residue "l ARG 12": "NH1" <-> "NH2" Residue "l ASP 20": "OD1" <-> "OD2" Residue "l ARG 63": "NH1" <-> "NH2" Residue "l ARG 69": "NH1" <-> "NH2" Residue "l ARG 127": "NH1" <-> "NH2" Residue "m ARG 14": "NH1" <-> "NH2" Residue "m TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 87": "NH1" <-> "NH2" Residue "n ARG 23": "NH1" <-> "NH2" Residue "n ARG 26": "NH1" <-> "NH2" Residue "n ARG 41": "NH1" <-> "NH2" Residue "o ARG 7": "NH1" <-> "NH2" Residue "o ARG 16": "NH1" <-> "NH2" Residue "o ARG 54": "NH1" <-> "NH2" Residue "o ARG 63": "NH1" <-> "NH2" Residue "o ARG 71": "NH1" <-> "NH2" Residue "o ARG 88": "NH1" <-> "NH2" Residue "p ARG 6": "NH1" <-> "NH2" Residue "p TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 19": "NH1" <-> "NH2" Residue "p ARG 29": "NH1" <-> "NH2" Residue "q TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 67": "NH1" <-> "NH2" Residue "r ARG 47": "NH1" <-> "NH2" Residue "s PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 73": "NH1" <-> "NH2" Residue "u ARG 18": "NH1" <-> "NH2" Residue "u ARG 35": "NH1" <-> "NH2" Residue "u PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ARG 66": "NH1" <-> "NH2" Residue "v ARG 90": "NH1" <-> "NH2" Residue "v TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ARG 166": "NH1" <-> "NH2" Residue "v ARG 177": "NH1" <-> "NH2" Residue "v TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 140672 Number of models: 1 Model: "" Number of chains: 53 Chain: "A" Number of atoms: 62277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2905, 62277 Classifications: {'RNA': 2905} Modifications used: {'rna2p_pur': 317, 'rna2p_pyr': 185, 'rna3p_pur': 1348, 'rna3p_pyr': 1055} Link IDs: {'rna2p': 502, 'rna3p': 2402} Chain breaks: 7 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' G%rna3p_pur:plan2': 1, ' G%rna3p_pur:plan': 1, ' A%rna3p_pur:plan2': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2445 Classifications: {'RNA': 115} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 9, 'rna3p_pur': 54, 'rna3p_pyr': 47} Link IDs: {'rna2p': 14, 'rna3p': 100} Chain: "C" Number of atoms: 2090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2090 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 256} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1627 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 8, 'TRANS': 206} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1572 Classifications: {'peptide': 206} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 9, 'TRANS': 196} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1315 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 166} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "G" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1248 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 7, 'TRANS': 165} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 11, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 68 Chain: "H" Number of atoms: 1149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1149 Classifications: {'peptide': 145} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 6, 'TRANS': 138} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "I" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 918 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "J" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1086 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 140} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "K" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1079 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 129} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "L" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 932 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 118} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "M" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 883 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 116} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "N" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 889 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 109} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "O" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 943 Classifications: {'peptide': 116} Link IDs: {'TRANS': 115} Chain: "P" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 790 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 99} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Q" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 838 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 105} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 715 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 86} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "S" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 770 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 97} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "T" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 722 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "U" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 75} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "V" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 379 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 47} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 541 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 66} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "X" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "Y" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 370 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 3, 'TRANS': 55} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "Z" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 360 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 44} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 17 Chain: "1" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 390 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 44} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "2" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 367 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "3" Number of atoms: 521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 521 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "4" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 295 Classifications: {'peptide': 37} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "a" Number of atoms: 32969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 32969 Classifications: {'RNA': 1539} Modifications used: {'rna2p_pur': 152, 'rna2p_pyr': 117, 'rna3p_pur': 716, 'rna3p_pyr': 554} Link IDs: {'rna2p': 268, 'rna3p': 1270} Chain breaks: 1 Chain: "b" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1819 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "c" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1501 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 3, 'TRANS': 198} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 42 Chain: "d" Number of atoms: 1497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1497 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 8, 'TRANS': 189} Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 83 Chain: "e" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1145 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 148} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "f" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 778 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 93} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "g" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1161 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 144} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "h" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1026 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 126} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "i" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 922 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 7, 'TRANS': 119} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 65 Chain: "j" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 752 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 90} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "k" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 810 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 106} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "l" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1037 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 126} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASP:plan': 3} Unresolved non-hydrogen planarities: 9 Chain: "m" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 727 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain breaks: 1 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 7, 'ASN:plan1': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 75 Chain: "n" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 487 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 57} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "o" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 723 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 86} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "p" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 694 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 83} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "q" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 621 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 1, 'TRANS': 78} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "r" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 445 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} 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: "s" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 636 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 75} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "t" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 591 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 80} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 10 Chain: "u" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 400 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 50} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "v" Number of atoms: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1333 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 3, 'TRANS': 158} Chain breaks: 1 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'ERY': 1} Classifications: {'undetermined': 1} Time building chain proxies: 54.59, per 1000 atoms: 0.39 Number of scatterers: 140672 At special positions: 0 Unit cell: (268.884, 241.142, 244.343, 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 105 16.00 P 4558 15.00 O 39462 8.00 N 25966 7.00 C 70581 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS 1 9 " - pdb=" SG CYS 1 12 " distance=2.02 Simple disulfide: pdb=" SG CYS 1 12 " - pdb=" SG CYS 1 36 " distance=2.02 Simple disulfide: pdb=" SG CYS 4 14 " - pdb=" SG CYS 4 27 " distance=2.04 Simple disulfide: pdb=" SG CYS n 27 " - pdb=" SG CYS n 40 " distance=2.03 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: 65.27 Conformation dependent library (CDL) restraints added in 6.6 seconds 10974 Ramachandran restraints generated. 5487 Oldfield, 0 Emsley, 5487 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10288 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 162 helices and 70 sheets defined 36.0% alpha, 18.0% beta 1231 base pairs and 2200 stacking pairs defined. Time for finding SS restraints: 71.57 Creating SS restraints... Processing helix chain 'C' and resid 10 through 15 removed outlier: 3.579A pdb=" N ARG C 14 " --> pdb=" O THR C 10 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ASN C 15 " --> pdb=" O ASN C 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 10 through 15' Processing helix chain 'C' and resid 131 through 136 removed outlier: 3.825A pdb=" N ILE C 135 " --> pdb=" O PRO C 131 " (cutoff:3.500A) Proline residue: C 136 - end of helix No H-bonds generated for 'chain 'C' and resid 131 through 136' Processing helix chain 'C' and resid 207 through 215 removed outlier: 3.664A pdb=" N SER C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY C 215 " --> pdb=" O SER C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 4.182A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ASN C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 226' Processing helix chain 'C' and resid 266 through 271 removed outlier: 3.564A pdb=" N ILE C 270 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N VAL C 271 " --> pdb=" O ASP C 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 266 through 271' Processing helix chain 'C' and resid 197 through 202 removed outlier: 3.573A pdb=" N HIS C 200 " --> pdb=" O ASN C 197 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU C 201 " --> pdb=" O LEU C 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 81 removed outlier: 3.689A pdb=" N LYS D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA D 80 " --> pdb=" O HIS D 76 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ASP D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 100 removed outlier: 4.380A pdb=" N TYR D 99 " --> pdb=" O ASP D 95 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLU D 100 " --> pdb=" O VAL D 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 95 through 100' Processing helix chain 'D' and resid 106 through 111 removed outlier: 5.040A pdb=" N VAL D 111 " --> pdb=" O ASP D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 129 through 135 removed outlier: 4.435A pdb=" N HIS D 134 " --> pdb=" O GLY D 129 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLY D 135 " --> pdb=" O ALA D 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 129 through 135' Processing helix chain 'E' and resid 29 through 45 removed outlier: 4.163A pdb=" N ARG E 45 " --> pdb=" O ARG E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 121 removed outlier: 3.502A pdb=" N GLN E 119 " --> pdb=" O SER E 115 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU E 120 " --> pdb=" O PHE E 116 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASN E 121 " --> pdb=" O LYS E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 147 removed outlier: 4.886A pdb=" N GLU E 147 " --> pdb=" O LEU E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 168 Processing helix chain 'E' and resid 182 through 190 removed outlier: 5.523A pdb=" N ASP E 190 " --> pdb=" O ILE E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 removed outlier: 3.578A pdb=" N LYS E 200 " --> pdb=" O GLU E 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 19 removed outlier: 4.619A pdb=" N PHE F 8 " --> pdb=" O LEU F 4 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N THR F 13 " --> pdb=" O ASN F 9 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN F 15 " --> pdb=" O GLU F 11 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU F 16 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N MET F 17 " --> pdb=" O THR F 13 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N LYS F 18 " --> pdb=" O GLU F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 62 removed outlier: 4.517A pdb=" N VAL F 49 " --> pdb=" O GLN F 45 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY F 62 " --> pdb=" O GLU F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 112 removed outlier: 3.536A pdb=" N LYS F 102 " --> pdb=" O GLU F 98 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER F 105 " --> pdb=" O ASP F 101 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL F 106 " --> pdb=" O LYS F 102 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N LEU F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) Proline residue: F 109 - end of helix removed outlier: 3.515A pdb=" N ARG F 112 " --> pdb=" O LEU F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 174 removed outlier: 4.209A pdb=" N ASN F 172 " --> pdb=" O GLU F 168 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N PHE F 173 " --> pdb=" O LEU F 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 8 removed outlier: 4.194A pdb=" N ILE G 8 " --> pdb=" O VAL G 4 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 81 removed outlier: 4.218A pdb=" N GLY G 66 " --> pdb=" O ARG G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 153 removed outlier: 3.948A pdb=" N VAL G 151 " --> pdb=" O ASN G 147 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ARG G 152 " --> pdb=" O ILE G 148 " (cutoff:3.500A) Proline residue: G 153 - end of helix Processing helix chain 'H' and resid 25 through 39 removed outlier: 3.970A pdb=" N GLU H 32 " --> pdb=" O ARG H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 64 removed outlier: 6.198A pdb=" N ILE H 63 " --> pdb=" O ASN H 59 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N GLU H 64 " --> pdb=" O ALA H 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 59 through 64' Processing helix chain 'H' and resid 89 through 97 removed outlier: 4.053A pdb=" N ASN H 97 " --> pdb=" O LEU H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 111 removed outlier: 3.751A pdb=" N MET H 109 " --> pdb=" O SER H 105 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU H 110 " --> pdb=" O ILE H 106 " (cutoff:3.500A) Proline residue: H 111 - end of helix Processing helix chain 'H' and resid 113 through 123 removed outlier: 3.627A pdb=" N LYS H 121 " --> pdb=" O GLU H 117 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS H 122 " --> pdb=" O LYS H 118 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU H 123 " --> pdb=" O GLN H 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 104 through 110 removed outlier: 4.637A pdb=" N GLU I 108 " --> pdb=" O ARG I 104 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLY I 109 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASN I 110 " --> pdb=" O LEU I 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 104 through 110' Processing helix chain 'I' and resid 111 through 118 Processing helix chain 'J' and resid 37 through 42 removed outlier: 4.001A pdb=" N ARG J 41 " --> pdb=" O GLY J 37 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N SER J 42 " --> pdb=" O GLN J 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 37 through 42' Processing helix chain 'J' and resid 56 through 62 removed outlier: 3.804A pdb=" N LEU J 61 " --> pdb=" O LEU J 57 " (cutoff:3.500A) Proline residue: J 62 - end of helix Processing helix chain 'J' and resid 78 through 84 removed outlier: 3.666A pdb=" N LEU J 82 " --> pdb=" O ASN J 78 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN J 83 " --> pdb=" O LEU J 79 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LYS J 84 " --> pdb=" O ASP J 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 78 through 84' Processing helix chain 'J' and resid 92 through 100 Processing helix chain 'J' and resid 129 through 140 removed outlier: 3.705A pdb=" N LYS J 139 " --> pdb=" O ALA J 135 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY J 140 " --> pdb=" O ILE J 136 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 59 removed outlier: 5.746A pdb=" N ILE K 47 " --> pdb=" O THR K 43 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU K 48 " --> pdb=" O SER K 44 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR K 57 " --> pdb=" O ALA K 53 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET K 58 " --> pdb=" O MET K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 126 removed outlier: 4.244A pdb=" N LYS K 124 " --> pdb=" O LEU K 120 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU K 125 " --> pdb=" O ALA K 121 " (cutoff:3.500A) Proline residue: K 126 - end of helix Processing helix chain 'L' and resid 9 through 28 Processing helix chain 'L' and resid 34 through 54 removed outlier: 4.786A pdb=" N SER L 42 " --> pdb=" O LYS L 38 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL L 43 " --> pdb=" O GLU L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 66 removed outlier: 3.722A pdb=" N LYS L 64 " --> pdb=" O ARG L 60 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N THR L 65 " --> pdb=" O ASN L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 94 removed outlier: 4.087A pdb=" N ILE L 89 " --> pdb=" O LEU L 85 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ALA L 90 " --> pdb=" O PHE L 86 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU L 91 " --> pdb=" O GLY L 87 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR L 93 " --> pdb=" O ILE L 89 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR L 94 " --> pdb=" O ALA L 90 " (cutoff:3.500A) Processing helix chain 'M' and resid 6 through 23 removed outlier: 4.141A pdb=" N VAL M 10 " --> pdb=" O ASP M 6 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR M 20 " --> pdb=" O ALA M 16 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ASN M 21 " --> pdb=" O ARG M 17 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU M 22 " --> pdb=" O VAL M 18 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N SER M 23 " --> pdb=" O ARG M 19 " (cutoff:3.500A) Processing helix chain 'M' and resid 68 through 86 removed outlier: 6.365A pdb=" N LEU M 72 " --> pdb=" O THR M 68 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA M 73 " --> pdb=" O LYS M 69 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASP M 86 " --> pdb=" O LYS M 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 116 removed outlier: 3.828A pdb=" N SER M 115 " --> pdb=" O ALA M 111 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY M 116 " --> pdb=" O ALA M 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 12 Processing helix chain 'N' and resid 99 through 106 removed outlier: 4.800A pdb=" N ARG N 103 " --> pdb=" O LEU N 99 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N SER N 104 " --> pdb=" O TYR N 100 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU N 105 " --> pdb=" O TYR N 101 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ARG N 106 " --> pdb=" O LEU N 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 99 through 106' Processing helix chain 'N' and resid 107 through 112 removed outlier: 3.826A pdb=" N ARG N 111 " --> pdb=" O GLY N 107 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE N 112 " --> pdb=" O LYS N 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 107 through 112' Processing helix chain 'O' and resid 8 through 22 removed outlier: 3.763A pdb=" N THR O 17 " --> pdb=" O ARG O 13 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS O 22 " --> pdb=" O ILE O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 25 through 31 removed outlier: 4.569A pdb=" N HIS O 29 " --> pdb=" O PHE O 25 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR O 30 " --> pdb=" O GLY O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 32 through 37 Processing helix chain 'O' and resid 39 through 73 removed outlier: 3.978A pdb=" N ARG O 51 " --> pdb=" O PHE O 47 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LYS O 54 " --> pdb=" O ARG O 50 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG O 55 " --> pdb=" O ARG O 51 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN O 71 " --> pdb=" O ALA O 67 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N HIS O 72 " --> pdb=" O ALA O 68 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU O 73 " --> pdb=" O ALA O 69 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 87 Processing helix chain 'O' and resid 91 through 102 Processing helix chain 'O' and resid 103 through 117 removed outlier: 3.581A pdb=" N ALA O 116 " --> pdb=" O LYS O 112 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU O 117 " --> pdb=" O ALA O 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 13 through 25 removed outlier: 3.537A pdb=" N VAL Q 17 " --> pdb=" O ALA Q 13 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU Q 19 " --> pdb=" O ARG Q 15 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL Q 20 " --> pdb=" O LYS Q 16 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU Q 23 " --> pdb=" O LEU Q 19 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE Q 24 " --> pdb=" O VAL Q 20 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG Q 25 " --> pdb=" O LEU Q 21 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 40 removed outlier: 6.228A pdb=" N ASN Q 40 " --> pdb=" O LEU Q 36 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 61 Processing helix chain 'R' and resid 2 through 8 removed outlier: 5.865A pdb=" N ILE R 6 " --> pdb=" O GLU R 2 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N LEU R 7 " --> pdb=" O ALA R 3 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N LYS R 8 " --> pdb=" O ARG R 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 2 through 8' Processing helix chain 'R' and resid 13 through 23 removed outlier: 3.903A pdb=" N GLU R 22 " --> pdb=" O GLU R 18 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP R 23 " --> pdb=" O ALA R 19 " (cutoff:3.500A) Processing helix chain 'R' and resid 34 through 46 Processing helix chain 'S' and resid 64 through 69 removed outlier: 4.741A pdb=" N VAL S 68 " --> pdb=" O HIS S 64 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N GLN S 69 " --> pdb=" O VAL S 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 64 through 69' Processing helix chain 'T' and resid 14 through 25 removed outlier: 3.533A pdb=" N SER T 24 " --> pdb=" O GLN T 20 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLY T 25 " --> pdb=" O LEU T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 44 through 56 Processing helix chain 'V' and resid 50 through 57 removed outlier: 4.128A pdb=" N SER V 56 " --> pdb=" O ARG V 52 " (cutoff:3.500A) Processing helix chain 'W' and resid 3 through 10 removed outlier: 4.861A pdb=" N ARG W 7 " --> pdb=" O ALA W 3 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASP W 8 " --> pdb=" O LYS W 4 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N THR W 10 " --> pdb=" O ILE W 6 " (cutoff:3.500A) Processing helix chain 'W' and resid 11 through 35 removed outlier: 4.993A pdb=" N GLU W 15 " --> pdb=" O THR W 11 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA W 33 " --> pdb=" O ARG W 29 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLY W 35 " --> pdb=" O GLN W 31 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 65 removed outlier: 4.682A pdb=" N ARG W 44 " --> pdb=" O THR W 40 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR W 45 " --> pdb=" O ALA W 41 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA W 57 " --> pdb=" O LEU W 53 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU W 61 " --> pdb=" O ALA W 57 " (cutoff:3.500A) Processing helix chain 'X' and resid 16 through 27 removed outlier: 3.628A pdb=" N GLY X 27 " --> pdb=" O VAL X 23 " (cutoff:3.500A) Processing helix chain 'X' and resid 40 through 51 removed outlier: 3.881A pdb=" N ARG X 44 " --> pdb=" O ASN X 40 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 18 removed outlier: 4.020A pdb=" N THR Z 18 " --> pdb=" O ASN Z 14 " (cutoff:3.500A) Processing helix chain '2' and resid 9 through 17 Processing helix chain '2' and resid 18 through 26 removed outlier: 4.123A pdb=" N THR 2 25 " --> pdb=" O LYS 2 21 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N LYS 2 26 " --> pdb=" O ARG 2 22 " (cutoff:3.500A) Processing helix chain '2' and resid 27 through 39 Processing helix chain '3' and resid 7 through 14 removed outlier: 3.545A pdb=" N LYS 3 12 " --> pdb=" O ARG 3 8 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG 3 13 " --> pdb=" O GLY 3 9 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL 3 14 " --> pdb=" O ALA 3 10 " (cutoff:3.500A) Processing helix chain '3' and resid 32 through 37 removed outlier: 5.030A pdb=" N LYS 3 36 " --> pdb=" O LEU 3 32 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N SER 3 37 " --> pdb=" O PHE 3 33 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 32 through 37' Processing helix chain '3' and resid 38 through 46 removed outlier: 4.036A pdb=" N ARG 3 45 " --> pdb=" O LYS 3 41 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LYS 3 46 " --> pdb=" O ARG 3 42 " (cutoff:3.500A) Processing helix chain '3' and resid 51 through 59 removed outlier: 3.892A pdb=" N ARG 3 57 " --> pdb=" O SER 3 53 " (cutoff:3.500A) Processing helix chain 'b' and resid 5 through 12 removed outlier: 4.022A pdb=" N LEU b 10 " --> pdb=" O MET b 6 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA b 12 " --> pdb=" O GLN b 8 " (cutoff:3.500A) Processing helix chain 'b' and resid 27 through 32 removed outlier: 5.721A pdb=" N PHE b 32 " --> pdb=" O LYS b 28 " (cutoff:3.500A) Processing helix chain 'b' and resid 42 through 64 removed outlier: 3.682A pdb=" N THR b 46 " --> pdb=" O ASP b 42 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N VAL b 47 " --> pdb=" O LEU b 43 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL b 50 " --> pdb=" O THR b 46 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU b 52 " --> pdb=" O LYS b 48 " (cutoff:3.500A) Processing helix chain 'b' and resid 73 through 88 removed outlier: 5.767A pdb=" N GLU b 78 " --> pdb=" O LYS b 74 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER b 79 " --> pdb=" O GLN b 75 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LYS b 81 " --> pdb=" O GLN b 77 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N SER b 82 " --> pdb=" O GLU b 78 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU b 85 " --> pdb=" O LYS b 81 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ARG b 86 " --> pdb=" O SER b 82 " (cutoff:3.500A) Processing helix chain 'b' and resid 103 through 123 removed outlier: 3.589A pdb=" N ILE b 107 " --> pdb=" O ASN b 103 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER b 108 " --> pdb=" O TYR b 104 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LYS b 109 " --> pdb=" O LYS b 105 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ARG b 110 " --> pdb=" O THR b 106 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE b 111 " --> pdb=" O ILE b 107 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS b 112 " --> pdb=" O SER b 108 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU b 118 " --> pdb=" O ILE b 114 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS b 119 " --> pdb=" O SER b 115 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP b 123 " --> pdb=" O LYS b 119 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 148 removed outlier: 3.611A pdb=" N GLU b 136 " --> pdb=" O LYS b 132 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG b 143 " --> pdb=" O LYS b 139 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE b 147 " --> pdb=" O ARG b 143 " (cutoff:3.500A) Processing helix chain 'b' and resid 149 through 155 removed outlier: 5.310A pdb=" N ASP b 153 " --> pdb=" O GLY b 149 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N MET b 154 " --> pdb=" O GLY b 150 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LYS b 155 " --> pdb=" O ILE b 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 149 through 155' Processing helix chain 'b' and resid 165 through 170 Processing helix chain 'b' and resid 171 through 180 removed outlier: 4.029A pdb=" N ASN b 180 " --> pdb=" O ALA b 176 " (cutoff:3.500A) Processing helix chain 'b' and resid 192 through 197 removed outlier: 4.546A pdb=" N ILE b 196 " --> pdb=" O ASP b 192 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ASP b 197 " --> pdb=" O PRO b 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 192 through 197' Processing helix chain 'b' and resid 206 through 226 removed outlier: 3.727A pdb=" N VAL b 210 " --> pdb=" O ALA b 206 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU b 213 " --> pdb=" O ALA b 209 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ALA b 215 " --> pdb=" O LYS b 211 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LYS b 216 " --> pdb=" O LEU b 212 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA b 218 " --> pdb=" O THR b 214 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE b 221 " --> pdb=" O MET b 217 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLN b 226 " --> pdb=" O LEU b 222 " (cutoff:3.500A) Processing helix chain 'b' and resid 124 through 129 removed outlier: 5.811A pdb=" N GLU b 127 " --> pdb=" O GLY b 124 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N VAL b 128 " --> pdb=" O LEU b 125 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU b 129 " --> pdb=" O PHE b 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 124 through 129' Processing helix chain 'c' and resid 6 through 12 removed outlier: 3.961A pdb=" N LEU c 10 " --> pdb=" O ASN c 6 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL c 12 " --> pdb=" O ILE c 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 6 through 12' Processing helix chain 'c' and resid 29 through 47 removed outlier: 3.578A pdb=" N HIS c 33 " --> pdb=" O ALA c 29 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ASP c 35 " --> pdb=" O LEU c 31 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE c 38 " --> pdb=" O GLU c 34 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS c 40 " --> pdb=" O LEU c 36 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N PHE c 41 " --> pdb=" O LYS c 37 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE c 42 " --> pdb=" O ILE c 38 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP c 43 " --> pdb=" O ARG c 39 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ASN c 44 " --> pdb=" O LYS c 40 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU c 46 " --> pdb=" O ILE c 42 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LYS c 47 " --> pdb=" O ASP c 43 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 77 removed outlier: 6.543A pdb=" N ILE c 76 " --> pdb=" O PRO c 72 " (cutoff:3.500A) Processing helix chain 'c' and resid 81 through 94 removed outlier: 4.013A pdb=" N LYS c 85 " --> pdb=" O SER c 81 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU c 86 " --> pdb=" O GLU c 82 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR c 94 " --> pdb=" O LEU c 90 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 126 removed outlier: 3.992A pdb=" N VAL c 115 " --> pdb=" O ASP c 111 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU c 123 " --> pdb=" O ILE c 119 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU c 124 " --> pdb=" O ALA c 120 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ASN c 125 " --> pdb=" O ARG c 121 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ARG c 126 " --> pdb=" O GLN c 122 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 144 removed outlier: 3.989A pdb=" N GLN c 133 " --> pdb=" O PHE c 129 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR c 138 " --> pdb=" O LYS c 134 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 15 removed outlier: 4.930A pdb=" N ARG d 13 " --> pdb=" O TRP d 9 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU d 15 " --> pdb=" O LYS d 11 " (cutoff:3.500A) Processing helix chain 'd' and resid 45 through 62 removed outlier: 3.692A pdb=" N LEU d 57 " --> pdb=" O GLU d 53 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR d 59 " --> pdb=" O GLN d 55 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU d 60 " --> pdb=" O LYS d 56 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 79 removed outlier: 5.437A pdb=" N ARG d 69 " --> pdb=" O GLU d 65 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN d 70 " --> pdb=" O ARG d 66 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR d 71 " --> pdb=" O GLN d 67 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE d 72 " --> pdb=" O PHE d 68 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP d 73 " --> pdb=" O ARG d 69 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE d 74 " --> pdb=" O ASN d 70 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N PHE d 79 " --> pdb=" O ALA d 75 " (cutoff:3.500A) Processing helix chain 'd' and resid 81 through 93 removed outlier: 3.534A pdb=" N PHE d 86 " --> pdb=" O HIS d 82 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N MET d 87 " --> pdb=" O GLY d 83 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ARG d 93 " --> pdb=" O LEU d 89 " (cutoff:3.500A) Processing helix chain 'd' and resid 94 through 100 removed outlier: 3.792A pdb=" N VAL d 98 " --> pdb=" O LEU d 94 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N TYR d 99 " --> pdb=" O ASP d 95 " (cutoff:3.500A) Processing helix chain 'd' and resid 106 through 117 removed outlier: 4.689A pdb=" N ALA d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU d 113 " --> pdb=" O GLN d 109 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN d 115 " --> pdb=" O ARG d 111 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY d 117 " --> pdb=" O LEU d 113 " (cutoff:3.500A) Processing helix chain 'd' and resid 148 through 159 removed outlier: 5.276A pdb=" N VAL d 152 " --> pdb=" O LEU d 148 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N GLU d 153 " --> pdb=" O ASN d 149 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N SER d 154 " --> pdb=" O ILE d 150 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL d 155 " --> pdb=" O ILE d 151 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU d 156 " --> pdb=" O VAL d 152 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN d 159 " --> pdb=" O VAL d 155 " (cutoff:3.500A) Processing helix chain 'd' and resid 181 through 186 removed outlier: 3.842A pdb=" N LEU d 185 " --> pdb=" O GLU d 181 " (cutoff:3.500A) Proline residue: d 186 - end of helix No H-bonds generated for 'chain 'd' and resid 181 through 186' Processing helix chain 'd' and resid 190 through 199 removed outlier: 4.418A pdb=" N ILE d 194 " --> pdb=" O ASN d 190 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N VAL d 195 " --> pdb=" O GLU d 191 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N GLU d 196 " --> pdb=" O GLN d 192 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N TYR d 197 " --> pdb=" O LEU d 193 " (cutoff:3.500A) Processing helix chain 'e' and resid 55 through 71 removed outlier: 4.166A pdb=" N ALA e 63 " --> pdb=" O ALA e 59 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP e 70 " --> pdb=" O ALA e 66 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU e 71 " --> pdb=" O ALA e 67 " (cutoff:3.500A) Processing helix chain 'e' and resid 109 through 119 removed outlier: 3.788A pdb=" N ALA e 113 " --> pdb=" O GLY e 109 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL e 114 " --> pdb=" O PRO e 110 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU e 115 " --> pdb=" O VAL e 111 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA e 118 " --> pdb=" O VAL e 114 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N GLY e 119 " --> pdb=" O LEU e 115 " (cutoff:3.500A) Processing helix chain 'e' and resid 132 through 147 removed outlier: 3.845A pdb=" N LEU e 144 " --> pdb=" O THR e 140 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN e 146 " --> pdb=" O ASP e 142 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU e 147 " --> pdb=" O GLY e 143 " (cutoff:3.500A) Processing helix chain 'e' and resid 149 through 158 removed outlier: 4.358A pdb=" N VAL e 153 " --> pdb=" O ASN e 149 " (cutoff:3.500A) Processing helix chain 'f' and resid 15 through 28 removed outlier: 3.660A pdb=" N LYS f 19 " --> pdb=" O GLU f 15 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG f 25 " --> pdb=" O ALA f 21 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE f 26 " --> pdb=" O LEU f 22 " (cutoff:3.500A) Processing helix chain 'f' and resid 70 through 81 removed outlier: 5.316A pdb=" N ASP f 74 " --> pdb=" O ASN f 70 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LYS f 81 " --> pdb=" O GLN f 77 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 removed outlier: 3.686A pdb=" N THR g 24 " --> pdb=" O SER g 20 " (cutoff:3.500A) Processing helix chain 'g' and resid 37 through 55 removed outlier: 3.896A pdb=" N ARG g 41 " --> pdb=" O GLY g 37 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE g 42 " --> pdb=" O THR g 38 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ASP g 48 " --> pdb=" O TYR g 44 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LEU g 49 " --> pdb=" O SER g 45 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N VAL g 50 " --> pdb=" O ALA g 46 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY g 55 " --> pdb=" O GLU g 51 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 71 removed outlier: 4.217A pdb=" N GLU g 63 " --> pdb=" O LEU g 59 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN g 67 " --> pdb=" O GLU g 63 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN g 68 " --> pdb=" O GLU g 64 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE g 69 " --> pdb=" O ALA g 65 " (cutoff:3.500A) Proline residue: g 71 - end of helix Processing helix chain 'g' and resid 92 through 109 removed outlier: 3.634A pdb=" N LEU g 101 " --> pdb=" O THR g 97 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N TRP g 103 " --> pdb=" O LEU g 99 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LEU g 104 " --> pdb=" O GLY g 100 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL g 105 " --> pdb=" O LEU g 101 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASN g 106 " --> pdb=" O ARG g 102 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR g 107 " --> pdb=" O TRP g 103 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA g 108 " --> pdb=" O LEU g 104 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ARG g 109 " --> pdb=" O VAL g 105 " (cutoff:3.500A) Processing helix chain 'g' and resid 116 through 129 removed outlier: 4.584A pdb=" N LEU g 120 " --> pdb=" O MET g 116 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ALA g 121 " --> pdb=" O GLU g 117 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE g 124 " --> pdb=" O LEU g 120 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU g 125 " --> pdb=" O ALA g 121 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASP g 126 " --> pdb=" O ASN g 122 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA g 127 " --> pdb=" O GLU g 123 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA g 128 " --> pdb=" O ILE g 124 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASN g 129 " --> pdb=" O LEU g 125 " (cutoff:3.500A) Processing helix chain 'g' and resid 134 through 149 removed outlier: 4.191A pdb=" N ARG g 138 " --> pdb=" O ALA g 134 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP g 140 " --> pdb=" O LYS g 136 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N THR g 141 " --> pdb=" O LYS g 137 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA g 145 " --> pdb=" O THR g 141 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N GLU g 146 " --> pdb=" O HIS g 142 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ALA g 147 " --> pdb=" O LYS g 143 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ASN g 148 " --> pdb=" O MET g 144 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS g 149 " --> pdb=" O ALA g 145 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 21 removed outlier: 3.582A pdb=" N ASP h 9 " --> pdb=" O ASP h 5 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU h 11 " --> pdb=" O ILE h 7 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL h 14 " --> pdb=" O MET h 10 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL h 20 " --> pdb=" O ASN h 16 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 44 removed outlier: 4.377A pdb=" N LYS h 34 " --> pdb=" O SER h 30 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLU h 35 " --> pdb=" O ASN h 31 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU h 40 " --> pdb=" O ILE h 36 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS h 41 " --> pdb=" O ALA h 37 " (cutoff:3.500A) Processing helix chain 'h' and resid 114 through 122 removed outlier: 3.595A pdb=" N LYS h 120 " --> pdb=" O LYS h 116 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ARG h 121 " --> pdb=" O GLU h 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 36 through 41 removed outlier: 3.973A pdb=" N TYR i 40 " --> pdb=" O ASP i 36 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU i 41 " --> pdb=" O VAL i 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 36 through 41' Processing helix chain 'i' and resid 44 through 56 removed outlier: 4.591A pdb=" N LEU i 48 " --> pdb=" O GLU i 44 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP i 49 " --> pdb=" O SER i 45 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASN i 51 " --> pdb=" O ILE i 47 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N GLN i 52 " --> pdb=" O LEU i 48 " (cutoff:3.500A) Proline residue: i 53 - end of helix removed outlier: 4.133A pdb=" N VAL i 56 " --> pdb=" O GLN i 52 " (cutoff:3.500A) Processing helix chain 'i' and resid 58 through 63 removed outlier: 4.471A pdb=" N ASN i 62 " --> pdb=" O GLU i 58 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR i 63 " --> pdb=" O THR i 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 58 through 63' Processing helix chain 'i' and resid 73 through 93 removed outlier: 4.509A pdb=" N GLN i 79 " --> pdb=" O THR i 75 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ALA i 80 " --> pdb=" O GLY i 76 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE i 81 " --> pdb=" O GLN i 77 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ARG i 82 " --> pdb=" O ALA i 78 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N HIS i 83 " --> pdb=" O GLN i 79 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA i 86 " --> pdb=" O ARG i 82 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG i 87 " --> pdb=" O HIS i 83 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA i 88 " --> pdb=" O GLY i 84 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU i 91 " --> pdb=" O ARG i 87 " (cutoff:3.500A) Processing helix chain 'i' and resid 96 through 101 Processing helix chain 'j' and resid 14 through 33 removed outlier: 4.133A pdb=" N GLN j 20 " --> pdb=" O ARG j 16 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE j 25 " --> pdb=" O SER j 21 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU j 27 " --> pdb=" O GLU j 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS j 30 " --> pdb=" O VAL j 26 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLY j 33 " --> pdb=" O ALA j 29 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 85 removed outlier: 3.589A pdb=" N VAL j 84 " --> pdb=" O THR j 80 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ASP j 85 " --> pdb=" O PRO j 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 80 through 85' Processing helix chain 'k' and resid 59 through 72 removed outlier: 4.346A pdb=" N ALA k 63 " --> pdb=" O THR k 59 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET k 65 " --> pdb=" O PHE k 61 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA k 66 " --> pdb=" O ALA k 62 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N SER k 67 " --> pdb=" O ALA k 63 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU k 68 " --> pdb=" O GLN k 64 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA k 70 " --> pdb=" O ALA k 66 " (cutoff:3.500A) Processing helix chain 'k' and resid 90 through 103 removed outlier: 4.960A pdb=" N GLU k 94 " --> pdb=" O GLY k 90 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N SER k 95 " --> pdb=" O PRO k 91 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA k 96 " --> pdb=" O GLY k 92 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ALA k 99 " --> pdb=" O SER k 95 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLN k 101 " --> pdb=" O ILE k 97 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ALA k 103 " --> pdb=" O ALA k 99 " (cutoff:3.500A) Processing helix chain 'k' and resid 46 through 51 removed outlier: 4.664A pdb=" N LEU k 50 " --> pdb=" O ALA k 47 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 11 removed outlier: 3.649A pdb=" N VAL l 8 " --> pdb=" O ILE l 4 " (cutoff:3.500A) Proline residue: l 11 - end of helix Processing helix chain 'l' and resid 21 through 26 removed outlier: 4.294A pdb=" N ASN l 25 " --> pdb=" O SER l 21 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N LYS l 26 " --> pdb=" O PRO l 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 21 through 26' Processing helix chain 'l' and resid 126 through 131 removed outlier: 4.595A pdb=" N TYR l 130 " --> pdb=" O GLY l 126 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N GLY l 131 " --> pdb=" O ARG l 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 126 through 131' Processing helix chain 'm' and resid 14 through 19 removed outlier: 4.341A pdb=" N LEU m 19 " --> pdb=" O VAL m 15 " (cutoff:3.500A) Processing helix chain 'm' and resid 27 through 32 removed outlier: 4.330A pdb=" N GLN m 31 " --> pdb=" O THR m 27 " (cutoff:3.500A) Processing helix chain 'm' and resid 33 through 38 removed outlier: 3.636A pdb=" N ALA m 37 " --> pdb=" O ILE m 33 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ASN m 38 " --> pdb=" O LEU m 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 33 through 38' Processing helix chain 'm' and resid 48 through 53 removed outlier: 4.467A pdb=" N LEU m 53 " --> pdb=" O THR m 49 " (cutoff:3.500A) Processing helix chain 'm' and resid 54 through 61 removed outlier: 4.323A pdb=" N GLU m 58 " --> pdb=" O GLY m 54 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL m 59 " --> pdb=" O ARG m 55 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP m 61 " --> pdb=" O ARG m 57 " (cutoff:3.500A) Processing helix chain 'm' and resid 67 through 84 removed outlier: 4.045A pdb=" N ARG m 71 " --> pdb=" O GLY m 67 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 94 removed outlier: 5.668A pdb=" N HIS m 91 " --> pdb=" O ARG m 87 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N GLY m 94 " --> pdb=" O ARG m 90 " (cutoff:3.500A) Processing helix chain 'n' and resid 2 through 12 removed outlier: 4.234A pdb=" N ALA n 8 " --> pdb=" O THR n 4 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS n 9 " --> pdb=" O SER n 5 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN n 10 " --> pdb=" O MET n 6 " (cutoff:3.500A) Processing helix chain 'n' and resid 40 through 51 removed outlier: 3.542A pdb=" N ARG n 45 " --> pdb=" O ARG n 41 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS n 50 " --> pdb=" O GLU n 46 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY n 51 " --> pdb=" O LEU n 47 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 15 removed outlier: 3.618A pdb=" N LYS o 8 " --> pdb=" O SER o 4 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LYS o 13 " --> pdb=" O ASN o 9 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU o 14 " --> pdb=" O GLU o 10 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 47 removed outlier: 3.823A pdb=" N GLN o 28 " --> pdb=" O SER o 24 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE o 29 " --> pdb=" O PRO o 25 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ALA o 30 " --> pdb=" O GLU o 26 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N VAL o 31 " --> pdb=" O VAL o 27 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU o 32 " --> pdb=" O GLN o 28 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU o 35 " --> pdb=" O VAL o 31 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.641A pdb=" N ARG o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU o 56 " --> pdb=" O SER o 52 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N MET o 59 " --> pdb=" O GLY o 55 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY o 61 " --> pdb=" O LEU o 57 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG o 62 " --> pdb=" O LYS o 58 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU o 66 " --> pdb=" O ARG o 62 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG o 71 " --> pdb=" O LEU o 67 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER o 72 " --> pdb=" O ASN o 68 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS o 73 " --> pdb=" O TYR o 69 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ASP o 74 " --> pdb=" O LEU o 70 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 removed outlier: 4.117A pdb=" N LEU o 85 " --> pdb=" O LEU o 81 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N GLY o 86 " --> pdb=" O ILE o 82 " (cutoff:3.500A) Processing helix chain 'p' and resid 54 through 64 removed outlier: 4.026A pdb=" N LEU p 58 " --> pdb=" O GLU p 54 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LYS p 59 " --> pdb=" O ALA p 55 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASN p 62 " --> pdb=" O LEU p 58 " (cutoff:3.500A) Processing helix chain 'p' and resid 69 through 79 removed outlier: 5.570A pdb=" N ASN p 73 " --> pdb=" O ASP p 69 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE p 74 " --> pdb=" O THR p 70 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU p 75 " --> pdb=" O VAL p 71 " (cutoff:3.500A) Processing helix chain 'p' and resid 80 through 89 removed outlier: 3.961A pdb=" N GLU p 86 " --> pdb=" O LYS p 82 " (cutoff:3.500A) Processing helix chain 'r' and resid 30 through 39 removed outlier: 3.989A pdb=" N LEU r 34 " --> pdb=" O ASP r 30 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ARG r 36 " --> pdb=" O GLU r 32 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHE r 37 " --> pdb=" O LEU r 33 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE r 38 " --> pdb=" O LEU r 34 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N SER r 39 " --> pdb=" O LYS r 35 " (cutoff:3.500A) Processing helix chain 'r' and resid 46 through 51 removed outlier: 3.869A pdb=" N THR r 50 " --> pdb=" O PRO r 46 " (cutoff:3.500A) Processing helix chain 'r' and resid 53 through 69 Processing helix chain 's' and resid 12 through 24 removed outlier: 5.480A pdb=" N MET s 16 " --> pdb=" O ASP s 12 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS s 17 " --> pdb=" O GLU s 13 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS s 18 " --> pdb=" O HIS s 14 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY s 24 " --> pdb=" O GLU s 20 " (cutoff:3.500A) Processing helix chain 't' and resid 4 through 41 removed outlier: 3.766A pdb=" N ILE t 8 " --> pdb=" O ILE t 4 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL t 11 " --> pdb=" O ALA t 7 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS t 12 " --> pdb=" O ILE t 8 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN t 24 " --> pdb=" O ARG t 20 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER t 26 " --> pdb=" O ILE t 22 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS t 33 " --> pdb=" O ARG t 29 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LYS t 36 " --> pdb=" O VAL t 32 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR t 37 " --> pdb=" O LYS t 33 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER t 40 " --> pdb=" O LYS t 36 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ASN t 41 " --> pdb=" O THR t 37 " (cutoff:3.500A) Processing helix chain 't' and resid 48 through 64 removed outlier: 4.459A pdb=" N LEU t 52 " --> pdb=" O GLU t 48 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS t 55 " --> pdb=" O SER t 51 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP t 58 " --> pdb=" O VAL t 54 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER t 63 " --> pdb=" O LYS t 59 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASN t 64 " --> pdb=" O ALA t 60 " (cutoff:3.500A) Processing helix chain 't' and resid 67 through 82 removed outlier: 3.728A pdb=" N GLN t 77 " --> pdb=" O ARG t 73 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR t 80 " --> pdb=" O SER t 76 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA t 81 " --> pdb=" O GLN t 77 " (cutoff:3.500A) Processing helix chain 'u' and resid 11 through 26 removed outlier: 3.978A pdb=" N ALA u 15 " --> pdb=" O SER u 11 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG u 21 " --> pdb=" O ARG u 17 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N SER u 26 " --> pdb=" O SER u 22 " (cutoff:3.500A) Processing helix chain 'u' and resid 27 through 36 removed outlier: 4.123A pdb=" N GLU u 31 " --> pdb=" O GLY u 27 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU u 36 " --> pdb=" O VAL u 32 " (cutoff:3.500A) Processing helix chain 'u' and resid 40 through 52 removed outlier: 4.718A pdb=" N ARG u 45 " --> pdb=" O PRO u 41 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N LYS u 46 " --> pdb=" O SER u 42 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA u 52 " --> pdb=" O LYS u 48 " (cutoff:3.500A) Processing helix chain 'v' and resid 14 through 34 removed outlier: 4.923A pdb=" N ARG v 18 " --> pdb=" O THR v 14 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N ASN v 19 " --> pdb=" O ASP v 15 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N TYR v 20 " --> pdb=" O ALA v 16 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE v 21 " --> pdb=" O ILE v 17 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLU v 22 " --> pdb=" O ARG v 18 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS v 27 " --> pdb=" O GLU v 23 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU v 28 " --> pdb=" O LYS v 24 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLU v 29 " --> pdb=" O ILE v 25 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ARG v 30 " --> pdb=" O GLY v 26 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N TYR v 31 " --> pdb=" O LYS v 27 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE v 32 " --> pdb=" O LEU v 28 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ASN v 33 " --> pdb=" O GLU v 29 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ASP v 34 " --> pdb=" O ARG v 30 " (cutoff:3.500A) Processing helix chain 'v' and resid 77 through 98 removed outlier: 4.109A pdb=" N ILE v 81 " --> pdb=" O GLY v 77 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS v 91 " --> pdb=" O ARG v 87 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS v 93 " --> pdb=" O VAL v 89 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE v 96 " --> pdb=" O TYR v 92 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ARG v 98 " --> pdb=" O THR v 94 " (cutoff:3.500A) Processing helix chain 'v' and resid 145 through 157 removed outlier: 4.105A pdb=" N LEU v 155 " --> pdb=" O LEU v 151 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LEU v 156 " --> pdb=" O GLN v 152 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'C' and resid 2 through 6 removed outlier: 6.638A pdb=" N ALA C 2 " --> pdb=" O ASP C 20 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP C 20 " --> pdb=" O ALA C 2 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N MET C 16 " --> pdb=" O TYR C 6 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'C' and resid 33 through 36 No H-bonds generated for sheet with id= 2 Processing sheet with id= 3, first strand: chain 'C' and resid 75 through 78 removed outlier: 4.775A pdb=" N GLN C 114 " --> pdb=" O VAL C 78 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 80 through 83 removed outlier: 3.647A pdb=" N SER C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ASN C 90 " --> pdb=" O ALA C 106 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'C' and resid 137 through 142 removed outlier: 7.409A pdb=" N VAL C 137 " --> pdb=" O GLY C 166 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N GLY C 166 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N THR C 139 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'D' and resid 3 through 7 removed outlier: 6.960A pdb=" N LYS D 3 " --> pdb=" O THR D 213 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASN D 176 " --> pdb=" O SER D 122 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'D' and resid 11 through 17 removed outlier: 3.756A pdb=" N GLY D 11 " --> pdb=" O VAL D 27 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU D 21 " --> pdb=" O GLY D 17 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLN D 187 " --> pdb=" O LEU D 196 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 33 through 36 removed outlier: 6.493A pdb=" N GLN D 50 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHE D 87 " --> pdb=" O PHE D 53 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'D' and resid 114 through 117 removed outlier: 4.470A pdb=" N ASP D 114 " --> pdb=" O VAL D 185 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'E' and resid 2 through 7 removed outlier: 8.276A pdb=" N ALA E 2 " --> pdb=" O GLU E 18 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLU E 18 " --> pdb=" O ALA E 2 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N TYR E 4 " --> pdb=" O SER E 16 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER E 16 " --> pdb=" O TYR E 4 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL E 6 " --> pdb=" O SER E 14 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'E' and resid 122 through 125 Processing sheet with id= 12, first strand: chain 'F' and resid 33 through 40 removed outlier: 3.615A pdb=" N VAL F 36 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N VAL F 89 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ALA F 87 " --> pdb=" O MET F 38 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL F 40 " --> pdb=" O ILE F 85 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ILE F 85 " --> pdb=" O VAL F 40 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'F' and resid 127 through 133 removed outlier: 6.643A pdb=" N ILE F 156 " --> pdb=" O TYR F 128 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'G' and resid 9 through 12 removed outlier: 4.129A pdb=" N ASP G 10 " --> pdb=" O ILE G 50 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASN G 48 " --> pdb=" O PRO G 12 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N THR G 49 " --> pdb=" O GLU G 46 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'G' and resid 15 through 20 removed outlier: 4.388A pdb=" N HIS G 23 " --> pdb=" O ASP G 20 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N GLY G 28 " --> pdb=" O GLY G 31 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLY G 31 " --> pdb=" O GLY G 28 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'G' and resid 94 through 99 removed outlier: 4.249A pdb=" N ASP G 102 " --> pdb=" O GLN G 99 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N LYS G 101 " --> pdb=" O ALA G 117 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA G 117 " --> pdb=" O LYS G 101 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'G' and resid 121 through 126 removed outlier: 6.503A pdb=" N VAL G 130 " --> pdb=" O GLU G 126 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N THR G 129 " --> pdb=" O LEU G 89 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'H' and resid 53 through 58 removed outlier: 5.077A pdb=" N ASP H 20 " --> pdb=" O TYR H 141 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'H' and resid 75 through 79 removed outlier: 7.048A pdb=" N GLY H 84 " --> pdb=" O SER H 79 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'I' and resid 6 through 9 removed outlier: 4.626A pdb=" N THR I 6 " --> pdb=" O THR I 21 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'I' and resid 37 through 41 removed outlier: 4.568A pdb=" N ASP I 37 " --> pdb=" O ILE I 62 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'I' and resid 63 through 66 removed outlier: 4.816A pdb=" N ARG I 64 " --> pdb=" O ALA I 83 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LYS I 66 " --> pdb=" O GLU I 81 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLU I 81 " --> pdb=" O LYS I 66 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'I' and resid 68 through 71 removed outlier: 4.223A pdb=" N SER I 75 " --> pdb=" O ARG I 71 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'J' and resid 74 through 77 Processing sheet with id= 25, first strand: chain 'J' and resid 121 through 124 removed outlier: 3.612A pdb=" N ALA J 142 " --> pdb=" O LEU J 121 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'K' and resid 63 through 66 removed outlier: 3.904A pdb=" N PHE K 104 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LYS K 128 " --> pdb=" O THR K 37 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'K' and resid 72 through 75 Processing sheet with id= 28, first strand: chain 'L' and resid 29 through 33 removed outlier: 5.993A pdb=" N ALA L 114 " --> pdb=" O PRO L 108 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N SER L 116 " --> pdb=" O GLN L 106 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'M' and resid 29 through 35 removed outlier: 5.891A pdb=" N ILE M 40 " --> pdb=" O SER M 58 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA M 54 " --> pdb=" O ILE M 44 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'N' and resid 39 through 47 removed outlier: 3.675A pdb=" N ARG N 39 " --> pdb=" O GLU N 36 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'N' and resid 51 through 55 removed outlier: 3.668A pdb=" N LYS N 51 " --> pdb=" O THR N 62 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLY N 55 " --> pdb=" O SER N 58 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'P' and resid 2 through 6 Processing sheet with id= 33, first strand: chain 'P' and resid 18 through 21 removed outlier: 4.370A pdb=" N GLN P 18 " --> pdb=" O ILE P 97 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS P 94 " --> pdb=" O ASN P 63 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASP P 31 " --> pdb=" O VAL P 62 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'P' and resid 66 through 77 No H-bonds generated for sheet with id= 34 Processing sheet with id= 35, first strand: chain 'Q' and resid 2 through 8 removed outlier: 6.662A pdb=" N VAL Q 104 " --> pdb=" O LYS Q 72 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'Q' and resid 73 through 79 removed outlier: 5.301A pdb=" N THR Q 98 " --> pdb=" O GLY Q 79 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'Q' and resid 81 through 87 removed outlier: 4.261A pdb=" N SER Q 92 " --> pdb=" O ARG Q 86 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'R' and resid 24 through 29 removed outlier: 4.389A pdb=" N ARG R 76 " --> pdb=" O VAL R 29 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LYS R 61 " --> pdb=" O THR R 72 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N LYS R 74 " --> pdb=" O LYS R 59 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LYS R 59 " --> pdb=" O LYS R 74 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ARG R 76 " --> pdb=" O ASN R 57 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASN R 57 " --> pdb=" O ARG R 76 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA R 78 " --> pdb=" O ILE R 55 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE R 55 " --> pdb=" O ALA R 78 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL R 80 " --> pdb=" O VAL R 53 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL R 53 " --> pdb=" O VAL R 80 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'S' and resid 39 through 44 removed outlier: 5.449A pdb=" N ASN S 39 " --> pdb=" O ALA S 61 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR S 59 " --> pdb=" O MET S 41 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'T' and resid 68 through 73 removed outlier: 5.680A pdb=" N ALA T 2 " --> pdb=" O VAL T 60 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU T 4 " --> pdb=" O GLU T 62 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASP T 76 " --> pdb=" O ASP T 90 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'U' and resid 53 through 56 removed outlier: 6.155A pdb=" N VAL U 89 " --> pdb=" O GLY U 56 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'U' and resid 58 through 62 removed outlier: 7.909A pdb=" N ASN U 58 " --> pdb=" O LYS U 70 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR U 66 " --> pdb=" O GLY U 62 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'V' and resid 13 through 19 removed outlier: 6.035A pdb=" N SER V 13 " --> pdb=" O TRP V 29 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ASN V 23 " --> pdb=" O SER V 19 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'X' and resid 32 through 38 removed outlier: 4.035A pdb=" N SER X 33 " --> pdb=" O LEU X 8 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain '1' and resid 2 through 7 No H-bonds generated for sheet with id= 45 Processing sheet with id= 46, first strand: chain '1' and resid 30 through 35 removed outlier: 5.318A pdb=" N ILE 1 30 " --> pdb=" O GLU 1 47 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain '3' and resid 22 through 25 removed outlier: 5.489A pdb=" N LEU 3 22 " --> pdb=" O VAL 3 50 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG 3 48 " --> pdb=" O ARG 3 24 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain '4' and resid 1 through 4 removed outlier: 7.053A pdb=" N HIS 4 32 " --> pdb=" O CYS 4 27 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N CYS 4 27 " --> pdb=" O HIS 4 32 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N VAL 4 23 " --> pdb=" O GLN 4 36 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'b' and resid 15 through 18 removed outlier: 6.979A pdb=" N HIS b 15 " --> pdb=" O ILE b 41 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE b 41 " --> pdb=" O HIS b 15 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N TYR b 39 " --> pdb=" O GLY b 17 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'b' and resid 67 through 71 removed outlier: 3.871A pdb=" N ILE b 186 " --> pdb=" O VAL b 163 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'c' and resid 54 through 58 removed outlier: 3.553A pdb=" N GLU c 55 " --> pdb=" O ALA c 66 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ALA c 66 " --> pdb=" O GLU c 55 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU c 57 " --> pdb=" O ASN c 64 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'c' and resid 164 through 170 removed outlier: 3.599A pdb=" N THR c 150 " --> pdb=" O TYR c 167 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLU c 169 " --> pdb=" O ILE c 148 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ILE c 148 " --> pdb=" O GLU c 169 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N GLY c 147 " --> pdb=" O TYR c 202 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR c 202 " --> pdb=" O GLY c 147 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLN c 151 " --> pdb=" O LYS c 198 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LYS c 198 " --> pdb=" O GLN c 151 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N SER c 153 " --> pdb=" O GLY c 196 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLY c 196 " --> pdb=" O SER c 153 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N GLY c 193 " --> pdb=" O THR c 190 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA c 188 " --> pdb=" O LEU c 195 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL c 197 " --> pdb=" O ALA c 186 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA c 186 " --> pdb=" O VAL c 197 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N VAL c 199 " --> pdb=" O ALA c 184 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA c 184 " --> pdb=" O VAL c 199 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'd' and resid 165 through 168 removed outlier: 6.147A pdb=" N ASN d 166 " --> pdb=" O THR d 175 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N THR d 173 " --> pdb=" O ASP d 168 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'e' and resid 11 through 17 removed outlier: 7.210A pdb=" N LEU e 36 " --> pdb=" O VAL e 16 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'e' and resid 84 through 88 removed outlier: 3.877A pdb=" N VAL e 94 " --> pdb=" O GLY e 87 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER e 93 " --> pdb=" O LEU e 128 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LYS e 97 " --> pdb=" O LEU e 124 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ASP e 122 " --> pdb=" O ALA e 99 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'f' and resid 40 through 44 removed outlier: 3.757A pdb=" N TYR f 60 " --> pdb=" O TRP f 43 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE f 59 " --> pdb=" O VAL f 10 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ILE f 9 " --> pdb=" O ARG f 88 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ARG f 88 " --> pdb=" O ILE f 9 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'g' and resid 72 through 77 No H-bonds generated for sheet with id= 57 Processing sheet with id= 58, first strand: chain 'h' and resid 23 through 29 removed outlier: 5.243A pdb=" N GLU h 23 " --> pdb=" O LEU h 64 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU h 25 " --> pdb=" O LEU h 62 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA h 29 " --> pdb=" O GLY h 58 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N GLY h 58 " --> pdb=" O ALA h 29 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'h' and resid 104 through 108 removed outlier: 6.793A pdb=" N LEU h 105 " --> pdb=" O ILE h 128 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE h 128 " --> pdb=" O LEU h 105 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'i' and resid 7 through 13 removed outlier: 4.465A pdb=" N TYR i 8 " --> pdb=" O LEU i 23 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY i 10 " --> pdb=" O VAL i 21 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG i 22 " --> pdb=" O LEU i 66 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU i 66 " --> pdb=" O ARG i 22 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'j' and resid 6 through 13 No H-bonds generated for sheet with id= 61 Processing sheet with id= 62, first strand: chain 'k' and resid 42 through 45 removed outlier: 3.816A pdb=" N SER k 43 " --> pdb=" O ILE k 34 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE k 31 " --> pdb=" O ARG k 24 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG k 24 " --> pdb=" O ILE k 31 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N THR k 81 " --> pdb=" O GLU k 17 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY k 19 " --> pdb=" O THR k 81 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLU k 83 " --> pdb=" O GLY k 19 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA k 21 " --> pdb=" O GLU k 83 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS k 87 " --> pdb=" O ILE k 23 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N SER k 25 " --> pdb=" O LYS k 87 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'l' and resid 42 through 45 removed outlier: 3.599A pdb=" N LYS l 43 " --> pdb=" O VAL l 95 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL l 95 " --> pdb=" O LYS l 43 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N LEU l 94 " --> pdb=" O VAL l 111 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG l 96 " --> pdb=" O HIS l 109 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'l' and resid 49 through 54 removed outlier: 4.830A pdb=" N LYS l 64 " --> pdb=" O ILE l 80 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL l 68 " --> pdb=" O ILE l 76 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'p' and resid 5 through 11 removed outlier: 3.678A pdb=" N VAL p 21 " --> pdb=" O ARG p 6 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR p 8 " --> pdb=" O ARG p 19 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR p 18 " --> pdb=" O TYR p 40 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY p 38 " --> pdb=" O ILE p 20 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASN p 41 " --> pdb=" O GLU p 49 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU p 49 " --> pdb=" O ASN p 41 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'q' and resid 8 through 12 removed outlier: 4.748A pdb=" N LYS q 8 " --> pdb=" O GLU q 65 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR q 10 " --> pdb=" O ILE q 63 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ARG q 74 " --> pdb=" O THR q 66 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'q' and resid 21 through 34 removed outlier: 5.629A pdb=" N LYS q 21 " --> pdb=" O ASP q 50 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASP q 50 " --> pdb=" O LYS q 21 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE q 23 " --> pdb=" O THR q 48 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR q 48 " --> pdb=" O ILE q 23 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL q 25 " --> pdb=" O TYR q 46 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR q 46 " --> pdb=" O VAL q 25 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL q 27 " --> pdb=" O LYS q 44 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS q 38 " --> pdb=" O HIS q 33 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 's' and resid 46 through 52 removed outlier: 4.050A pdb=" N HIS s 47 " --> pdb=" O VAL s 62 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'v' and resid 38 through 46 removed outlier: 3.868A pdb=" N VAL v 39 " --> pdb=" O PRO v 59 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASN v 71 " --> pdb=" O THR v 52 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU v 60 " --> pdb=" O VAL v 63 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N VAL v 63 " --> pdb=" O LEU v 60 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'v' and resid 160 through 164 1361 hydrogen bonds defined for protein. 4011 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3048 hydrogen bonds 4844 hydrogen bond angles 0 basepair planarities 1231 basepair parallelities 2200 stacking parallelities Total time for adding SS restraints: 197.48 Time building geometry restraints manager: 70.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.07 - 1.39: 56612 1.39 - 1.70: 96125 1.70 - 2.01: 208 2.01 - 2.33: 0 2.33 - 2.64: 6 Bond restraints: 152951 Sorted by residual: bond pdb=" C1' G A 393 " pdb=" N9 G A 393 " ideal model delta sigma weight residual 1.475 2.638 -1.163 1.50e-02 4.44e+03 6.01e+03 bond pdb=" N9 A A 332 " pdb=" C8 A A 332 " ideal model delta sigma weight residual 1.373 2.539 -1.166 2.00e-02 2.50e+03 3.40e+03 bond pdb=" N7 A A 332 " pdb=" C5 A A 332 " ideal model delta sigma weight residual 1.388 2.542 -1.154 2.00e-02 2.50e+03 3.33e+03 bond pdb=" C8 A A 332 " pdb=" N7 A A 332 " ideal model delta sigma weight residual 1.311 2.430 -1.119 2.00e-02 2.50e+03 3.13e+03 bond pdb=" N9 A A 332 " pdb=" C4 A A 332 " ideal model delta sigma weight residual 1.374 2.463 -1.089 2.00e-02 2.50e+03 2.97e+03 ... (remaining 152946 not shown) Histogram of bond angle deviations from ideal: 40.24 - 64.30: 2 64.30 - 88.37: 27 88.37 - 112.43: 106474 112.43 - 136.50: 122383 136.50 - 160.56: 232 Bond angle restraints: 229118 Sorted by residual: angle pdb=" C8 G A 393 " pdb=" N9 G A 393 " pdb=" C4 G A 393 " ideal model delta sigma weight residual 106.40 40.24 66.16 3.00e+00 1.11e-01 4.86e+02 angle pdb=" C8 G A 393 " pdb=" N7 G A 393 " pdb=" C5 G A 393 " ideal model delta sigma weight residual 104.30 53.69 50.61 3.00e+00 1.11e-01 2.85e+02 angle pdb=" C5' G A 990 " pdb=" C4' G A 990 " pdb=" O4' G A 990 " ideal model delta sigma weight residual 109.80 132.85 -23.05 1.50e+00 4.44e-01 2.36e+02 angle pdb=" O4' C A 644 " pdb=" C1' C A 644 " pdb=" N1 C A 644 " ideal model delta sigma weight residual 108.50 127.91 -19.41 1.50e+00 4.44e-01 1.67e+02 angle pdb=" C2' G A 393 " pdb=" C1' G A 393 " pdb=" N9 G A 393 " ideal model delta sigma weight residual 112.00 130.45 -18.45 1.50e+00 4.44e-01 1.51e+02 ... (remaining 229113 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 82313 36.00 - 71.99: 13868 71.99 - 107.99: 1286 107.99 - 143.98: 69 143.98 - 179.98: 74 Dihedral angle restraints: 97610 sinusoidal: 81639 harmonic: 15971 Sorted by residual: dihedral pdb=" C4' U A1174 " pdb=" C3' U A1174 " pdb=" C2' U A1174 " pdb=" C1' U A1174 " ideal model delta sinusoidal sigma weight residual 36.00 -52.83 88.83 1 8.00e+00 1.56e-02 1.47e+02 dihedral pdb=" CA ALA P 50 " pdb=" C ALA P 50 " pdb=" N PRO P 51 " pdb=" CA PRO P 51 " ideal model delta harmonic sigma weight residual 180.00 119.47 60.53 0 5.00e+00 4.00e-02 1.47e+02 dihedral pdb=" O4' U A1174 " pdb=" C2' U A1174 " pdb=" C1' U A1174 " pdb=" C3' U A1174 " ideal model delta sinusoidal sigma weight residual 25.00 -58.10 83.10 1 8.00e+00 1.56e-02 1.32e+02 ... (remaining 97607 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.517: 29343 0.517 - 1.035: 105 1.035 - 1.552: 10 1.552 - 2.070: 4 2.070 - 2.587: 5 Chirality restraints: 29467 Sorted by residual: chirality pdb=" C16 ERY A3001 " pdb=" C15 ERY A3001 " pdb=" C17 ERY A3001 " pdb=" C19 ERY A3001 " both_signs ideal model delta sigma weight residual False 2.68 0.09 2.59 2.00e-01 2.50e+01 1.67e+02 chirality pdb=" C1' C A2077 " pdb=" O4' C A2077 " pdb=" C2' C A2077 " pdb=" N1 C A2077 " both_signs ideal model delta sigma weight residual False 2.47 -0.06 2.53 2.00e-01 2.50e+01 1.60e+02 chirality pdb=" C1' A A1289 " pdb=" O4' A A1289 " pdb=" C2' A A1289 " pdb=" N9 A A1289 " both_signs ideal model delta sigma weight residual False 2.46 -0.01 2.47 2.00e-01 2.50e+01 1.53e+02 ... (remaining 29464 not shown) Planarity restraints: 12075 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 557 " -0.116 2.00e-02 2.50e+03 6.59e-02 1.30e+02 pdb=" N9 G A 557 " 0.181 2.00e-02 2.50e+03 pdb=" C8 G A 557 " 0.022 2.00e-02 2.50e+03 pdb=" N7 G A 557 " -0.060 2.00e-02 2.50e+03 pdb=" C5 G A 557 " -0.024 2.00e-02 2.50e+03 pdb=" C6 G A 557 " 0.011 2.00e-02 2.50e+03 pdb=" O6 G A 557 " -0.005 2.00e-02 2.50e+03 pdb=" N1 G A 557 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G A 557 " -0.031 2.00e-02 2.50e+03 pdb=" N2 G A 557 " 0.007 2.00e-02 2.50e+03 pdb=" N3 G A 557 " 0.000 2.00e-02 2.50e+03 pdb=" C4 G A 557 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A2045 " -0.126 2.00e-02 2.50e+03 6.66e-02 1.22e+02 pdb=" N9 A A2045 " -0.038 2.00e-02 2.50e+03 pdb=" C8 A A2045 " 0.077 2.00e-02 2.50e+03 pdb=" N7 A A2045 " 0.047 2.00e-02 2.50e+03 pdb=" C5 A A2045 " 0.025 2.00e-02 2.50e+03 pdb=" C6 A A2045 " -0.074 2.00e-02 2.50e+03 pdb=" N6 A A2045 " -0.060 2.00e-02 2.50e+03 pdb=" N1 A A2045 " -0.025 2.00e-02 2.50e+03 pdb=" C2 A A2045 " 0.013 2.00e-02 2.50e+03 pdb=" N3 A A2045 " 0.070 2.00e-02 2.50e+03 pdb=" C4 A A2045 " 0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 648 " -0.126 2.00e-02 2.50e+03 6.24e-02 1.17e+02 pdb=" N9 G A 648 " 0.140 2.00e-02 2.50e+03 pdb=" C8 G A 648 " 0.026 2.00e-02 2.50e+03 pdb=" N7 G A 648 " -0.019 2.00e-02 2.50e+03 pdb=" C5 G A 648 " 0.004 2.00e-02 2.50e+03 pdb=" C6 G A 648 " 0.042 2.00e-02 2.50e+03 pdb=" O6 G A 648 " -0.056 2.00e-02 2.50e+03 pdb=" N1 G A 648 " -0.033 2.00e-02 2.50e+03 pdb=" C2 G A 648 " 0.057 2.00e-02 2.50e+03 pdb=" N2 G A 648 " -0.030 2.00e-02 2.50e+03 pdb=" N3 G A 648 " 0.002 2.00e-02 2.50e+03 pdb=" C4 G A 648 " -0.007 2.00e-02 2.50e+03 ... (remaining 12072 not shown) Histogram of nonbonded interaction distances: 0.92 - 1.71: 17 1.71 - 2.51: 2033 2.51 - 3.31: 150091 3.31 - 4.10: 471210 4.10 - 4.90: 680054 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1303405 Sorted by model distance: nonbonded pdb=" O2 U A 12 " pdb=" N6 A A 571 " model vdw 0.917 2.520 nonbonded pdb=" N6 A A 28 " pdb=" N3 G A 557 " model vdw 1.012 2.600 nonbonded pdb=" N7 A A 28 " pdb=" N2 G A 557 " model vdw 1.133 2.600 nonbonded pdb=" N3 G A1250 " pdb=" N6 A A1275 " model vdw 1.184 2.600 nonbonded pdb=" O4 U A 860 " pdb=" N6 A A1231 " model vdw 1.219 2.520 ... (remaining 1303400 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.120 Extract box with map and model: 18.360 Check model and map are aligned: 1.530 Set scattering table: 1.040 Process input model: 497.350 Find NCS groups from input model: 2.630 Set up NCS constraints: 0.320 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:10.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 535.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6210 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 : 0.021 1.166 152951 Z= 1.239 Angle : 2.128 66.162 229118 Z= 0.976 Chirality : 0.108 2.587 29467 Planarity : 0.011 0.109 12075 Dihedral : 26.575 179.977 87310 Min Nonbonded Distance : 0.917 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.70 % Favored : 90.23 % Rotamer: Outliers : 19.66 % Allowed : 15.11 % Favored : 65.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.28 % 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: -4.36 (0.09), residues: 5487 helix: -3.51 (0.09), residues: 1452 sheet: -2.05 (0.15), residues: 983 loop : -2.93 (0.09), residues: 3052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.004 TRP O 61 HIS 0.022 0.003 HIS Z 40 PHE 0.040 0.004 PHE P 2 TYR 0.033 0.004 TYR H 126 ARG 0.020 0.002 ARG J 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10974 Ramachandran restraints generated. 5487 Oldfield, 0 Emsley, 5487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10974 Ramachandran restraints generated. 5487 Oldfield, 0 Emsley, 5487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1614 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 873 poor density : 741 time to evaluate : 6.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL L 122 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THR V 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7286 (mt-10) REVERT: C 168 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6372 (mt-10) REVERT: D 21 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6620 (tp30) REVERT: D 27 VAL cc_start: 0.9016 (OUTLIER) cc_final: 0.8814 (m) REVERT: D 193 LYS cc_start: 0.8788 (mttp) cc_final: 0.8567 (mttm) REVERT: E 205 VAL cc_start: 0.7935 (m) cc_final: 0.7706 (t) REVERT: F 81 GLU cc_start: 0.4634 (mm-30) cc_final: 0.4120 (mp0) REVERT: F 149 VAL cc_start: 0.3192 (OUTLIER) cc_final: 0.2988 (t) REVERT: F 161 ASN cc_start: 0.6485 (OUTLIER) cc_final: 0.5583 (t0) REVERT: G 2 SER cc_start: 0.5481 (p) cc_final: 0.5193 (p) REVERT: G 30 LYS cc_start: 0.4224 (mtmt) cc_final: 0.3977 (mtmt) REVERT: G 158 LYS cc_start: 0.4977 (mttt) cc_final: 0.4755 (mttt) REVERT: H 144 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.7364 (mmt-90) REVERT: I 2 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8606 (mp) REVERT: I 66 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8248 (mtpp) REVERT: I 81 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8082 (pm20) REVERT: I 105 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7714 (mp0) REVERT: K 116 GLU cc_start: 0.7985 (tp30) cc_final: 0.7503 (tp30) REVERT: L 8 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8256 (mtt-85) REVERT: M 86 ASP cc_start: 0.4044 (OUTLIER) cc_final: 0.3434 (m-30) REVERT: N 65 LYS cc_start: 0.8964 (pttt) cc_final: 0.8722 (ptmm) REVERT: O 51 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.7117 (mtt180) REVERT: O 59 LYS cc_start: 0.8633 (ttpt) cc_final: 0.8344 (ttmm) REVERT: P 10 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8486 (mttp) REVERT: P 26 ASP cc_start: 0.6734 (OUTLIER) cc_final: 0.6462 (p0) REVERT: R 14 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6944 (mt-10) REVERT: R 64 ARG cc_start: 0.7436 (tpp-160) cc_final: 0.6705 (tpp-160) REVERT: S 3 ILE cc_start: 0.6734 (pt) cc_final: 0.6344 (pt) REVERT: T 7 ILE cc_start: 0.8231 (mp) cc_final: 0.7976 (mp) REVERT: T 20 GLN cc_start: 0.7939 (tt0) cc_final: 0.7724 (mt0) REVERT: W 2 LYS cc_start: 0.1965 (OUTLIER) cc_final: 0.1631 (ttpp) REVERT: W 47 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7378 (mtp180) REVERT: Y 38 GLU cc_start: 0.4369 (OUTLIER) cc_final: 0.3625 (mm-30) REVERT: 1 44 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7413 (tp) REVERT: 1 46 ARG cc_start: 0.7100 (ttm110) cc_final: 0.6485 (ttt-90) REVERT: 3 45 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8104 (mtp180) REVERT: 4 25 VAL cc_start: 0.8786 (OUTLIER) cc_final: 0.8556 (t) REVERT: b 6 MET cc_start: 0.2277 (mmt) cc_final: 0.1943 (mpt) REVERT: b 7 LYS cc_start: 0.2151 (OUTLIER) cc_final: 0.1424 (mmmt) REVERT: b 11 GLU cc_start: 0.3166 (OUTLIER) cc_final: 0.2856 (tm-30) REVERT: b 22 ARG cc_start: 0.2683 (mmm-85) cc_final: 0.2078 (mtm180) REVERT: b 27 MET cc_start: 0.2017 (mmm) cc_final: 0.1402 (mtt) REVERT: b 51 ASP cc_start: 0.4637 (OUTLIER) cc_final: 0.4407 (p0) REVERT: b 62 GLU cc_start: 0.2152 (OUTLIER) cc_final: 0.1927 (tm-30) REVERT: b 126 PHE cc_start: 0.0679 (OUTLIER) cc_final: 0.0363 (p90) REVERT: b 154 MET cc_start: 0.0992 (ttt) cc_final: 0.0443 (tmt) REVERT: b 187 VAL cc_start: 0.1478 (OUTLIER) cc_final: 0.1221 (t) REVERT: b 208 ARG cc_start: 0.3209 (mtp85) cc_final: 0.2723 (pmm-80) REVERT: b 217 MET cc_start: 0.2056 (tpp) cc_final: 0.1841 (tpt) REVERT: c 36 LEU cc_start: 0.1210 (OUTLIER) cc_final: 0.0653 (tp) REVERT: c 57 GLU cc_start: 0.1446 (OUTLIER) cc_final: 0.0905 (tp30) REVERT: c 71 LYS cc_start: 0.2108 (ptpt) cc_final: 0.1201 (tptt) REVERT: c 163 ARG cc_start: 0.2903 (mtm110) cc_final: 0.2040 (mtt-85) REVERT: c 165 GLU cc_start: 0.2635 (OUTLIER) cc_final: 0.1330 (tt0) REVERT: c 174 LEU cc_start: 0.1750 (OUTLIER) cc_final: 0.1424 (pt) REVERT: d 61 TYR cc_start: 0.1970 (OUTLIER) cc_final: 0.0984 (m-80) REVERT: d 84 GLU cc_start: 0.4744 (OUTLIER) cc_final: 0.4444 (mm-30) REVERT: d 87 MET cc_start: 0.1070 (mmm) cc_final: 0.0705 (mtt) REVERT: d 111 ARG cc_start: 0.1779 (OUTLIER) cc_final: 0.0623 (tmt170) REVERT: d 115 ASN cc_start: 0.3275 (OUTLIER) cc_final: 0.2103 (p0) REVERT: e 10 GLU cc_start: 0.1971 (OUTLIER) cc_final: 0.0748 (mm-30) REVERT: e 65 GLU cc_start: 0.2271 (OUTLIER) cc_final: 0.1449 (tt0) REVERT: e 106 ILE cc_start: 0.1337 (OUTLIER) cc_final: 0.1058 (tt) REVERT: e 163 GLU cc_start: 0.1481 (OUTLIER) cc_final: 0.1043 (mm-30) REVERT: f 76 PHE cc_start: 0.2968 (OUTLIER) cc_final: 0.2659 (t80) REVERT: g 9 LYS cc_start: 0.1105 (OUTLIER) cc_final: 0.0656 (mmmm) REVERT: g 36 ARG cc_start: 0.3176 (tpp80) cc_final: 0.2690 (mmt180) REVERT: g 38 THR cc_start: 0.1686 (OUTLIER) cc_final: 0.1300 (p) REVERT: g 94 GLU cc_start: 0.2397 (OUTLIER) cc_final: 0.2079 (mt-10) REVERT: g 120 LEU cc_start: 0.2324 (OUTLIER) cc_final: 0.1778 (pt) REVERT: g 125 LEU cc_start: 0.2407 (OUTLIER) cc_final: 0.2167 (mt) REVERT: h 3 MET cc_start: 0.2912 (ppp) cc_final: 0.2248 (tpt) REVERT: h 39 ILE cc_start: 0.2614 (OUTLIER) cc_final: 0.2369 (mp) REVERT: h 82 LYS cc_start: 0.4224 (OUTLIER) cc_final: 0.3565 (mmmt) REVERT: h 103 ILE cc_start: 0.3366 (OUTLIER) cc_final: 0.3031 (mp) REVERT: h 105 LEU cc_start: 0.2372 (OUTLIER) cc_final: 0.1991 (pt) REVERT: h 120 LYS cc_start: 0.3274 (OUTLIER) cc_final: 0.2983 (mmtm) REVERT: i 101 LYS cc_start: 0.0470 (OUTLIER) cc_final: 0.0143 (tptm) REVERT: i 112 MET cc_start: 0.3216 (pmm) cc_final: 0.2854 (tpp) REVERT: j 11 LYS cc_start: 0.2357 (OUTLIER) cc_final: 0.1936 (mptt) REVERT: j 31 ARG cc_start: 0.2538 (OUTLIER) cc_final: 0.2015 (ppt170) REVERT: j 65 PHE cc_start: 0.0808 (OUTLIER) cc_final: 0.0482 (m-80) REVERT: j 88 MET cc_start: 0.3240 (OUTLIER) cc_final: 0.1940 (ttp) REVERT: k 37 GLU cc_start: 0.2761 (OUTLIER) cc_final: 0.1777 (mt-10) REVERT: l 9 ARG cc_start: 0.1646 (ttp-170) cc_final: 0.0824 (tmm-80) REVERT: l 67 ARG cc_start: 0.4449 (OUTLIER) cc_final: 0.3861 (tpp80) REVERT: l 99 ARG cc_start: 0.3711 (OUTLIER) cc_final: 0.3454 (ttm-80) REVERT: m 55 ARG cc_start: 0.3471 (mtm-85) cc_final: 0.3238 (tmt170) REVERT: n 3 LYS cc_start: 0.0991 (OUTLIER) cc_final: 0.0538 (tptm) REVERT: n 52 GLN cc_start: 0.3059 (OUTLIER) cc_final: 0.1712 (tp-100) REVERT: o 3 ILE cc_start: 0.2101 (OUTLIER) cc_final: 0.1569 (tp) REVERT: o 8 LYS cc_start: 0.1843 (OUTLIER) cc_final: 0.1420 (tptt) REVERT: o 15 TYR cc_start: 0.2481 (OUTLIER) cc_final: 0.0943 (m-10) REVERT: o 28 GLN cc_start: 0.2288 (OUTLIER) cc_final: 0.1786 (pt0) REVERT: o 42 HIS cc_start: 0.2604 (OUTLIER) cc_final: 0.2146 (t-170) REVERT: o 47 LYS cc_start: 0.3125 (OUTLIER) cc_final: 0.2405 (mtpt) REVERT: p 4 LYS cc_start: 0.2791 (OUTLIER) cc_final: 0.2510 (tptt) REVERT: p 78 GLU cc_start: 0.2817 (OUTLIER) cc_final: 0.2470 (tt0) REVERT: q 45 LYS cc_start: 0.4174 (mtmp) cc_final: 0.2903 (mmmm) REVERT: q 51 GLU cc_start: 0.2173 (OUTLIER) cc_final: 0.1351 (mm-30) REVERT: q 77 LEU cc_start: 0.3196 (OUTLIER) cc_final: 0.2927 (mm) REVERT: r 70 MET cc_start: 0.1638 (mmt) cc_final: 0.0056 (ptt) REVERT: s 28 LYS cc_start: 0.2666 (OUTLIER) cc_final: 0.2236 (mmmt) REVERT: s 32 LYS cc_start: -0.0095 (OUTLIER) cc_final: -0.0544 (ptpt) REVERT: t 22 ILE cc_start: 0.5702 (OUTLIER) cc_final: 0.5226 (tt) REVERT: t 73 ARG cc_start: 0.2250 (OUTLIER) cc_final: 0.1138 (tpt90) REVERT: u 17 ARG cc_start: 0.2233 (OUTLIER) cc_final: 0.1882 (mtt180) REVERT: u 21 ARG cc_start: 0.2957 (OUTLIER) cc_final: 0.2474 (ttm-80) REVERT: v 3 ARG cc_start: 0.0645 (OUTLIER) cc_final: -0.0696 (pmm-80) REVERT: v 45 LYS cc_start: 0.1261 (OUTLIER) cc_final: -0.0480 (tmtt) REVERT: v 144 MET cc_start: 0.1510 (OUTLIER) cc_final: 0.1061 (pmt) REVERT: v 165 ASP cc_start: 0.2866 (OUTLIER) cc_final: 0.2586 (t70) outliers start: 873 outliers final: 302 residues processed: 1469 average time/residue: 2.0712 time to fit residues: 4350.1526 Evaluate side-chains 957 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 384 poor density : 573 time to evaluate : 5.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 60 ARG Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 274 ARG Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 24 SER Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 109 PRO Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 161 ASN Chi-restraints excluded: chain G residue 3 ARG Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 120 ASN Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 136 GLN Chi-restraints excluded: chain H residue 144 ARG Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 66 LYS Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 51 GLU Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 64 ARG Chi-restraints excluded: chain J residue 71 ARG Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 99 SER Chi-restraints excluded: chain J residue 103 LYS Chi-restraints excluded: chain J residue 107 SER Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 39 THR Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 45 GLU Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 6 ASP Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 86 ASP Chi-restraints excluded: chain M residue 87 LYS Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 115 SER Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain N residue 52 ARG Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 73 GLU Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 51 ARG Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain O residue 90 ILE Chi-restraints excluded: chain P residue 10 LYS Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 26 ASP Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 63 ASN Chi-restraints excluded: chain P residue 67 ARG Chi-restraints excluded: chain P residue 79 ARG Chi-restraints excluded: chain P residue 98 ASP Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 14 GLU Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 65 VAL Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 79 THR Chi-restraints excluded: chain S residue 93 ILE Chi-restraints excluded: chain S residue 97 SER Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain U residue 24 SER Chi-restraints excluded: chain U residue 72 ASP Chi-restraints excluded: chain U residue 75 VAL Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain U residue 88 SER Chi-restraints excluded: chain W residue 2 LYS Chi-restraints excluded: chain W residue 14 ILE Chi-restraints excluded: chain W residue 25 LEU Chi-restraints excluded: chain W residue 47 ARG Chi-restraints excluded: chain W residue 63 GLU Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 15 ARG Chi-restraints excluded: chain X residue 18 THR Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 35 VAL Chi-restraints excluded: chain X residue 46 GLN Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 5 ILE Chi-restraints excluded: chain Y residue 38 GLU Chi-restraints excluded: chain Z residue 7 ARG Chi-restraints excluded: chain Z residue 8 THR Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 30 CYS Chi-restraints excluded: chain 1 residue 36 CYS Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 1 residue 44 LEU Chi-restraints excluded: chain 2 residue 31 VAL Chi-restraints excluded: chain 3 residue 14 VAL Chi-restraints excluded: chain 3 residue 30 SER Chi-restraints excluded: chain 3 residue 31 HIS Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 45 ARG Chi-restraints excluded: chain 3 residue 65 LYS Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain b residue 7 LYS Chi-restraints excluded: chain b residue 11 GLU Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 51 ASP Chi-restraints excluded: chain b residue 58 LYS Chi-restraints excluded: chain b residue 60 VAL Chi-restraints excluded: chain b residue 62 GLU Chi-restraints excluded: chain b residue 89 GLN Chi-restraints excluded: chain b residue 116 GLU Chi-restraints excluded: chain b residue 126 PHE Chi-restraints excluded: chain b residue 128 VAL Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 187 VAL Chi-restraints excluded: chain c residue 32 LEU Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain c residue 42 ILE Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain c residue 78 LYS Chi-restraints excluded: chain c residue 105 ILE Chi-restraints excluded: chain c residue 108 VAL Chi-restraints excluded: chain c residue 113 ARG Chi-restraints excluded: chain c residue 115 VAL Chi-restraints excluded: chain c residue 118 ASN Chi-restraints excluded: chain c residue 128 SER Chi-restraints excluded: chain c residue 165 GLU Chi-restraints excluded: chain c residue 167 TYR Chi-restraints excluded: chain c residue 174 LEU Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 197 VAL Chi-restraints excluded: chain c residue 201 ILE Chi-restraints excluded: chain d residue 10 LYS Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 51 LEU Chi-restraints excluded: chain d residue 52 ARG Chi-restraints excluded: chain d residue 58 ARG Chi-restraints excluded: chain d residue 61 TYR Chi-restraints excluded: chain d residue 71 THR Chi-restraints excluded: chain d residue 84 GLU Chi-restraints excluded: chain d residue 111 ARG Chi-restraints excluded: chain d residue 115 ASN Chi-restraints excluded: chain d residue 156 GLU Chi-restraints excluded: chain e residue 10 GLU Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 65 GLU Chi-restraints excluded: chain e residue 72 VAL Chi-restraints excluded: chain e residue 81 THR Chi-restraints excluded: chain e residue 106 ILE Chi-restraints excluded: chain e residue 141 ILE Chi-restraints excluded: chain e residue 163 GLU Chi-restraints excluded: chain f residue 20 LYS Chi-restraints excluded: chain f residue 57 ASP Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 73 THR Chi-restraints excluded: chain f residue 76 PHE Chi-restraints excluded: chain f residue 84 ASP Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 87 ILE Chi-restraints excluded: chain g residue 9 LYS Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 38 THR Chi-restraints excluded: chain g residue 41 ARG Chi-restraints excluded: chain g residue 94 GLU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain g residue 125 LEU Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 135 VAL Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 24 LYS Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 62 LEU Chi-restraints excluded: chain h residue 70 ASP Chi-restraints excluded: chain h residue 82 LYS Chi-restraints excluded: chain h residue 96 LYS Chi-restraints excluded: chain h residue 103 ILE Chi-restraints excluded: chain h residue 105 LEU Chi-restraints excluded: chain h residue 112 VAL Chi-restraints excluded: chain h residue 113 ILE Chi-restraints excluded: chain h residue 120 LYS Chi-restraints excluded: chain i residue 40 TYR Chi-restraints excluded: chain i residue 56 VAL Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 101 LYS Chi-restraints excluded: chain i residue 129 PHE Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 11 LYS Chi-restraints excluded: chain j residue 27 GLU Chi-restraints excluded: chain j residue 31 ARG Chi-restraints excluded: chain j residue 65 PHE Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain k residue 37 GLU Chi-restraints excluded: chain k residue 59 THR Chi-restraints excluded: chain k residue 64 GLN Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 97 ILE Chi-restraints excluded: chain k residue 101 GLN Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 36 THR Chi-restraints excluded: chain l residue 42 GLN Chi-restraints excluded: chain l residue 47 CYS Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 62 LEU Chi-restraints excluded: chain l residue 63 ARG Chi-restraints excluded: chain l residue 67 ARG Chi-restraints excluded: chain l residue 99 ARG Chi-restraints excluded: chain l residue 100 VAL Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain l residue 115 LEU Chi-restraints excluded: chain l residue 129 LEU Chi-restraints excluded: chain m residue 35 GLU Chi-restraints excluded: chain m residue 57 ARG Chi-restraints excluded: chain m residue 63 TYR Chi-restraints excluded: chain m residue 64 LYS Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain m residue 108 THR Chi-restraints excluded: chain n residue 3 LYS Chi-restraints excluded: chain n residue 4 THR Chi-restraints excluded: chain n residue 31 HIS Chi-restraints excluded: chain n residue 38 LYS Chi-restraints excluded: chain n residue 44 PHE Chi-restraints excluded: chain n residue 45 ARG Chi-restraints excluded: chain n residue 52 GLN Chi-restraints excluded: chain n residue 53 ILE Chi-restraints excluded: chain o residue 3 ILE Chi-restraints excluded: chain o residue 8 LYS Chi-restraints excluded: chain o residue 15 TYR Chi-restraints excluded: chain o residue 28 GLN Chi-restraints excluded: chain o residue 42 HIS Chi-restraints excluded: chain o residue 47 LYS Chi-restraints excluded: chain o residue 74 ASP Chi-restraints excluded: chain o residue 80 GLU Chi-restraints excluded: chain o residue 81 LEU Chi-restraints excluded: chain p residue 4 LYS Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 78 GLU Chi-restraints excluded: chain q residue 48 THR Chi-restraints excluded: chain q residue 51 GLU Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain q residue 76 ARG Chi-restraints excluded: chain q residue 77 LEU Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 24 THR Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 50 THR Chi-restraints excluded: chain r residue 60 LEU Chi-restraints excluded: chain s residue 28 LYS Chi-restraints excluded: chain s residue 31 ILE Chi-restraints excluded: chain s residue 32 LYS Chi-restraints excluded: chain s residue 48 THR Chi-restraints excluded: chain t residue 22 ILE Chi-restraints excluded: chain t residue 73 ARG Chi-restraints excluded: chain u residue 17 ARG Chi-restraints excluded: chain u residue 21 ARG Chi-restraints excluded: chain u residue 33 ARG Chi-restraints excluded: chain v residue 3 ARG Chi-restraints excluded: chain v residue 4 PHE Chi-restraints excluded: chain v residue 14 THR Chi-restraints excluded: chain v residue 17 ILE Chi-restraints excluded: chain v residue 28 LEU Chi-restraints excluded: chain v residue 44 VAL Chi-restraints excluded: chain v residue 45 LYS Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 57 THR Chi-restraints excluded: chain v residue 74 LEU Chi-restraints excluded: chain v residue 78 ILE Chi-restraints excluded: chain v residue 85 LEU Chi-restraints excluded: chain v residue 88 GLN Chi-restraints excluded: chain v residue 137 LYS Chi-restraints excluded: chain v residue 144 MET Chi-restraints excluded: chain v residue 150 VAL Chi-restraints excluded: chain v residue 155 LEU Chi-restraints excluded: chain v residue 165 ASP Chi-restraints excluded: chain v residue 168 THR Chi-restraints excluded: chain v residue 184 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 835 optimal weight: 20.0000 chunk 750 optimal weight: 7.9990 chunk 416 optimal weight: 0.9980 chunk 256 optimal weight: 0.8980 chunk 506 optimal weight: 2.9990 chunk 400 optimal weight: 6.9990 chunk 775 optimal weight: 9.9990 chunk 300 optimal weight: 0.9990 chunk 471 optimal weight: 8.9990 chunk 577 optimal weight: 0.9980 chunk 899 optimal weight: 9.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 114 GLN C 153 GLN C 199 GLN C 226 ASN C 230 HIS C 232 HIS D 33 ASN D 47 ASN D 76 HIS E 75 GLN E 162 ASN E 174 GLN F 45 GLN F 135 GLN G 74 ASN G 97 GLN H 3 GLN H 24 GLN I 4 GLN J 54 GLN ** K 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 46 GLN K 71 HIS M 39 HIS M 43 GLN M 48 ASN O 44 GLN O 81 ASN P 18 GLN Q 61 ASN Q 95 ASN R 37 GLN R 54 ASN ** R 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 ASN S 67 ASN T 88 HIS U 37 GLN W 36 GLN X 19 GLN Y 3 GLN 1 25 ASN 1 40 ASN 2 7 GLN 2 17 HIS 3 35 ASN 3 40 GLN 3 43 GLN 3 60 GLN b 24 ASN b 103 ASN c 151 GLN c 166 GLN d 55 GLN d 67 GLN d 85 ASN ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 118 HIS d 137 GLN f 27 ASN f 53 ASN f 70 ASN f 77 GLN ** g 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 130 ASN g 148 ASN h 22 HIS i 16 ASN i 29 ASN i 62 ASN ** i 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 128 GLN j 15 HIS k 64 GLN l 39 ASN l 85 HIS l 86 ASN n 11 GLN o 28 GLN ** p 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 49 HIS s 22 GLN s 43 ASN ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 21 ASN ** t 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 62 GLN t 64 ASN t 69 ASN v 88 GLN v 152 GLN v 186 GLN Total number of N/Q/H flips: 84 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5928 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.625 152951 Z= 0.288 Angle : 0.931 62.239 229118 Z= 0.452 Chirality : 0.053 2.102 29467 Planarity : 0.006 0.074 12075 Dihedral : 26.531 179.949 77551 Min Nonbonded Distance : 1.409 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 11.55 % Allowed : 22.68 % Favored : 65.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.10), residues: 5487 helix: -2.09 (0.11), residues: 1540 sheet: -1.52 (0.16), residues: 965 loop : -2.46 (0.10), residues: 2982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 61 HIS 0.007 0.001 HIS Z 40 PHE 0.029 0.002 PHE g 47 TYR 0.027 0.002 TYR d 61 ARG 0.009 0.001 ARG J 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10974 Ramachandran restraints generated. 5487 Oldfield, 0 Emsley, 5487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10974 Ramachandran restraints generated. 5487 Oldfield, 0 Emsley, 5487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1188 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 513 poor density : 675 time to evaluate : 5.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 100 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7123 (mp0) REVERT: D 159 ASP cc_start: 0.7182 (OUTLIER) cc_final: 0.6927 (m-30) REVERT: E 200 LYS cc_start: 0.8417 (mmtm) cc_final: 0.8054 (mtmm) REVERT: F 17 MET cc_start: 0.4127 (mmm) cc_final: 0.3821 (mmp) REVERT: F 81 GLU cc_start: 0.4422 (mm-30) cc_final: 0.4144 (mm-30) REVERT: F 94 GLU cc_start: 0.6481 (OUTLIER) cc_final: 0.6256 (tp30) REVERT: F 110 ARG cc_start: 0.3907 (OUTLIER) cc_final: 0.3662 (mpp80) REVERT: G 2 SER cc_start: 0.5543 (p) cc_final: 0.4949 (t) REVERT: G 30 LYS cc_start: 0.4166 (OUTLIER) cc_final: 0.3819 (mttt) REVERT: G 41 MET cc_start: 0.5518 (mpp) cc_final: 0.5313 (mmt) REVERT: G 158 LYS cc_start: 0.5105 (mttt) cc_final: 0.4565 (mmtt) REVERT: G 163 ARG cc_start: 0.6323 (ptp-170) cc_final: 0.6116 (ptm160) REVERT: G 167 GLU cc_start: 0.5790 (tt0) cc_final: 0.5563 (tt0) REVERT: H 12 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8737 (mm) REVERT: H 144 ARG cc_start: 0.7382 (mpt180) cc_final: 0.7090 (mmt-90) REVERT: J 51 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8438 (mt-10) REVERT: J 71 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.6541 (ptm160) REVERT: J 73 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7122 (mm-30) REVERT: L 45 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7174 (mt-10) REVERT: M 86 ASP cc_start: 0.4033 (OUTLIER) cc_final: 0.3701 (m-30) REVERT: M 87 LYS cc_start: 0.3642 (OUTLIER) cc_final: 0.2427 (pmtt) REVERT: N 91 ARG cc_start: 0.8139 (mmt180) cc_final: 0.7914 (mpt180) REVERT: O 16 LYS cc_start: 0.8308 (ptpt) cc_final: 0.8060 (pttt) REVERT: O 74 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.7880 (ttt) REVERT: O 108 GLN cc_start: 0.8251 (tt0) cc_final: 0.8037 (tt0) REVERT: P 26 ASP cc_start: 0.6564 (OUTLIER) cc_final: 0.6264 (p0) REVERT: Q 11 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7951 (mmm160) REVERT: R 64 ARG cc_start: 0.7300 (tpp-160) cc_final: 0.6967 (tpp-160) REVERT: S 3 ILE cc_start: 0.6314 (pt) cc_final: 0.5825 (pt) REVERT: S 56 ILE cc_start: 0.6170 (OUTLIER) cc_final: 0.5952 (pp) REVERT: T 7 ILE cc_start: 0.8112 (mp) cc_final: 0.7854 (mp) REVERT: W 2 LYS cc_start: 0.1471 (OUTLIER) cc_final: 0.1206 (ttpp) REVERT: X 40 ASN cc_start: 0.7122 (m-40) cc_final: 0.6894 (m-40) REVERT: 2 41 LYS cc_start: 0.8002 (tmtm) cc_final: 0.7795 (tptt) REVERT: 3 48 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7515 (mmm-85) REVERT: b 11 GLU cc_start: 0.3154 (OUTLIER) cc_final: 0.2937 (tm-30) REVERT: b 22 ARG cc_start: 0.2584 (mmm-85) cc_final: 0.2051 (mtm110) REVERT: b 59 GLN cc_start: 0.3841 (OUTLIER) cc_final: 0.3403 (mt0) REVERT: b 62 GLU cc_start: 0.2176 (OUTLIER) cc_final: 0.1930 (tm-30) REVERT: b 83 GLU cc_start: 0.2296 (OUTLIER) cc_final: 0.1993 (mp0) REVERT: b 95 ARG cc_start: 0.1496 (OUTLIER) cc_final: 0.0858 (tmm160) REVERT: b 126 PHE cc_start: 0.0780 (OUTLIER) cc_final: 0.0558 (p90) REVERT: b 154 MET cc_start: 0.1014 (ttt) cc_final: 0.0776 (tmt) REVERT: b 168 LYS cc_start: 0.4340 (mttt) cc_final: 0.2834 (tttt) REVERT: b 170 ARG cc_start: 0.3585 (tpt170) cc_final: 0.3364 (tpm-80) REVERT: b 187 VAL cc_start: 0.1700 (OUTLIER) cc_final: 0.1419 (t) REVERT: b 213 LEU cc_start: 0.2447 (OUTLIER) cc_final: 0.2022 (tp) REVERT: b 214 THR cc_start: 0.1013 (OUTLIER) cc_final: 0.0765 (m) REVERT: c 57 GLU cc_start: 0.1514 (OUTLIER) cc_final: 0.0902 (mm-30) REVERT: c 105 ILE cc_start: 0.1839 (OUTLIER) cc_final: 0.1507 (pp) REVERT: c 163 ARG cc_start: 0.2741 (mtm110) cc_final: 0.1898 (mpt-90) REVERT: c 165 GLU cc_start: 0.2193 (OUTLIER) cc_final: 0.1315 (mt-10) REVERT: d 5 ARG cc_start: 0.1847 (mtm110) cc_final: 0.0453 (tpt170) REVERT: d 85 ASN cc_start: 0.4209 (OUTLIER) cc_final: 0.3858 (m110) REVERT: d 87 MET cc_start: 0.1696 (mmm) cc_final: 0.0912 (mpt) REVERT: d 89 LEU cc_start: 0.1352 (OUTLIER) cc_final: 0.1018 (mm) REVERT: d 139 ILE cc_start: 0.1938 (OUTLIER) cc_final: 0.1182 (mp) REVERT: d 153 GLU cc_start: 0.1645 (OUTLIER) cc_final: 0.0904 (tp30) REVERT: e 10 GLU cc_start: 0.1935 (OUTLIER) cc_final: 0.0987 (mm-30) REVERT: e 163 GLU cc_start: 0.1423 (OUTLIER) cc_final: 0.0860 (mm-30) REVERT: g 10 ARG cc_start: 0.1353 (mtm180) cc_final: -0.0021 (ptm160) REVERT: g 36 ARG cc_start: 0.3434 (tpp80) cc_final: 0.2869 (mmt180) REVERT: g 38 THR cc_start: 0.1268 (OUTLIER) cc_final: 0.1006 (p) REVERT: h 3 MET cc_start: 0.2812 (OUTLIER) cc_final: 0.2170 (tpt) REVERT: h 39 ILE cc_start: 0.2637 (OUTLIER) cc_final: 0.2201 (mp) REVERT: h 82 LYS cc_start: 0.3808 (OUTLIER) cc_final: 0.3445 (tppt) REVERT: i 20 ARG cc_start: 0.2337 (pmt170) cc_final: 0.2027 (pmt170) REVERT: i 35 ARG cc_start: 0.2257 (ptm160) cc_final: 0.1633 (tpt-90) REVERT: i 40 TYR cc_start: 0.1299 (OUTLIER) cc_final: 0.1069 (t80) REVERT: i 46 LEU cc_start: 0.2018 (OUTLIER) cc_final: 0.1430 (tt) REVERT: i 101 LYS cc_start: 0.0437 (OUTLIER) cc_final: 0.0222 (tptm) REVERT: i 112 MET cc_start: 0.3054 (pmm) cc_final: 0.2637 (tpp) REVERT: j 10 LEU cc_start: 0.2380 (OUTLIER) cc_final: 0.2115 (tt) REVERT: j 11 LYS cc_start: 0.3452 (OUTLIER) cc_final: 0.2119 (tppp) REVERT: j 65 PHE cc_start: 0.0822 (OUTLIER) cc_final: 0.0502 (m-80) REVERT: j 88 MET cc_start: 0.3222 (OUTLIER) cc_final: 0.2221 (ttm) REVERT: l 3 THR cc_start: 0.3102 (OUTLIER) cc_final: 0.2569 (p) REVERT: l 9 ARG cc_start: 0.1740 (ttp-170) cc_final: 0.0743 (tmm-80) REVERT: l 10 LYS cc_start: 0.4848 (tptm) cc_final: 0.4633 (ttpt) REVERT: l 12 ARG cc_start: 0.3559 (mmt-90) cc_final: 0.3229 (tpp-160) REVERT: l 18 LYS cc_start: 0.4034 (ttmt) cc_final: 0.3821 (tttm) REVERT: l 67 ARG cc_start: 0.4438 (OUTLIER) cc_final: 0.3853 (tpp80) REVERT: l 99 ARG cc_start: 0.3632 (OUTLIER) cc_final: 0.3422 (ttm-80) REVERT: n 31 HIS cc_start: -0.0119 (OUTLIER) cc_final: -0.1216 (m170) REVERT: n 52 GLN cc_start: 0.3166 (OUTLIER) cc_final: 0.1823 (tp-100) REVERT: o 3 ILE cc_start: 0.2184 (OUTLIER) cc_final: 0.1581 (tp) REVERT: o 8 LYS cc_start: 0.1582 (OUTLIER) cc_final: 0.1276 (tmtt) REVERT: o 15 TYR cc_start: 0.2173 (OUTLIER) cc_final: 0.0740 (m-10) REVERT: o 28 GLN cc_start: 0.2712 (OUTLIER) cc_final: 0.2040 (pt0) REVERT: o 42 HIS cc_start: 0.2484 (OUTLIER) cc_final: 0.2012 (t-170) REVERT: o 47 LYS cc_start: 0.2523 (OUTLIER) cc_final: 0.2057 (ttpt) REVERT: q 14 VAL cc_start: 0.1705 (OUTLIER) cc_final: 0.1314 (p) REVERT: q 45 LYS cc_start: 0.3524 (mtmp) cc_final: 0.3138 (mmmt) REVERT: q 51 GLU cc_start: 0.2143 (OUTLIER) cc_final: 0.1331 (mm-30) REVERT: q 77 LEU cc_start: 0.3024 (OUTLIER) cc_final: 0.2758 (mm) REVERT: r 70 MET cc_start: 0.1822 (mmt) cc_final: 0.0268 (ptt) REVERT: t 16 LYS cc_start: 0.3133 (ptmt) cc_final: 0.2887 (ptpp) REVERT: t 73 ARG cc_start: 0.2129 (OUTLIER) cc_final: 0.0889 (mtp-110) REVERT: u 21 ARG cc_start: 0.2905 (OUTLIER) cc_final: 0.2474 (ttm-80) REVERT: v 3 ARG cc_start: 0.1113 (OUTLIER) cc_final: -0.0602 (pmm-80) REVERT: v 4 PHE cc_start: -0.0319 (OUTLIER) cc_final: -0.0729 (m-10) REVERT: v 45 LYS cc_start: 0.1526 (OUTLIER) cc_final: -0.0352 (tmtt) REVERT: v 144 MET cc_start: 0.1227 (OUTLIER) cc_final: 0.0898 (pmt) REVERT: v 151 LEU cc_start: 0.0215 (OUTLIER) cc_final: -0.0279 (mm) REVERT: v 155 LEU cc_start: 0.0960 (OUTLIER) cc_final: 0.0424 (tt) outliers start: 513 outliers final: 192 residues processed: 1086 average time/residue: 2.1079 time to fit residues: 3245.8791 Evaluate side-chains 824 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 564 time to evaluate : 5.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 110 ARG Chi-restraints excluded: chain F residue 120 LYS Chi-restraints excluded: chain G residue 3 ARG Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 120 ASN Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 114 ARG Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 51 GLU Chi-restraints excluded: chain J residue 64 ARG Chi-restraints excluded: chain J residue 71 ARG Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain L residue 45 GLU Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain M residue 6 ASP Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 86 ASP Chi-restraints excluded: chain M residue 87 LYS Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 115 SER Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 84 GLU Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 74 MET Chi-restraints excluded: chain O residue 90 ILE Chi-restraints excluded: chain P residue 26 ASP Chi-restraints excluded: chain P residue 63 ASN Chi-restraints excluded: chain P residue 67 ARG Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 93 ILE Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain U residue 72 ASP Chi-restraints excluded: chain U residue 75 VAL Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain W residue 2 LYS Chi-restraints excluded: chain W residue 25 LEU Chi-restraints excluded: chain W residue 63 GLU Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain Y residue 5 ILE Chi-restraints excluded: chain Z residue 7 ARG Chi-restraints excluded: chain Z residue 8 THR Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 30 CYS Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 2 residue 31 VAL Chi-restraints excluded: chain 3 residue 30 SER Chi-restraints excluded: chain 3 residue 31 HIS Chi-restraints excluded: chain 3 residue 48 ARG Chi-restraints excluded: chain 4 residue 2 LYS Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 11 GLU Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 59 GLN Chi-restraints excluded: chain b residue 60 VAL Chi-restraints excluded: chain b residue 62 GLU Chi-restraints excluded: chain b residue 83 GLU Chi-restraints excluded: chain b residue 95 ARG Chi-restraints excluded: chain b residue 100 LEU Chi-restraints excluded: chain b residue 101 LEU Chi-restraints excluded: chain b residue 116 GLU Chi-restraints excluded: chain b residue 126 PHE Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 187 VAL Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain b residue 214 THR Chi-restraints excluded: chain b residue 221 ILE Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain c residue 78 LYS Chi-restraints excluded: chain c residue 93 LEU Chi-restraints excluded: chain c residue 94 THR Chi-restraints excluded: chain c residue 105 ILE Chi-restraints excluded: chain c residue 113 ARG Chi-restraints excluded: chain c residue 115 VAL Chi-restraints excluded: chain c residue 118 ASN Chi-restraints excluded: chain c residue 160 ASP Chi-restraints excluded: chain c residue 165 GLU Chi-restraints excluded: chain c residue 167 TYR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 197 VAL Chi-restraints excluded: chain c residue 201 ILE Chi-restraints excluded: chain d residue 10 LYS Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 71 THR Chi-restraints excluded: chain d residue 85 ASN Chi-restraints excluded: chain d residue 89 LEU Chi-restraints excluded: chain d residue 103 LEU Chi-restraints excluded: chain d residue 111 ARG Chi-restraints excluded: chain d residue 139 ILE Chi-restraints excluded: chain d residue 153 GLU Chi-restraints excluded: chain e residue 10 GLU Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 72 VAL Chi-restraints excluded: chain e residue 141 ILE Chi-restraints excluded: chain e residue 163 GLU Chi-restraints excluded: chain f residue 14 ILE Chi-restraints excluded: chain f residue 20 LYS Chi-restraints excluded: chain f residue 57 ASP Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 73 THR Chi-restraints excluded: chain f residue 74 ASP Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 87 ILE Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 38 THR Chi-restraints excluded: chain g residue 64 GLU Chi-restraints excluded: chain g residue 94 GLU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 137 LYS Chi-restraints excluded: chain g residue 144 MET Chi-restraints excluded: chain h residue 3 MET Chi-restraints excluded: chain h residue 24 LYS Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 70 ASP Chi-restraints excluded: chain h residue 82 LYS Chi-restraints excluded: chain h residue 96 LYS Chi-restraints excluded: chain h residue 112 VAL Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain i residue 17 SER Chi-restraints excluded: chain i residue 40 TYR Chi-restraints excluded: chain i residue 46 LEU Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 101 LYS Chi-restraints excluded: chain i residue 129 PHE Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 11 LYS Chi-restraints excluded: chain j residue 27 GLU Chi-restraints excluded: chain j residue 65 PHE Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain k residue 59 THR Chi-restraints excluded: chain k residue 69 THR Chi-restraints excluded: chain k residue 101 GLN Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 36 THR Chi-restraints excluded: chain l residue 42 GLN Chi-restraints excluded: chain l residue 47 CYS Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 62 LEU Chi-restraints excluded: chain l residue 67 ARG Chi-restraints excluded: chain l residue 99 ARG Chi-restraints excluded: chain l residue 100 VAL Chi-restraints excluded: chain l residue 115 LEU Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain m residue 35 GLU Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 64 LYS Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain m residue 108 THR Chi-restraints excluded: chain n residue 4 THR Chi-restraints excluded: chain n residue 31 HIS Chi-restraints excluded: chain n residue 38 LYS Chi-restraints excluded: chain n residue 44 PHE Chi-restraints excluded: chain n residue 52 GLN Chi-restraints excluded: chain o residue 3 ILE Chi-restraints excluded: chain o residue 8 LYS Chi-restraints excluded: chain o residue 11 ILE Chi-restraints excluded: chain o residue 15 TYR Chi-restraints excluded: chain o residue 17 VAL Chi-restraints excluded: chain o residue 28 GLN Chi-restraints excluded: chain o residue 42 HIS Chi-restraints excluded: chain o residue 47 LYS Chi-restraints excluded: chain o residue 53 ARG Chi-restraints excluded: chain o residue 74 ASP Chi-restraints excluded: chain o residue 81 LEU Chi-restraints excluded: chain p residue 54 GLU Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain q residue 48 THR Chi-restraints excluded: chain q residue 51 GLU Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain q residue 76 ARG Chi-restraints excluded: chain q residue 77 LEU Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 50 THR Chi-restraints excluded: chain r residue 75 TYR Chi-restraints excluded: chain s residue 31 ILE Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain t residue 73 ARG Chi-restraints excluded: chain u residue 21 ARG Chi-restraints excluded: chain v residue 3 ARG Chi-restraints excluded: chain v residue 4 PHE Chi-restraints excluded: chain v residue 28 LEU Chi-restraints excluded: chain v residue 44 VAL Chi-restraints excluded: chain v residue 45 LYS Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 57 THR Chi-restraints excluded: chain v residue 74 LEU Chi-restraints excluded: chain v residue 89 VAL Chi-restraints excluded: chain v residue 94 THR Chi-restraints excluded: chain v residue 137 LYS Chi-restraints excluded: chain v residue 144 MET Chi-restraints excluded: chain v residue 151 LEU Chi-restraints excluded: chain v residue 155 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 499 optimal weight: 5.9990 chunk 279 optimal weight: 4.9990 chunk 748 optimal weight: 40.0000 chunk 612 optimal weight: 30.0000 chunk 248 optimal weight: 9.9990 chunk 900 optimal weight: 10.0000 chunk 972 optimal weight: 0.5980 chunk 802 optimal weight: 20.0000 chunk 893 optimal weight: 0.8980 chunk 307 optimal weight: 7.9990 chunk 722 optimal weight: 40.0000 overall best weight: 4.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 133 GLN C 199 GLN E 174 GLN G 147 ASN H 3 GLN I 3 GLN J 17 ASN J 70 ASN K 25 ASN L 68 ASN P 63 ASN Q 95 ASN R 73 ASN S 39 ASN ** T 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 78 GLN ** W 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 31 GLN 1 25 ASN 1 40 ASN 3 43 GLN b 94 GLN b 203 ASN ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 27 ASN f 69 ASN ** g 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 28 ASN ** i 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 101 GLN ** p 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 57 HIS ** s 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 33 ASN v 158 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6136 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.602 152951 Z= 0.431 Angle : 1.098 62.983 229118 Z= 0.526 Chirality : 0.060 2.161 29467 Planarity : 0.006 0.076 12075 Dihedral : 26.436 179.948 77154 Min Nonbonded Distance : 1.511 Molprobity Statistics. All-atom Clashscore : 20.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.51 % Favored : 91.45 % Rotamer: Outliers : 10.16 % Allowed : 24.57 % Favored : 65.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.07 % 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: -2.80 (0.10), residues: 5487 helix: -1.54 (0.12), residues: 1548 sheet: -1.16 (0.16), residues: 994 loop : -2.32 (0.10), residues: 2945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 250 HIS 0.012 0.002 HIS p 72 PHE 0.030 0.002 PHE g 47 TYR 0.026 0.002 TYR H 126 ARG 0.009 0.001 ARG Q 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10974 Ramachandran restraints generated. 5487 Oldfield, 0 Emsley, 5487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10974 Ramachandran restraints generated. 5487 Oldfield, 0 Emsley, 5487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1022 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 451 poor density : 571 time to evaluate : 5.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 71 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.8001 (mtpp) REVERT: C 274 ARG cc_start: 0.7214 (tpp80) cc_final: 0.6998 (tpp80) REVERT: D 100 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7133 (mp0) REVERT: D 159 ASP cc_start: 0.7381 (OUTLIER) cc_final: 0.7073 (m-30) REVERT: E 157 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7507 (tt0) REVERT: E 200 LYS cc_start: 0.8530 (mmtm) cc_final: 0.8106 (mtmm) REVERT: F 17 MET cc_start: 0.3900 (mmm) cc_final: 0.3585 (mmp) REVERT: F 81 GLU cc_start: 0.4216 (mm-30) cc_final: 0.3987 (mm-30) REVERT: F 110 ARG cc_start: 0.3937 (OUTLIER) cc_final: 0.3634 (mpp80) REVERT: G 2 SER cc_start: 0.5567 (p) cc_final: 0.4944 (t) REVERT: G 30 LYS cc_start: 0.4131 (OUTLIER) cc_final: 0.3756 (mttt) REVERT: G 87 LEU cc_start: 0.5400 (OUTLIER) cc_final: 0.5049 (pt) REVERT: H 12 ILE cc_start: 0.9111 (OUTLIER) cc_final: 0.8828 (mm) REVERT: H 114 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8345 (ptp-170) REVERT: I 4 GLN cc_start: 0.8066 (tt0) cc_final: 0.7653 (tt0) REVERT: I 5 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8122 (mm-30) REVERT: M 87 LYS cc_start: 0.3828 (OUTLIER) cc_final: 0.2805 (pmtt) REVERT: M 115 SER cc_start: 0.7305 (OUTLIER) cc_final: 0.6921 (p) REVERT: O 19 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8305 (tptt) REVERT: O 108 GLN cc_start: 0.8336 (tt0) cc_final: 0.8058 (tt0) REVERT: P 26 ASP cc_start: 0.6792 (OUTLIER) cc_final: 0.6275 (p0) REVERT: Q 11 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7972 (mmm160) REVERT: R 64 ARG cc_start: 0.7269 (tpp-160) cc_final: 0.7012 (tpp-160) REVERT: S 56 ILE cc_start: 0.6652 (OUTLIER) cc_final: 0.6376 (pp) REVERT: S 93 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7919 (pt) REVERT: S 95 LYS cc_start: 0.7540 (OUTLIER) cc_final: 0.7311 (mmtm) REVERT: T 7 ILE cc_start: 0.8222 (mp) cc_final: 0.7973 (mp) REVERT: W 2 LYS cc_start: 0.1802 (OUTLIER) cc_final: 0.1492 (ttpp) REVERT: 2 41 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7663 (tttm) REVERT: 3 59 LYS cc_start: 0.8265 (ttpp) cc_final: 0.7703 (ttmm) REVERT: 4 20 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.7922 (mppt) REVERT: b 6 MET cc_start: 0.3277 (OUTLIER) cc_final: 0.2795 (mpt) REVERT: b 11 GLU cc_start: 0.3285 (OUTLIER) cc_final: 0.2904 (tm-30) REVERT: b 22 ARG cc_start: 0.2737 (mmm-85) cc_final: 0.2126 (mtm110) REVERT: b 95 ARG cc_start: 0.1531 (OUTLIER) cc_final: 0.0871 (tmm160) REVERT: b 143 ARG cc_start: 0.1760 (ttm170) cc_final: 0.0990 (mmm-85) REVERT: b 168 LYS cc_start: 0.4564 (mttt) cc_final: 0.3132 (tttt) REVERT: b 170 ARG cc_start: 0.3532 (tpt170) cc_final: 0.3291 (tpm-80) REVERT: b 177 ARG cc_start: 0.2605 (mmt180) cc_final: 0.2067 (mpt180) REVERT: b 199 VAL cc_start: 0.1555 (OUTLIER) cc_final: 0.1289 (m) REVERT: b 208 ARG cc_start: 0.3026 (mtp85) cc_final: 0.2256 (ptm-80) REVERT: b 213 LEU cc_start: 0.2181 (OUTLIER) cc_final: 0.1846 (tp) REVERT: c 3 GLN cc_start: 0.1508 (OUTLIER) cc_final: -0.0641 (pp30) REVERT: c 45 GLU cc_start: 0.2569 (OUTLIER) cc_final: 0.2361 (pt0) REVERT: c 57 GLU cc_start: 0.1495 (OUTLIER) cc_final: 0.0867 (mm-30) REVERT: c 78 LYS cc_start: 0.3036 (OUTLIER) cc_final: 0.2685 (mtpp) REVERT: c 105 ILE cc_start: 0.1868 (OUTLIER) cc_final: 0.1523 (pp) REVERT: c 123 LEU cc_start: 0.2412 (OUTLIER) cc_final: 0.2199 (mt) REVERT: c 163 ARG cc_start: 0.2767 (mtm110) cc_final: 0.1942 (mpt180) REVERT: d 5 ARG cc_start: 0.1712 (mtm110) cc_final: 0.0351 (mmm-85) REVERT: d 26 LEU cc_start: 0.3527 (OUTLIER) cc_final: 0.2916 (pp) REVERT: d 35 GLN cc_start: 0.1664 (OUTLIER) cc_final: 0.0920 (tm-30) REVERT: d 65 GLU cc_start: 0.3023 (tt0) cc_final: 0.2217 (tt0) REVERT: d 87 MET cc_start: 0.1588 (mmm) cc_final: 0.0961 (mpt) REVERT: d 89 LEU cc_start: 0.1331 (OUTLIER) cc_final: 0.0714 (mp) REVERT: d 153 GLU cc_start: 0.1743 (OUTLIER) cc_final: 0.1049 (tp30) REVERT: d 156 GLU cc_start: 0.2080 (OUTLIER) cc_final: 0.1774 (mm-30) REVERT: e 10 GLU cc_start: 0.2084 (OUTLIER) cc_final: 0.1168 (mm-30) REVERT: e 163 GLU cc_start: 0.1475 (OUTLIER) cc_final: 0.0658 (pt0) REVERT: g 10 ARG cc_start: 0.1644 (mtm180) cc_final: 0.0434 (ptm-80) REVERT: g 38 THR cc_start: 0.1470 (OUTLIER) cc_final: 0.1132 (p) REVERT: h 3 MET cc_start: 0.3194 (ppp) cc_final: 0.2328 (tpt) REVERT: h 39 ILE cc_start: 0.2135 (OUTLIER) cc_final: 0.1814 (mm) REVERT: h 82 LYS cc_start: 0.3713 (OUTLIER) cc_final: 0.3365 (mmmt) REVERT: h 96 LYS cc_start: 0.1751 (OUTLIER) cc_final: 0.1367 (pttm) REVERT: h 105 LEU cc_start: 0.1273 (OUTLIER) cc_final: 0.1031 (mm) REVERT: i 20 ARG cc_start: 0.2430 (OUTLIER) cc_final: 0.2187 (pmt170) REVERT: i 35 ARG cc_start: 0.2366 (ptm160) cc_final: 0.1649 (tpt-90) REVERT: i 40 TYR cc_start: 0.1387 (OUTLIER) cc_final: 0.1173 (t80) REVERT: i 46 LEU cc_start: 0.1883 (OUTLIER) cc_final: 0.1324 (tt) REVERT: j 11 LYS cc_start: 0.3514 (OUTLIER) cc_final: 0.2479 (tppp) REVERT: j 88 MET cc_start: 0.2912 (OUTLIER) cc_final: 0.2045 (ttm) REVERT: l 3 THR cc_start: 0.2849 (OUTLIER) cc_final: 0.2349 (p) REVERT: l 9 ARG cc_start: 0.1994 (ttp-170) cc_final: 0.0590 (tmm-80) REVERT: l 12 ARG cc_start: 0.3627 (mmt-90) cc_final: 0.3358 (tpp-160) REVERT: l 33 LYS cc_start: 0.5619 (mppt) cc_final: 0.4983 (ptmt) REVERT: l 67 ARG cc_start: 0.4402 (OUTLIER) cc_final: 0.3811 (tpp80) REVERT: l 99 ARG cc_start: 0.3870 (OUTLIER) cc_final: 0.3557 (ttm-80) REVERT: m 74 ASN cc_start: 0.3246 (OUTLIER) cc_final: 0.2920 (t0) REVERT: n 31 HIS cc_start: 0.0462 (OUTLIER) cc_final: -0.1275 (m170) REVERT: n 52 GLN cc_start: 0.3718 (OUTLIER) cc_final: 0.2200 (tm-30) REVERT: o 3 ILE cc_start: 0.2247 (OUTLIER) cc_final: 0.1627 (tp) REVERT: o 15 TYR cc_start: 0.2094 (OUTLIER) cc_final: 0.0908 (m-10) REVERT: o 28 GLN cc_start: 0.1854 (OUTLIER) cc_final: 0.1451 (pt0) REVERT: o 47 LYS cc_start: 0.2743 (OUTLIER) cc_final: 0.2159 (ttpt) REVERT: q 8 LYS cc_start: 0.1915 (OUTLIER) cc_final: 0.1335 (mmtm) REVERT: q 45 LYS cc_start: 0.3563 (mtmp) cc_final: 0.3187 (mmmt) REVERT: r 70 MET cc_start: 0.1642 (mmt) cc_final: 0.0884 (mpp) REVERT: t 73 ARG cc_start: 0.2308 (OUTLIER) cc_final: 0.1110 (ttp-170) REVERT: u 18 ARG cc_start: 0.1957 (OUTLIER) cc_final: 0.1461 (tmm160) REVERT: v 3 ARG cc_start: 0.1098 (OUTLIER) cc_final: -0.0587 (pmm-80) REVERT: v 4 PHE cc_start: -0.1213 (OUTLIER) cc_final: -0.1532 (m-10) REVERT: v 37 ASN cc_start: 0.0771 (OUTLIER) cc_final: 0.0470 (m-40) REVERT: v 45 LYS cc_start: 0.1217 (OUTLIER) cc_final: -0.0805 (tmtt) REVERT: v 144 MET cc_start: 0.1640 (OUTLIER) cc_final: 0.1290 (pmt) REVERT: v 184 LEU cc_start: 0.1876 (OUTLIER) cc_final: 0.1571 (mm) outliers start: 451 outliers final: 245 residues processed: 942 average time/residue: 2.1666 time to fit residues: 2891.8774 Evaluate side-chains 859 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 313 poor density : 546 time to evaluate : 5.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 71 LYS Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 3 ASN Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 157 GLU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 24 SER Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 110 ARG Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain G residue 3 ARG Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 39 GLU Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 120 ASN Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 114 ARG Chi-restraints excluded: chain I residue 5 GLU Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 59 LYS Chi-restraints excluded: chain I residue 116 SER Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 64 ARG Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 82 ARG Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain L residue 45 GLU Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain M residue 6 ASP Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 87 LYS Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 115 SER Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 84 GLU Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 19 LYS Chi-restraints excluded: chain O residue 74 MET Chi-restraints excluded: chain O residue 90 ILE Chi-restraints excluded: chain P residue 26 ASP Chi-restraints excluded: chain P residue 36 ASP Chi-restraints excluded: chain P residue 63 ASN Chi-restraints excluded: chain P residue 67 ARG Chi-restraints excluded: chain Q residue 4 LYS Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 14 GLU Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain R residue 28 ASP Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 26 THR Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 93 ILE Chi-restraints excluded: chain S residue 95 LYS Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 43 VAL Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain U residue 72 ASP Chi-restraints excluded: chain U residue 75 VAL Chi-restraints excluded: chain W residue 2 LYS Chi-restraints excluded: chain W residue 14 ILE Chi-restraints excluded: chain W residue 25 LEU Chi-restraints excluded: chain W residue 63 GLU Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain Y residue 5 ILE Chi-restraints excluded: chain Z residue 7 ARG Chi-restraints excluded: chain Z residue 8 THR Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 28 THR Chi-restraints excluded: chain Z residue 30 CYS Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 2 residue 31 VAL Chi-restraints excluded: chain 2 residue 41 LYS Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 3 residue 14 VAL Chi-restraints excluded: chain 3 residue 31 HIS Chi-restraints excluded: chain 3 residue 55 MET Chi-restraints excluded: chain 4 residue 2 LYS Chi-restraints excluded: chain 4 residue 20 LYS Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 11 GLU Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 60 VAL Chi-restraints excluded: chain b residue 89 GLN Chi-restraints excluded: chain b residue 95 ARG Chi-restraints excluded: chain b residue 101 LEU Chi-restraints excluded: chain b residue 116 GLU Chi-restraints excluded: chain b residue 128 VAL Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 187 VAL Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain b residue 221 ILE Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain c residue 78 LYS Chi-restraints excluded: chain c residue 94 THR Chi-restraints excluded: chain c residue 105 ILE Chi-restraints excluded: chain c residue 113 ARG Chi-restraints excluded: chain c residue 118 ASN Chi-restraints excluded: chain c residue 123 LEU Chi-restraints excluded: chain c residue 160 ASP Chi-restraints excluded: chain c residue 167 TYR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 197 VAL Chi-restraints excluded: chain c residue 201 ILE Chi-restraints excluded: chain d residue 10 LYS Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 35 GLN Chi-restraints excluded: chain d residue 71 THR Chi-restraints excluded: chain d residue 89 LEU Chi-restraints excluded: chain d residue 103 LEU Chi-restraints excluded: chain d residue 111 ARG Chi-restraints excluded: chain d residue 139 ILE Chi-restraints excluded: chain d residue 153 GLU Chi-restraints excluded: chain d residue 156 GLU Chi-restraints excluded: chain e residue 10 GLU Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 68 LYS Chi-restraints excluded: chain e residue 72 VAL Chi-restraints excluded: chain e residue 106 ILE Chi-restraints excluded: chain e residue 141 ILE Chi-restraints excluded: chain e residue 163 GLU Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 14 ILE Chi-restraints excluded: chain f residue 20 LYS Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 87 ILE Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 38 THR Chi-restraints excluded: chain g residue 48 ASP Chi-restraints excluded: chain g residue 59 LEU Chi-restraints excluded: chain g residue 64 GLU Chi-restraints excluded: chain g residue 70 MET Chi-restraints excluded: chain g residue 94 GLU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 137 LYS Chi-restraints excluded: chain g residue 144 MET Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 24 LYS Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 70 ASP Chi-restraints excluded: chain h residue 82 LYS Chi-restraints excluded: chain h residue 96 LYS Chi-restraints excluded: chain h residue 105 LEU Chi-restraints excluded: chain h residue 113 ILE Chi-restraints excluded: chain i residue 17 SER Chi-restraints excluded: chain i residue 20 ARG Chi-restraints excluded: chain i residue 40 TYR Chi-restraints excluded: chain i residue 46 LEU Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 129 PHE Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 11 LYS Chi-restraints excluded: chain j residue 27 GLU Chi-restraints excluded: chain j residue 64 GLN Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain k residue 59 THR Chi-restraints excluded: chain k residue 94 GLU Chi-restraints excluded: chain k residue 100 LEU Chi-restraints excluded: chain k residue 101 GLN Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 36 THR Chi-restraints excluded: chain l residue 42 GLN Chi-restraints excluded: chain l residue 47 CYS Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 62 LEU Chi-restraints excluded: chain l residue 67 ARG Chi-restraints excluded: chain l residue 73 ASN Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain l residue 99 ARG Chi-restraints excluded: chain l residue 100 VAL Chi-restraints excluded: chain l residue 115 LEU Chi-restraints excluded: chain m residue 13 LYS Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain m residue 35 GLU Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 74 ASN Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain m residue 108 THR Chi-restraints excluded: chain n residue 4 THR Chi-restraints excluded: chain n residue 31 HIS Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 38 LYS Chi-restraints excluded: chain n residue 50 LYS Chi-restraints excluded: chain n residue 52 GLN Chi-restraints excluded: chain o residue 3 ILE Chi-restraints excluded: chain o residue 15 TYR Chi-restraints excluded: chain o residue 17 VAL Chi-restraints excluded: chain o residue 28 GLN Chi-restraints excluded: chain o residue 47 LYS Chi-restraints excluded: chain o residue 74 ASP Chi-restraints excluded: chain o residue 81 LEU Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 54 GLU Chi-restraints excluded: chain p residue 80 ILE Chi-restraints excluded: chain q residue 8 LYS Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain q residue 48 THR Chi-restraints excluded: chain q residue 51 GLU Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain q residue 76 ARG Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 50 THR Chi-restraints excluded: chain r residue 75 TYR Chi-restraints excluded: chain s residue 28 LYS Chi-restraints excluded: chain s residue 29 GLN Chi-restraints excluded: chain s residue 31 ILE Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain t residue 73 ARG Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 18 ARG Chi-restraints excluded: chain u residue 33 ARG Chi-restraints excluded: chain v residue 3 ARG Chi-restraints excluded: chain v residue 4 PHE Chi-restraints excluded: chain v residue 17 ILE Chi-restraints excluded: chain v residue 28 LEU Chi-restraints excluded: chain v residue 37 ASN Chi-restraints excluded: chain v residue 44 VAL Chi-restraints excluded: chain v residue 45 LYS Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 52 THR Chi-restraints excluded: chain v residue 57 THR Chi-restraints excluded: chain v residue 74 LEU Chi-restraints excluded: chain v residue 89 VAL Chi-restraints excluded: chain v residue 94 THR Chi-restraints excluded: chain v residue 137 LYS Chi-restraints excluded: chain v residue 144 MET Chi-restraints excluded: chain v residue 151 LEU Chi-restraints excluded: chain v residue 162 VAL Chi-restraints excluded: chain v residue 184 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 889 optimal weight: 9.9990 chunk 677 optimal weight: 40.0000 chunk 467 optimal weight: 5.9990 chunk 99 optimal weight: 0.5980 chunk 429 optimal weight: 3.9990 chunk 604 optimal weight: 50.0000 chunk 903 optimal weight: 8.9990 chunk 956 optimal weight: 30.0000 chunk 472 optimal weight: 9.9990 chunk 856 optimal weight: 8.9990 chunk 257 optimal weight: 5.9990 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 133 GLN C 199 GLN E 174 GLN G 147 ASN H 3 GLN J 70 ASN Q 28 ASN Q 95 ASN S 39 ASN ** S 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 38 ASN T 78 GLN W 31 GLN 1 25 ASN 2 17 HIS 3 43 GLN ** b 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 3 GLN c 166 GLN ** c 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 70 ASN d 85 ASN ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 68 ASN ** p 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 47 HIS ** s 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 97 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6188 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.601 152951 Z= 0.475 Angle : 1.163 62.573 229118 Z= 0.555 Chirality : 0.062 2.158 29467 Planarity : 0.007 0.079 12075 Dihedral : 26.465 179.867 77098 Min Nonbonded Distance : 1.501 Molprobity Statistics. All-atom Clashscore : 21.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.89 % Favored : 91.07 % Rotamer: Outliers : 10.88 % Allowed : 25.07 % Favored : 64.05 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % 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: -2.65 (0.10), residues: 5487 helix: -1.36 (0.12), residues: 1545 sheet: -1.14 (0.16), residues: 1004 loop : -2.24 (0.10), residues: 2938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP C 250 HIS 0.016 0.002 HIS e 83 PHE 0.041 0.003 PHE s 44 TYR 0.026 0.002 TYR O 32 ARG 0.014 0.001 ARG d 93 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10974 Ramachandran restraints generated. 5487 Oldfield, 0 Emsley, 5487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10974 Ramachandran restraints generated. 5487 Oldfield, 0 Emsley, 5487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1066 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 483 poor density : 583 time to evaluate : 10.041 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "VAL J 145 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 71 LYS cc_start: 0.8155 (mttp) cc_final: 0.7923 (mtpp) REVERT: C 123 ASP cc_start: 0.6932 (p0) cc_final: 0.6575 (m-30) REVERT: D 100 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7132 (mp0) REVERT: D 159 ASP cc_start: 0.7343 (OUTLIER) cc_final: 0.7085 (m-30) REVERT: E 200 LYS cc_start: 0.8540 (mmtm) cc_final: 0.8155 (mtmm) REVERT: F 17 MET cc_start: 0.3813 (mmm) cc_final: 0.3489 (mmp) REVERT: F 57 LEU cc_start: 0.5665 (OUTLIER) cc_final: 0.5386 (tt) REVERT: F 81 GLU cc_start: 0.4148 (mm-30) cc_final: 0.3859 (mm-30) REVERT: F 110 ARG cc_start: 0.4113 (OUTLIER) cc_final: 0.3754 (mpp80) REVERT: G 25 THR cc_start: 0.5970 (OUTLIER) cc_final: 0.5572 (m) REVERT: G 30 LYS cc_start: 0.4365 (OUTLIER) cc_final: 0.3954 (mttt) REVERT: G 87 LEU cc_start: 0.5585 (OUTLIER) cc_final: 0.5257 (pt) REVERT: H 12 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8936 (mm) REVERT: H 85 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8802 (tp) REVERT: I 5 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8269 (mp0) REVERT: M 87 LYS cc_start: 0.3854 (OUTLIER) cc_final: 0.2763 (pmtt) REVERT: O 19 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8257 (tptt) REVERT: O 51 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.8621 (mtt180) REVERT: O 89 ASP cc_start: 0.7039 (m-30) cc_final: 0.6791 (m-30) REVERT: O 108 GLN cc_start: 0.8347 (tt0) cc_final: 0.8104 (tt0) REVERT: P 10 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8639 (mtmm) REVERT: Q 11 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7054 (mmm160) REVERT: R 64 ARG cc_start: 0.7316 (tpp-160) cc_final: 0.7058 (tpp-160) REVERT: R 65 MET cc_start: 0.6238 (ttt) cc_final: 0.5519 (ptm) REVERT: S 56 ILE cc_start: 0.7072 (OUTLIER) cc_final: 0.6861 (pp) REVERT: T 7 ILE cc_start: 0.8312 (mp) cc_final: 0.8031 (mp) REVERT: T 21 LEU cc_start: 0.8859 (tt) cc_final: 0.8644 (tp) REVERT: T 57 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.6407 (tpt-90) REVERT: W 2 LYS cc_start: 0.2256 (OUTLIER) cc_final: 0.1852 (ttpp) REVERT: W 30 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.7657 (t80) REVERT: X 20 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.7801 (mtp180) REVERT: Z 41 ARG cc_start: 0.6222 (OUTLIER) cc_final: 0.5180 (mtt-85) REVERT: 2 41 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7821 (tptt) REVERT: 3 59 LYS cc_start: 0.8286 (ttpp) cc_final: 0.7732 (ttmm) REVERT: b 6 MET cc_start: 0.3277 (OUTLIER) cc_final: 0.2733 (mpt) REVERT: b 11 GLU cc_start: 0.3062 (OUTLIER) cc_final: 0.2223 (pt0) REVERT: b 22 ARG cc_start: 0.2861 (mmm-85) cc_final: 0.2231 (mtm110) REVERT: b 35 ARG cc_start: 0.2911 (ttt90) cc_final: 0.1956 (mtt-85) REVERT: b 59 GLN cc_start: 0.3725 (OUTLIER) cc_final: 0.3295 (mt0) REVERT: b 62 GLU cc_start: 0.2273 (OUTLIER) cc_final: 0.1792 (pp20) REVERT: b 143 ARG cc_start: 0.1946 (ttm170) cc_final: 0.0974 (mmm-85) REVERT: b 157 MET cc_start: 0.2598 (OUTLIER) cc_final: 0.2215 (pmm) REVERT: b 168 LYS cc_start: 0.4461 (mttt) cc_final: 0.2949 (tttt) REVERT: b 169 GLU cc_start: 0.3636 (OUTLIER) cc_final: 0.3168 (mm-30) REVERT: b 177 ARG cc_start: 0.2801 (mmt180) cc_final: 0.2193 (mpt180) REVERT: b 208 ARG cc_start: 0.2991 (mtp85) cc_final: 0.2339 (ppp-140) REVERT: b 213 LEU cc_start: 0.2587 (OUTLIER) cc_final: 0.2039 (tp) REVERT: c 3 GLN cc_start: 0.1865 (OUTLIER) cc_final: -0.1119 (pp30) REVERT: c 57 GLU cc_start: 0.1602 (OUTLIER) cc_final: 0.1038 (tp30) REVERT: c 78 LYS cc_start: 0.3049 (OUTLIER) cc_final: 0.2692 (mtpp) REVERT: c 105 ILE cc_start: 0.1870 (OUTLIER) cc_final: 0.1494 (pp) REVERT: c 123 LEU cc_start: 0.2086 (OUTLIER) cc_final: 0.1866 (mt) REVERT: c 163 ARG cc_start: 0.2911 (mtm110) cc_final: 0.2038 (mpt180) REVERT: d 5 ARG cc_start: 0.2289 (mtm110) cc_final: 0.0686 (mmt-90) REVERT: d 26 LEU cc_start: 0.3772 (OUTLIER) cc_final: 0.3153 (pp) REVERT: d 35 GLN cc_start: 0.1541 (OUTLIER) cc_final: 0.0777 (tm-30) REVERT: d 49 LEU cc_start: 0.4518 (tm) cc_final: 0.4201 (tp) REVERT: d 63 MET cc_start: 0.2645 (OUTLIER) cc_final: 0.2282 (tpt) REVERT: d 65 GLU cc_start: 0.2884 (tt0) cc_final: 0.2303 (tt0) REVERT: d 87 MET cc_start: 0.1395 (mmm) cc_final: 0.0770 (mpt) REVERT: d 89 LEU cc_start: 0.1665 (OUTLIER) cc_final: 0.1184 (mm) REVERT: d 103 LEU cc_start: 0.1742 (OUTLIER) cc_final: 0.0872 (mt) REVERT: d 124 LYS cc_start: 0.2072 (tptp) cc_final: 0.1651 (tptt) REVERT: d 153 GLU cc_start: 0.1920 (OUTLIER) cc_final: 0.1294 (tp30) REVERT: d 156 GLU cc_start: 0.2409 (OUTLIER) cc_final: 0.1649 (mm-30) REVERT: e 10 GLU cc_start: 0.2052 (OUTLIER) cc_final: 0.1150 (mm-30) REVERT: e 136 MET cc_start: 0.3689 (OUTLIER) cc_final: 0.2755 (tpt) REVERT: e 163 GLU cc_start: 0.1321 (OUTLIER) cc_final: 0.0587 (pt0) REVERT: f 74 ASP cc_start: 0.1843 (OUTLIER) cc_final: 0.1575 (p0) REVERT: g 36 ARG cc_start: 0.3084 (tpp80) cc_final: 0.2537 (mmt180) REVERT: g 94 GLU cc_start: 0.2436 (OUTLIER) cc_final: 0.1912 (mt-10) REVERT: h 3 MET cc_start: 0.3112 (OUTLIER) cc_final: 0.2413 (pmm) REVERT: h 11 LEU cc_start: 0.1995 (tp) cc_final: 0.1684 (mp) REVERT: h 39 ILE cc_start: 0.2301 (OUTLIER) cc_final: 0.1966 (mm) REVERT: h 53 GLU cc_start: 0.2555 (OUTLIER) cc_final: 0.0887 (pm20) REVERT: h 82 LYS cc_start: 0.3815 (OUTLIER) cc_final: 0.3547 (mmmt) REVERT: i 20 ARG cc_start: 0.2247 (OUTLIER) cc_final: 0.2042 (pmt170) REVERT: i 35 ARG cc_start: 0.2600 (ptm160) cc_final: 0.1962 (tpt-90) REVERT: i 40 TYR cc_start: 0.1490 (OUTLIER) cc_final: 0.1208 (t80) REVERT: i 46 LEU cc_start: 0.2116 (OUTLIER) cc_final: 0.1592 (tt) REVERT: j 11 LYS cc_start: 0.3449 (OUTLIER) cc_final: 0.2469 (tppp) REVERT: j 31 ARG cc_start: 0.2845 (OUTLIER) cc_final: 0.1070 (ppt170) REVERT: j 88 MET cc_start: 0.2604 (OUTLIER) cc_final: 0.1785 (ttm) REVERT: l 9 ARG cc_start: 0.2086 (ttp-170) cc_final: 0.0657 (tmm-80) REVERT: l 12 ARG cc_start: 0.3855 (mmt-90) cc_final: 0.3588 (tpp-160) REVERT: l 33 LYS cc_start: 0.5790 (mppt) cc_final: 0.4782 (ptmt) REVERT: l 67 ARG cc_start: 0.4330 (OUTLIER) cc_final: 0.3656 (tpp80) REVERT: l 89 GLU cc_start: 0.2966 (OUTLIER) cc_final: 0.2570 (tt0) REVERT: l 99 ARG cc_start: 0.3816 (OUTLIER) cc_final: 0.3435 (ttm-80) REVERT: n 31 HIS cc_start: 0.0703 (OUTLIER) cc_final: -0.1469 (m170) REVERT: n 52 GLN cc_start: 0.3702 (OUTLIER) cc_final: 0.2187 (tm-30) REVERT: o 3 ILE cc_start: 0.2334 (OUTLIER) cc_final: 0.1727 (tp) REVERT: o 15 TYR cc_start: 0.2585 (OUTLIER) cc_final: 0.1162 (m-10) REVERT: o 28 GLN cc_start: 0.1953 (OUTLIER) cc_final: 0.1467 (pt0) REVERT: o 47 LYS cc_start: 0.2809 (OUTLIER) cc_final: 0.2239 (mtpt) REVERT: p 59 LYS cc_start: 0.3678 (OUTLIER) cc_final: 0.3153 (ptpp) REVERT: q 34 LYS cc_start: 0.3245 (OUTLIER) cc_final: 0.2938 (tttt) REVERT: q 45 LYS cc_start: 0.3505 (mtmp) cc_final: 0.3237 (mmmm) REVERT: q 77 LEU cc_start: 0.3961 (OUTLIER) cc_final: 0.2947 (pp) REVERT: r 70 MET cc_start: 0.1794 (mmt) cc_final: 0.0878 (mpp) REVERT: s 66 MET cc_start: 0.2207 (mpt) cc_final: 0.1321 (ppp) REVERT: t 16 LYS cc_start: 0.3291 (ptmt) cc_final: 0.2599 (pttt) REVERT: t 73 ARG cc_start: 0.2335 (OUTLIER) cc_final: 0.1181 (ttp-170) REVERT: u 12 LEU cc_start: 0.0680 (OUTLIER) cc_final: 0.0457 (mt) REVERT: u 17 ARG cc_start: 0.2193 (OUTLIER) cc_final: 0.1472 (mtt180) REVERT: v 4 PHE cc_start: -0.1269 (OUTLIER) cc_final: -0.1502 (m-10) REVERT: v 37 ASN cc_start: 0.1039 (OUTLIER) cc_final: 0.0702 (m-40) REVERT: v 45 LYS cc_start: 0.1810 (OUTLIER) cc_final: -0.0590 (tmtt) REVERT: v 144 MET cc_start: 0.1255 (OUTLIER) cc_final: 0.1005 (pmt) outliers start: 483 outliers final: 270 residues processed: 980 average time/residue: 2.1799 time to fit residues: 3038.5099 Evaluate side-chains 896 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 345 poor density : 551 time to evaluate : 5.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 193 LYS Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 3 ASN Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 24 SER Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 110 ARG Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain G residue 3 ARG Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 39 GLU Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 97 GLN Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 120 ASN Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 118 LYS Chi-restraints excluded: chain I residue 5 GLU Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 59 LYS Chi-restraints excluded: chain I residue 116 SER Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 82 ARG Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 34 GLU Chi-restraints excluded: chain L residue 45 GLU Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain M residue 6 ASP Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 59 LYS Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 80 ILE Chi-restraints excluded: chain M residue 87 LYS Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain N residue 12 LYS Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 84 GLU Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 19 LYS Chi-restraints excluded: chain O residue 51 ARG Chi-restraints excluded: chain O residue 74 MET Chi-restraints excluded: chain O residue 90 ILE Chi-restraints excluded: chain P residue 10 LYS Chi-restraints excluded: chain P residue 26 ASP Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 63 ASN Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain S residue 3 ILE Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 26 THR Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 93 ILE Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 43 VAL Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 57 ARG Chi-restraints excluded: chain U residue 72 ASP Chi-restraints excluded: chain U residue 75 VAL Chi-restraints excluded: chain W residue 2 LYS Chi-restraints excluded: chain W residue 14 ILE Chi-restraints excluded: chain W residue 25 LEU Chi-restraints excluded: chain W residue 30 PHE Chi-restraints excluded: chain W residue 63 GLU Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 20 ARG Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain Y residue 5 ILE Chi-restraints excluded: chain Z residue 7 ARG Chi-restraints excluded: chain Z residue 8 THR Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 28 THR Chi-restraints excluded: chain Z residue 30 CYS Chi-restraints excluded: chain Z residue 41 ARG Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 2 residue 31 VAL Chi-restraints excluded: chain 2 residue 41 LYS Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 3 residue 14 VAL Chi-restraints excluded: chain 3 residue 31 HIS Chi-restraints excluded: chain 3 residue 55 MET Chi-restraints excluded: chain 4 residue 2 LYS Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 11 GLU Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 59 GLN Chi-restraints excluded: chain b residue 60 VAL Chi-restraints excluded: chain b residue 62 GLU Chi-restraints excluded: chain b residue 89 GLN Chi-restraints excluded: chain b residue 101 LEU Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain b residue 105 LYS Chi-restraints excluded: chain b residue 116 GLU Chi-restraints excluded: chain b residue 157 MET Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 169 GLU Chi-restraints excluded: chain b residue 187 VAL Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain c residue 78 LYS Chi-restraints excluded: chain c residue 94 THR Chi-restraints excluded: chain c residue 105 ILE Chi-restraints excluded: chain c residue 113 ARG Chi-restraints excluded: chain c residue 118 ASN Chi-restraints excluded: chain c residue 123 LEU Chi-restraints excluded: chain c residue 160 ASP Chi-restraints excluded: chain c residue 167 TYR Chi-restraints excluded: chain c residue 197 VAL Chi-restraints excluded: chain c residue 201 ILE Chi-restraints excluded: chain d residue 4 PHE Chi-restraints excluded: chain d residue 10 LYS Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 35 GLN Chi-restraints excluded: chain d residue 63 MET Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 71 THR Chi-restraints excluded: chain d residue 89 LEU Chi-restraints excluded: chain d residue 103 LEU Chi-restraints excluded: chain d residue 111 ARG Chi-restraints excluded: chain d residue 139 ILE Chi-restraints excluded: chain d residue 153 GLU Chi-restraints excluded: chain d residue 156 GLU Chi-restraints excluded: chain e residue 10 GLU Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 68 LYS Chi-restraints excluded: chain e residue 72 VAL Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 81 THR Chi-restraints excluded: chain e residue 106 ILE Chi-restraints excluded: chain e residue 136 MET Chi-restraints excluded: chain e residue 141 ILE Chi-restraints excluded: chain e residue 163 GLU Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 7 MET Chi-restraints excluded: chain f residue 14 ILE Chi-restraints excluded: chain f residue 20 LYS Chi-restraints excluded: chain f residue 38 LEU Chi-restraints excluded: chain f residue 42 ASP Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 68 ASP Chi-restraints excluded: chain f residue 74 ASP Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 87 ILE Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 48 ASP Chi-restraints excluded: chain g residue 64 GLU Chi-restraints excluded: chain g residue 70 MET Chi-restraints excluded: chain g residue 94 GLU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 144 MET Chi-restraints excluded: chain h residue 3 MET Chi-restraints excluded: chain h residue 13 ARG Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain h residue 47 LYS Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 70 ASP Chi-restraints excluded: chain h residue 82 LYS Chi-restraints excluded: chain h residue 96 LYS Chi-restraints excluded: chain h residue 112 VAL Chi-restraints excluded: chain h residue 113 ILE Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 20 ARG Chi-restraints excluded: chain i residue 37 VAL Chi-restraints excluded: chain i residue 40 TYR Chi-restraints excluded: chain i residue 46 LEU Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 129 PHE Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 11 LYS Chi-restraints excluded: chain j residue 27 GLU Chi-restraints excluded: chain j residue 31 ARG Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 66 GLU Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain k residue 100 LEU Chi-restraints excluded: chain k residue 101 GLN Chi-restraints excluded: chain k residue 121 CYS Chi-restraints excluded: chain l residue 36 THR Chi-restraints excluded: chain l residue 42 GLN Chi-restraints excluded: chain l residue 47 CYS Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 62 LEU Chi-restraints excluded: chain l residue 67 ARG Chi-restraints excluded: chain l residue 73 ASN Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain l residue 89 GLU Chi-restraints excluded: chain l residue 99 ARG Chi-restraints excluded: chain l residue 100 VAL Chi-restraints excluded: chain l residue 115 LEU Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain m residue 57 ARG Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 63 TYR Chi-restraints excluded: chain m residue 79 ARG Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain n residue 4 THR Chi-restraints excluded: chain n residue 31 HIS Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 38 LYS Chi-restraints excluded: chain n residue 50 LYS Chi-restraints excluded: chain n residue 52 GLN Chi-restraints excluded: chain o residue 3 ILE Chi-restraints excluded: chain o residue 11 ILE Chi-restraints excluded: chain o residue 15 TYR Chi-restraints excluded: chain o residue 17 VAL Chi-restraints excluded: chain o residue 28 GLN Chi-restraints excluded: chain o residue 47 LYS Chi-restraints excluded: chain o residue 74 ASP Chi-restraints excluded: chain o residue 81 LEU Chi-restraints excluded: chain p residue 10 LEU Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 59 LYS Chi-restraints excluded: chain p residue 80 ILE Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain q residue 15 VAL Chi-restraints excluded: chain q residue 34 LYS Chi-restraints excluded: chain q residue 48 THR Chi-restraints excluded: chain q residue 51 GLU Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain q residue 76 ARG Chi-restraints excluded: chain q residue 77 LEU Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 24 THR Chi-restraints excluded: chain r residue 50 THR Chi-restraints excluded: chain s residue 31 ILE Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain t residue 73 ARG Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 12 LEU Chi-restraints excluded: chain u residue 17 ARG Chi-restraints excluded: chain u residue 33 ARG Chi-restraints excluded: chain v residue 4 PHE Chi-restraints excluded: chain v residue 17 ILE Chi-restraints excluded: chain v residue 28 LEU Chi-restraints excluded: chain v residue 30 ARG Chi-restraints excluded: chain v residue 37 ASN Chi-restraints excluded: chain v residue 44 VAL Chi-restraints excluded: chain v residue 45 LYS Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 52 THR Chi-restraints excluded: chain v residue 57 THR Chi-restraints excluded: chain v residue 74 LEU Chi-restraints excluded: chain v residue 89 VAL Chi-restraints excluded: chain v residue 94 THR Chi-restraints excluded: chain v residue 144 MET Chi-restraints excluded: chain v residue 151 LEU Chi-restraints excluded: chain v residue 162 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 796 optimal weight: 9.9990 chunk 543 optimal weight: 0.5980 chunk 13 optimal weight: 20.0000 chunk 712 optimal weight: 40.0000 chunk 394 optimal weight: 9.9990 chunk 816 optimal weight: 7.9990 chunk 661 optimal weight: 40.0000 chunk 1 optimal weight: 1.9990 chunk 488 optimal weight: 1.9990 chunk 858 optimal weight: 10.0000 chunk 241 optimal weight: 10.0000 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 133 GLN C 199 GLN E 174 GLN G 111 HIS G 147 ASN H 3 GLN H 11 ASN J 70 ASN M 15 HIS Q 28 ASN Q 95 ASN S 39 ASN T 13 GLN 1 25 ASN b 44 GLN c 151 GLN ** c 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 59 ASN ** o 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 73 ASN r 25 HIS ** r 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6175 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.599 152951 Z= 0.433 Angle : 1.081 62.696 229118 Z= 0.517 Chirality : 0.059 2.164 29467 Planarity : 0.007 0.076 12075 Dihedral : 26.339 179.595 77063 Min Nonbonded Distance : 1.504 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.40 % Favored : 91.56 % Rotamer: Outliers : 10.02 % Allowed : 26.46 % Favored : 63.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.07 % 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: -2.48 (0.11), residues: 5487 helix: -1.14 (0.12), residues: 1558 sheet: -1.05 (0.16), residues: 988 loop : -2.18 (0.11), residues: 2941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 250 HIS 0.028 0.002 HIS S 44 PHE 0.039 0.002 PHE g 47 TYR 0.023 0.002 TYR O 32 ARG 0.016 0.001 ARG d 93 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10974 Ramachandran restraints generated. 5487 Oldfield, 0 Emsley, 5487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10974 Ramachandran restraints generated. 5487 Oldfield, 0 Emsley, 5487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1019 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 445 poor density : 574 time to evaluate : 6.037 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL J 145 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 3 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8334 (mt) REVERT: C 207 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8447 (ptmm) REVERT: D 100 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7143 (mp0) REVERT: D 159 ASP cc_start: 0.7501 (OUTLIER) cc_final: 0.7229 (m-30) REVERT: E 200 LYS cc_start: 0.8567 (mmtm) cc_final: 0.8163 (mtmm) REVERT: F 17 MET cc_start: 0.3816 (mmm) cc_final: 0.3592 (mmp) REVERT: F 33 LYS cc_start: 0.6457 (pttt) cc_final: 0.6244 (pttt) REVERT: F 81 GLU cc_start: 0.3962 (mm-30) cc_final: 0.3670 (mm-30) REVERT: F 110 ARG cc_start: 0.4039 (OUTLIER) cc_final: 0.3813 (mpp80) REVERT: G 30 LYS cc_start: 0.4302 (OUTLIER) cc_final: 0.3784 (mttt) REVERT: G 87 LEU cc_start: 0.5654 (OUTLIER) cc_final: 0.5239 (pt) REVERT: G 121 ILE cc_start: 0.6559 (OUTLIER) cc_final: 0.6324 (mp) REVERT: H 12 ILE cc_start: 0.9270 (OUTLIER) cc_final: 0.9015 (mm) REVERT: H 85 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8813 (tp) REVERT: I 4 GLN cc_start: 0.8064 (tt0) cc_final: 0.7674 (tt0) REVERT: I 5 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8257 (mp0) REVERT: J 70 ASN cc_start: 0.8370 (OUTLIER) cc_final: 0.8161 (p0) REVERT: L 31 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.7078 (tt0) REVERT: M 87 LYS cc_start: 0.3823 (OUTLIER) cc_final: 0.2790 (pmtt) REVERT: O 51 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8628 (mtt-85) REVERT: O 59 LYS cc_start: 0.8564 (ttpt) cc_final: 0.8240 (ttmm) REVERT: O 89 ASP cc_start: 0.7021 (m-30) cc_final: 0.6730 (m-30) REVERT: O 108 GLN cc_start: 0.8300 (tt0) cc_final: 0.8075 (tt0) REVERT: Q 11 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.8030 (mmm160) REVERT: R 65 MET cc_start: 0.6307 (ttt) cc_final: 0.5526 (ptm) REVERT: T 7 ILE cc_start: 0.8288 (mp) cc_final: 0.8006 (mp) REVERT: T 21 LEU cc_start: 0.8856 (tt) cc_final: 0.8640 (tp) REVERT: T 57 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.6478 (tpt-90) REVERT: W 2 LYS cc_start: 0.1975 (OUTLIER) cc_final: 0.1538 (ttpp) REVERT: W 30 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.7640 (t80) REVERT: Z 41 ARG cc_start: 0.6625 (OUTLIER) cc_final: 0.5629 (mtt-85) REVERT: 2 15 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.7881 (mptm) REVERT: 2 41 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7852 (tptt) REVERT: 3 59 LYS cc_start: 0.8279 (ttpp) cc_final: 0.7784 (ttmm) REVERT: b 6 MET cc_start: 0.3383 (OUTLIER) cc_final: 0.2918 (mpt) REVERT: b 11 GLU cc_start: 0.2788 (OUTLIER) cc_final: 0.2022 (pt0) REVERT: b 22 ARG cc_start: 0.2610 (mmm-85) cc_final: 0.1936 (mtm110) REVERT: b 35 ARG cc_start: 0.2860 (ttt90) cc_final: 0.1903 (mtt-85) REVERT: b 62 GLU cc_start: 0.2329 (OUTLIER) cc_final: 0.1861 (pp20) REVERT: b 143 ARG cc_start: 0.1773 (ttm170) cc_final: 0.0972 (mmm-85) REVERT: b 168 LYS cc_start: 0.4556 (mttt) cc_final: 0.2986 (tttt) REVERT: b 169 GLU cc_start: 0.3536 (OUTLIER) cc_final: 0.3119 (mm-30) REVERT: b 208 ARG cc_start: 0.3208 (mtp85) cc_final: 0.2463 (ptm-80) REVERT: b 213 LEU cc_start: 0.2498 (OUTLIER) cc_final: 0.2136 (tp) REVERT: c 3 GLN cc_start: 0.1350 (OUTLIER) cc_final: -0.0938 (pp30) REVERT: c 57 GLU cc_start: 0.1452 (OUTLIER) cc_final: 0.0953 (tp30) REVERT: c 78 LYS cc_start: 0.3032 (OUTLIER) cc_final: 0.2536 (mtpp) REVERT: c 105 ILE cc_start: 0.1620 (OUTLIER) cc_final: 0.1264 (pp) REVERT: c 163 ARG cc_start: 0.2844 (mtm110) cc_final: 0.1992 (mpt90) REVERT: d 5 ARG cc_start: 0.2321 (mtm110) cc_final: 0.0615 (mmt-90) REVERT: d 26 LEU cc_start: 0.3936 (OUTLIER) cc_final: 0.3313 (pp) REVERT: d 35 GLN cc_start: 0.1510 (OUTLIER) cc_final: 0.0797 (tm-30) REVERT: d 49 LEU cc_start: 0.4939 (OUTLIER) cc_final: 0.4665 (tp) REVERT: d 63 MET cc_start: 0.3298 (pp-130) cc_final: 0.2743 (mtt) REVERT: d 65 GLU cc_start: 0.2754 (tt0) cc_final: 0.2233 (tt0) REVERT: d 87 MET cc_start: 0.1577 (mmm) cc_final: 0.0891 (mpt) REVERT: d 89 LEU cc_start: 0.1345 (OUTLIER) cc_final: 0.0995 (mm) REVERT: d 124 LYS cc_start: 0.1977 (tptp) cc_final: 0.1573 (tptt) REVERT: d 153 GLU cc_start: 0.1741 (OUTLIER) cc_final: 0.1288 (tp30) REVERT: d 156 GLU cc_start: 0.2302 (OUTLIER) cc_final: 0.1625 (mt-10) REVERT: d 196 GLU cc_start: 0.3250 (OUTLIER) cc_final: 0.2464 (pm20) REVERT: e 10 GLU cc_start: 0.2153 (OUTLIER) cc_final: 0.1222 (mm-30) REVERT: e 13 GLU cc_start: 0.2364 (OUTLIER) cc_final: 0.1402 (mm-30) REVERT: e 136 MET cc_start: 0.3255 (tpt) cc_final: 0.2290 (tpt) REVERT: f 14 ILE cc_start: 0.1335 (OUTLIER) cc_final: 0.0813 (tp) REVERT: g 9 LYS cc_start: 0.2093 (OUTLIER) cc_final: 0.1810 (mmmt) REVERT: g 36 ARG cc_start: 0.3277 (tpp80) cc_final: 0.2739 (mmt180) REVERT: g 94 GLU cc_start: 0.2321 (OUTLIER) cc_final: 0.1820 (mt-10) REVERT: h 3 MET cc_start: 0.2951 (OUTLIER) cc_final: 0.2190 (pmm) REVERT: h 39 ILE cc_start: 0.2022 (OUTLIER) cc_final: 0.1766 (mm) REVERT: h 53 GLU cc_start: 0.2640 (OUTLIER) cc_final: 0.1144 (pm20) REVERT: h 64 LEU cc_start: 0.2517 (mp) cc_final: 0.2312 (mt) REVERT: h 82 LYS cc_start: 0.3773 (OUTLIER) cc_final: 0.3511 (tptt) REVERT: i 35 ARG cc_start: 0.2603 (ptm160) cc_final: 0.1964 (tpt-90) REVERT: i 46 LEU cc_start: 0.2108 (OUTLIER) cc_final: 0.1586 (tt) REVERT: i 114 GLU cc_start: 0.2529 (OUTLIER) cc_final: 0.2054 (tm-30) REVERT: j 11 LYS cc_start: 0.3607 (OUTLIER) cc_final: 0.2563 (tppp) REVERT: j 31 ARG cc_start: 0.2928 (OUTLIER) cc_final: 0.1024 (ppt170) REVERT: j 88 MET cc_start: 0.2891 (OUTLIER) cc_final: 0.1975 (ttm) REVERT: l 9 ARG cc_start: 0.2166 (ttp-170) cc_final: 0.0730 (tmm-80) REVERT: l 33 LYS cc_start: 0.5979 (mppt) cc_final: 0.5548 (mmtm) REVERT: l 67 ARG cc_start: 0.4378 (OUTLIER) cc_final: 0.3684 (tpp80) REVERT: l 89 GLU cc_start: 0.2945 (OUTLIER) cc_final: 0.2547 (tt0) REVERT: l 99 ARG cc_start: 0.3791 (OUTLIER) cc_final: 0.3515 (ttm-80) REVERT: m 35 GLU cc_start: 0.3437 (OUTLIER) cc_final: 0.2768 (tm-30) REVERT: n 6 MET cc_start: 0.1864 (mpp) cc_final: 0.0689 (tpt) REVERT: n 31 HIS cc_start: 0.0568 (OUTLIER) cc_final: -0.1592 (m170) REVERT: n 52 GLN cc_start: 0.3670 (OUTLIER) cc_final: 0.2326 (tp-100) REVERT: o 3 ILE cc_start: 0.2356 (OUTLIER) cc_final: 0.1999 (tt) REVERT: o 15 TYR cc_start: 0.2614 (OUTLIER) cc_final: 0.1164 (m-10) REVERT: o 28 GLN cc_start: 0.2226 (OUTLIER) cc_final: 0.1596 (pt0) REVERT: o 74 ASP cc_start: 0.1980 (OUTLIER) cc_final: 0.0410 (m-30) REVERT: p 81 MET cc_start: 0.3551 (mmm) cc_final: 0.3250 (mmm) REVERT: q 38 LYS cc_start: 0.4706 (tttp) cc_final: 0.4284 (ttpt) REVERT: q 77 LEU cc_start: 0.3902 (OUTLIER) cc_final: 0.3589 (tm) REVERT: r 45 LEU cc_start: 0.2690 (OUTLIER) cc_final: 0.1449 (pt) REVERT: r 70 MET cc_start: 0.1734 (mmt) cc_final: 0.0254 (ptt) REVERT: t 16 LYS cc_start: 0.3332 (ptmt) cc_final: 0.2691 (pttt) REVERT: t 73 ARG cc_start: 0.2223 (OUTLIER) cc_final: 0.1018 (mtp-110) REVERT: u 17 ARG cc_start: 0.2204 (OUTLIER) cc_final: 0.1536 (mtt180) REVERT: v 4 PHE cc_start: -0.1278 (OUTLIER) cc_final: -0.1503 (m-10) REVERT: v 30 ARG cc_start: 0.2016 (OUTLIER) cc_final: 0.1582 (tpm170) REVERT: v 45 LYS cc_start: 0.1063 (OUTLIER) cc_final: -0.1102 (tmtt) outliers start: 445 outliers final: 252 residues processed: 939 average time/residue: 2.1765 time to fit residues: 2896.1755 Evaluate side-chains 877 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 321 poor density : 556 time to evaluate : 5.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 193 LYS Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 3 ASN Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 24 SER Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 110 ARG Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain G residue 3 ARG Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 39 GLU Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 97 GLN Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 120 ASN Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain I residue 5 GLU Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 59 LYS Chi-restraints excluded: chain I residue 116 SER Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 70 ASN Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 82 ARG Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 31 GLU Chi-restraints excluded: chain L residue 34 GLU Chi-restraints excluded: chain L residue 45 GLU Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain M residue 6 ASP Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 87 LYS Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 84 GLU Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 51 ARG Chi-restraints excluded: chain O residue 74 MET Chi-restraints excluded: chain O residue 90 ILE Chi-restraints excluded: chain P residue 26 ASP Chi-restraints excluded: chain P residue 63 ASN Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 14 GLU Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain S residue 3 ILE Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 26 THR Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 93 ILE Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 43 VAL Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 57 ARG Chi-restraints excluded: chain U residue 72 ASP Chi-restraints excluded: chain U residue 75 VAL Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain W residue 2 LYS Chi-restraints excluded: chain W residue 14 ILE Chi-restraints excluded: chain W residue 20 SER Chi-restraints excluded: chain W residue 25 LEU Chi-restraints excluded: chain W residue 30 PHE Chi-restraints excluded: chain W residue 63 GLU Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain Y residue 5 ILE Chi-restraints excluded: chain Z residue 7 ARG Chi-restraints excluded: chain Z residue 8 THR Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 28 THR Chi-restraints excluded: chain Z residue 30 CYS Chi-restraints excluded: chain Z residue 41 ARG Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 2 residue 14 SER Chi-restraints excluded: chain 2 residue 15 LYS Chi-restraints excluded: chain 2 residue 31 VAL Chi-restraints excluded: chain 2 residue 41 LYS Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 3 residue 14 VAL Chi-restraints excluded: chain 3 residue 31 HIS Chi-restraints excluded: chain 3 residue 55 MET Chi-restraints excluded: chain 4 residue 2 LYS Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 11 GLU Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 60 VAL Chi-restraints excluded: chain b residue 62 GLU Chi-restraints excluded: chain b residue 101 LEU Chi-restraints excluded: chain b residue 105 LYS Chi-restraints excluded: chain b residue 116 GLU Chi-restraints excluded: chain b residue 169 GLU Chi-restraints excluded: chain b residue 187 VAL Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 35 ASP Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain c residue 78 LYS Chi-restraints excluded: chain c residue 94 THR Chi-restraints excluded: chain c residue 105 ILE Chi-restraints excluded: chain c residue 113 ARG Chi-restraints excluded: chain c residue 118 ASN Chi-restraints excluded: chain c residue 160 ASP Chi-restraints excluded: chain c residue 167 TYR Chi-restraints excluded: chain c residue 183 TYR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 201 ILE Chi-restraints excluded: chain d residue 10 LYS Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 35 GLN Chi-restraints excluded: chain d residue 49 LEU Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 71 THR Chi-restraints excluded: chain d residue 89 LEU Chi-restraints excluded: chain d residue 111 ARG Chi-restraints excluded: chain d residue 139 ILE Chi-restraints excluded: chain d residue 153 GLU Chi-restraints excluded: chain d residue 156 GLU Chi-restraints excluded: chain d residue 196 GLU Chi-restraints excluded: chain e residue 10 GLU Chi-restraints excluded: chain e residue 13 GLU Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 72 VAL Chi-restraints excluded: chain e residue 106 ILE Chi-restraints excluded: chain e residue 141 ILE Chi-restraints excluded: chain e residue 163 GLU Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 14 ILE Chi-restraints excluded: chain f residue 20 LYS Chi-restraints excluded: chain f residue 38 LEU Chi-restraints excluded: chain f residue 42 ASP Chi-restraints excluded: chain f residue 68 ASP Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 87 ILE Chi-restraints excluded: chain g residue 9 LYS Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 64 GLU Chi-restraints excluded: chain g residue 94 GLU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 144 MET Chi-restraints excluded: chain h residue 3 MET Chi-restraints excluded: chain h residue 13 ARG Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 24 LYS Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain h residue 47 LYS Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 70 ASP Chi-restraints excluded: chain h residue 82 LYS Chi-restraints excluded: chain h residue 96 LYS Chi-restraints excluded: chain h residue 112 VAL Chi-restraints excluded: chain h residue 113 ILE Chi-restraints excluded: chain i residue 37 VAL Chi-restraints excluded: chain i residue 40 TYR Chi-restraints excluded: chain i residue 46 LEU Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 112 MET Chi-restraints excluded: chain i residue 114 GLU Chi-restraints excluded: chain i residue 129 PHE Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 11 LYS Chi-restraints excluded: chain j residue 31 ARG Chi-restraints excluded: chain j residue 64 GLN Chi-restraints excluded: chain j residue 66 GLU Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain k residue 69 THR Chi-restraints excluded: chain k residue 100 LEU Chi-restraints excluded: chain k residue 101 GLN Chi-restraints excluded: chain k residue 121 CYS Chi-restraints excluded: chain l residue 36 THR Chi-restraints excluded: chain l residue 42 GLN Chi-restraints excluded: chain l residue 47 CYS Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 62 LEU Chi-restraints excluded: chain l residue 67 ARG Chi-restraints excluded: chain l residue 73 ASN Chi-restraints excluded: chain l residue 80 ILE Chi-restraints excluded: chain l residue 89 GLU Chi-restraints excluded: chain l residue 99 ARG Chi-restraints excluded: chain l residue 100 VAL Chi-restraints excluded: chain l residue 115 LEU Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain m residue 35 GLU Chi-restraints excluded: chain m residue 57 ARG Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 63 TYR Chi-restraints excluded: chain m residue 79 ARG Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain m residue 108 THR Chi-restraints excluded: chain n residue 4 THR Chi-restraints excluded: chain n residue 31 HIS Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 38 LYS Chi-restraints excluded: chain n residue 50 LYS Chi-restraints excluded: chain n residue 52 GLN Chi-restraints excluded: chain o residue 3 ILE Chi-restraints excluded: chain o residue 15 TYR Chi-restraints excluded: chain o residue 28 GLN Chi-restraints excluded: chain o residue 74 ASP Chi-restraints excluded: chain o residue 81 LEU Chi-restraints excluded: chain p residue 10 LEU Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 32 ARG Chi-restraints excluded: chain p residue 80 ILE Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain q residue 48 THR Chi-restraints excluded: chain q residue 51 GLU Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain q residue 76 ARG Chi-restraints excluded: chain q residue 77 LEU Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 50 THR Chi-restraints excluded: chain s residue 31 ILE Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain t residue 73 ARG Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 17 ARG Chi-restraints excluded: chain v residue 4 PHE Chi-restraints excluded: chain v residue 17 ILE Chi-restraints excluded: chain v residue 28 LEU Chi-restraints excluded: chain v residue 30 ARG Chi-restraints excluded: chain v residue 44 VAL Chi-restraints excluded: chain v residue 45 LYS Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 52 THR Chi-restraints excluded: chain v residue 57 THR Chi-restraints excluded: chain v residue 74 LEU Chi-restraints excluded: chain v residue 89 VAL Chi-restraints excluded: chain v residue 94 THR Chi-restraints excluded: chain v residue 151 LEU Chi-restraints excluded: chain v residue 162 VAL Chi-restraints excluded: chain v residue 184 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 321 optimal weight: 0.9980 chunk 861 optimal weight: 0.0070 chunk 189 optimal weight: 30.0000 chunk 561 optimal weight: 0.7980 chunk 236 optimal weight: 4.9990 chunk 957 optimal weight: 9.9990 chunk 795 optimal weight: 9.9990 chunk 443 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 316 optimal weight: 3.9990 chunk 502 optimal weight: 2.9990 overall best weight: 1.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 133 GLN C 199 GLN E 174 GLN G 147 ASN H 3 GLN H 11 ASN ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 43 GLN Q 65 ASN Q 95 ASN S 39 ASN ** S 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 37 GLN 1 25 ASN b 44 GLN ** c 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 151 GLN ** c 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6041 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.600 152951 Z= 0.292 Angle : 0.848 62.685 229118 Z= 0.410 Chirality : 0.051 2.150 29467 Planarity : 0.005 0.105 12075 Dihedral : 26.088 179.837 77046 Min Nonbonded Distance : 1.504 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.51 % Favored : 92.47 % Rotamer: Outliers : 8.27 % Allowed : 28.20 % Favored : 63.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.00 % 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: -2.22 (0.11), residues: 5487 helix: -0.78 (0.13), residues: 1573 sheet: -1.00 (0.16), residues: 981 loop : -2.07 (0.11), residues: 2933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 250 HIS 0.019 0.001 HIS S 44 PHE 0.028 0.002 PHE g 47 TYR 0.027 0.001 TYR s 61 ARG 0.009 0.001 ARG O 58 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10974 Ramachandran restraints generated. 5487 Oldfield, 0 Emsley, 5487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10974 Ramachandran restraints generated. 5487 Oldfield, 0 Emsley, 5487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 950 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 367 poor density : 583 time to evaluate : 6.112 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "VAL J 145 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 100 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7089 (mp0) REVERT: D 104 GLU cc_start: 0.7396 (mm-30) cc_final: 0.7140 (mm-30) REVERT: E 200 LYS cc_start: 0.8544 (mmtm) cc_final: 0.8108 (mtmm) REVERT: F 17 MET cc_start: 0.3902 (mmm) cc_final: 0.3643 (mmp) REVERT: F 110 ARG cc_start: 0.4062 (OUTLIER) cc_final: 0.3703 (mpp80) REVERT: G 30 LYS cc_start: 0.4288 (OUTLIER) cc_final: 0.3866 (mptt) REVERT: G 87 LEU cc_start: 0.5373 (OUTLIER) cc_final: 0.4921 (pt) REVERT: G 121 ILE cc_start: 0.6642 (OUTLIER) cc_final: 0.6431 (mp) REVERT: H 85 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8713 (tp) REVERT: I 4 GLN cc_start: 0.7906 (tt0) cc_final: 0.7452 (tt0) REVERT: I 5 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8092 (mm-30) REVERT: M 87 LYS cc_start: 0.3426 (OUTLIER) cc_final: 0.3001 (pmtt) REVERT: O 51 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8586 (mtt-85) REVERT: O 74 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.7922 (ttt) REVERT: O 108 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7962 (tt0) REVERT: R 64 ARG cc_start: 0.7332 (ttm170) cc_final: 0.6815 (mtp85) REVERT: S 19 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7880 (ttmm) REVERT: S 93 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7872 (pt) REVERT: T 7 ILE cc_start: 0.8267 (mp) cc_final: 0.8002 (mp) REVERT: T 21 LEU cc_start: 0.8771 (tt) cc_final: 0.8561 (tp) REVERT: W 2 LYS cc_start: 0.1730 (OUTLIER) cc_final: 0.1380 (ttpp) REVERT: W 30 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.7571 (t80) REVERT: 4 20 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8055 (mppt) REVERT: b 11 GLU cc_start: 0.2692 (OUTLIER) cc_final: 0.1934 (pt0) REVERT: b 22 ARG cc_start: 0.2692 (mmm-85) cc_final: 0.1853 (mtm110) REVERT: b 35 ARG cc_start: 0.2769 (ttt90) cc_final: 0.1807 (mtp85) REVERT: b 59 GLN cc_start: 0.3736 (OUTLIER) cc_final: 0.3149 (mt0) REVERT: b 62 GLU cc_start: 0.2162 (OUTLIER) cc_final: 0.1791 (pp20) REVERT: b 95 ARG cc_start: 0.1430 (ptt180) cc_final: 0.0598 (ttm170) REVERT: b 143 ARG cc_start: 0.1776 (ttm170) cc_final: 0.0961 (mmm-85) REVERT: b 168 LYS cc_start: 0.4537 (mttt) cc_final: 0.3018 (tttt) REVERT: b 169 GLU cc_start: 0.3596 (OUTLIER) cc_final: 0.3039 (mm-30) REVERT: b 170 ARG cc_start: 0.2335 (tpm170) cc_final: 0.2035 (tpm-80) REVERT: b 208 ARG cc_start: 0.3353 (mtp85) cc_final: 0.2659 (ptm-80) REVERT: b 213 LEU cc_start: 0.2535 (OUTLIER) cc_final: 0.1941 (tp) REVERT: c 57 GLU cc_start: 0.1318 (OUTLIER) cc_final: 0.0956 (tp30) REVERT: c 78 LYS cc_start: 0.2998 (OUTLIER) cc_final: 0.2512 (mtpp) REVERT: c 105 ILE cc_start: 0.1137 (OUTLIER) cc_final: 0.0628 (tp) REVERT: c 123 LEU cc_start: 0.1452 (mt) cc_final: 0.1241 (mm) REVERT: c 163 ARG cc_start: 0.2738 (mtm110) cc_final: 0.1919 (mpt90) REVERT: d 5 ARG cc_start: 0.2169 (mtm110) cc_final: 0.0603 (mmt-90) REVERT: d 26 LEU cc_start: 0.4017 (OUTLIER) cc_final: 0.3379 (pp) REVERT: d 49 LEU cc_start: 0.4837 (OUTLIER) cc_final: 0.4574 (tp) REVERT: d 63 MET cc_start: 0.2936 (OUTLIER) cc_final: 0.2703 (mtt) REVERT: d 77 LYS cc_start: 0.3641 (tmtt) cc_final: 0.3291 (tttt) REVERT: d 87 MET cc_start: 0.1322 (mmm) cc_final: 0.0571 (mpt) REVERT: d 134 LYS cc_start: 0.2571 (mptt) cc_final: 0.1234 (tptt) REVERT: d 153 GLU cc_start: 0.1801 (mm-30) cc_final: 0.1524 (tp30) REVERT: d 156 GLU cc_start: 0.2028 (OUTLIER) cc_final: 0.1580 (mm-30) REVERT: d 165 LEU cc_start: 0.1936 (OUTLIER) cc_final: 0.0687 (mt) REVERT: d 196 GLU cc_start: 0.2659 (pm20) cc_final: 0.2109 (pm20) REVERT: e 10 GLU cc_start: 0.2601 (OUTLIER) cc_final: 0.1311 (mm-30) REVERT: e 13 GLU cc_start: 0.2348 (OUTLIER) cc_final: 0.1465 (mp0) REVERT: e 136 MET cc_start: 0.3660 (tpt) cc_final: 0.2758 (tpt) REVERT: e 163 GLU cc_start: 0.1780 (OUTLIER) cc_final: 0.0989 (pt0) REVERT: g 36 ARG cc_start: 0.3046 (tpp80) cc_final: 0.2757 (mmt180) REVERT: g 70 MET cc_start: 0.1164 (mmm) cc_final: 0.0696 (mmt) REVERT: g 94 GLU cc_start: 0.2620 (OUTLIER) cc_final: 0.2032 (mt-10) REVERT: h 3 MET cc_start: 0.2843 (OUTLIER) cc_final: 0.2027 (pmm) REVERT: h 39 ILE cc_start: 0.1717 (OUTLIER) cc_final: 0.1492 (mm) REVERT: h 53 GLU cc_start: 0.2866 (OUTLIER) cc_final: 0.1148 (pm20) REVERT: h 64 LEU cc_start: 0.2449 (mp) cc_final: 0.2231 (mt) REVERT: h 82 LYS cc_start: 0.3568 (OUTLIER) cc_final: 0.3352 (tptp) REVERT: i 20 ARG cc_start: 0.2340 (pmt170) cc_final: 0.1995 (pmt-80) REVERT: i 35 ARG cc_start: 0.2420 (ptm160) cc_final: 0.1891 (ttt-90) REVERT: i 46 LEU cc_start: 0.1955 (OUTLIER) cc_final: 0.1438 (tt) REVERT: i 66 LEU cc_start: 0.1344 (OUTLIER) cc_final: 0.1059 (pt) REVERT: i 114 GLU cc_start: 0.2492 (OUTLIER) cc_final: 0.2098 (tm-30) REVERT: j 11 LYS cc_start: 0.3763 (OUTLIER) cc_final: 0.2612 (tppp) REVERT: j 66 GLU cc_start: 0.0541 (OUTLIER) cc_final: -0.1054 (pp20) REVERT: j 88 MET cc_start: 0.3421 (OUTLIER) cc_final: 0.2426 (ttm) REVERT: l 9 ARG cc_start: 0.2385 (ttp-170) cc_final: 0.1010 (tmm-80) REVERT: l 33 LYS cc_start: 0.6016 (mppt) cc_final: 0.5611 (mmtm) REVERT: l 67 ARG cc_start: 0.4449 (OUTLIER) cc_final: 0.3808 (tpp80) REVERT: l 99 ARG cc_start: 0.3536 (OUTLIER) cc_final: 0.3205 (ttm-80) REVERT: m 63 TYR cc_start: 0.2112 (OUTLIER) cc_final: 0.1871 (p90) REVERT: n 6 MET cc_start: 0.1659 (mpp) cc_final: 0.0642 (tpt) REVERT: n 52 GLN cc_start: 0.3520 (OUTLIER) cc_final: 0.2365 (tp-100) REVERT: o 3 ILE cc_start: 0.2335 (OUTLIER) cc_final: 0.1996 (tt) REVERT: o 15 TYR cc_start: 0.2428 (OUTLIER) cc_final: 0.1039 (m-10) REVERT: o 28 GLN cc_start: 0.2000 (OUTLIER) cc_final: 0.1559 (pt0) REVERT: o 74 ASP cc_start: 0.1855 (OUTLIER) cc_final: 0.0302 (m-30) REVERT: p 32 ARG cc_start: 0.3487 (OUTLIER) cc_final: 0.3152 (pmt170) REVERT: p 81 MET cc_start: 0.3470 (mmm) cc_final: 0.3252 (mmm) REVERT: q 38 LYS cc_start: 0.4614 (tttp) cc_final: 0.4267 (ttpt) REVERT: q 43 SER cc_start: 0.1129 (OUTLIER) cc_final: 0.0925 (t) REVERT: q 77 LEU cc_start: 0.3798 (OUTLIER) cc_final: 0.2889 (pp) REVERT: r 70 MET cc_start: 0.1885 (mmt) cc_final: 0.0534 (ptt) REVERT: u 17 ARG cc_start: 0.2137 (OUTLIER) cc_final: 0.1436 (mtt180) REVERT: v 4 PHE cc_start: -0.1121 (OUTLIER) cc_final: -0.1477 (m-10) REVERT: v 37 ASN cc_start: 0.1226 (OUTLIER) cc_final: 0.0868 (m-40) REVERT: v 45 LYS cc_start: 0.1119 (OUTLIER) cc_final: -0.0817 (tmtt) outliers start: 367 outliers final: 204 residues processed: 881 average time/residue: 2.2106 time to fit residues: 2747.3348 Evaluate side-chains 814 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 552 time to evaluate : 5.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 3 ASN Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 110 ARG Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 120 ASN Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 118 LYS Chi-restraints excluded: chain I residue 5 GLU Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 59 LYS Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 82 ARG Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain L residue 34 GLU Chi-restraints excluded: chain L residue 45 GLU Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain M residue 6 ASP Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 87 LYS Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 84 GLU Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 51 ARG Chi-restraints excluded: chain O residue 74 MET Chi-restraints excluded: chain O residue 90 ILE Chi-restraints excluded: chain O residue 108 GLN Chi-restraints excluded: chain P residue 26 ASP Chi-restraints excluded: chain P residue 63 ASN Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 14 GLU Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 93 ILE Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain U residue 72 ASP Chi-restraints excluded: chain U residue 75 VAL Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain W residue 2 LYS Chi-restraints excluded: chain W residue 14 ILE Chi-restraints excluded: chain W residue 25 LEU Chi-restraints excluded: chain W residue 30 PHE Chi-restraints excluded: chain W residue 63 GLU Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain Z residue 7 ARG Chi-restraints excluded: chain Z residue 8 THR Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 30 CYS Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 2 residue 31 VAL Chi-restraints excluded: chain 3 residue 14 VAL Chi-restraints excluded: chain 4 residue 7 VAL Chi-restraints excluded: chain 4 residue 20 LYS Chi-restraints excluded: chain b residue 11 GLU Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 59 GLN Chi-restraints excluded: chain b residue 60 VAL Chi-restraints excluded: chain b residue 62 GLU Chi-restraints excluded: chain b residue 101 LEU Chi-restraints excluded: chain b residue 105 LYS Chi-restraints excluded: chain b residue 116 GLU Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 169 GLU Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 187 VAL Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 35 ASP Chi-restraints excluded: chain c residue 42 ILE Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain c residue 78 LYS Chi-restraints excluded: chain c residue 94 THR Chi-restraints excluded: chain c residue 105 ILE Chi-restraints excluded: chain c residue 113 ARG Chi-restraints excluded: chain c residue 167 TYR Chi-restraints excluded: chain c residue 183 TYR Chi-restraints excluded: chain c residue 197 VAL Chi-restraints excluded: chain c residue 201 ILE Chi-restraints excluded: chain d residue 4 PHE Chi-restraints excluded: chain d residue 10 LYS Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 49 LEU Chi-restraints excluded: chain d residue 63 MET Chi-restraints excluded: chain d residue 71 THR Chi-restraints excluded: chain d residue 103 LEU Chi-restraints excluded: chain d residue 156 GLU Chi-restraints excluded: chain d residue 165 LEU Chi-restraints excluded: chain e residue 10 GLU Chi-restraints excluded: chain e residue 13 GLU Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 72 VAL Chi-restraints excluded: chain e residue 91 SER Chi-restraints excluded: chain e residue 106 ILE Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain e residue 141 ILE Chi-restraints excluded: chain e residue 163 GLU Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 14 ILE Chi-restraints excluded: chain f residue 20 LYS Chi-restraints excluded: chain f residue 38 LEU Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 68 ASP Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 87 ILE Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 64 GLU Chi-restraints excluded: chain g residue 94 GLU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain h residue 3 MET Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 24 LYS Chi-restraints excluded: chain h residue 26 GLU Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain h residue 47 LYS Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 70 ASP Chi-restraints excluded: chain h residue 82 LYS Chi-restraints excluded: chain h residue 112 VAL Chi-restraints excluded: chain h residue 113 ILE Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 37 VAL Chi-restraints excluded: chain i residue 40 TYR Chi-restraints excluded: chain i residue 46 LEU Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 66 LEU Chi-restraints excluded: chain i residue 112 MET Chi-restraints excluded: chain i residue 114 GLU Chi-restraints excluded: chain i residue 129 PHE Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 11 LYS Chi-restraints excluded: chain j residue 66 GLU Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain k residue 100 LEU Chi-restraints excluded: chain k residue 101 GLN Chi-restraints excluded: chain l residue 36 THR Chi-restraints excluded: chain l residue 42 GLN Chi-restraints excluded: chain l residue 47 CYS Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 62 LEU Chi-restraints excluded: chain l residue 67 ARG Chi-restraints excluded: chain l residue 73 ASN Chi-restraints excluded: chain l residue 99 ARG Chi-restraints excluded: chain l residue 100 VAL Chi-restraints excluded: chain l residue 115 LEU Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain m residue 57 ARG Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 63 TYR Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain m residue 108 THR Chi-restraints excluded: chain n residue 4 THR Chi-restraints excluded: chain n residue 31 HIS Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 38 LYS Chi-restraints excluded: chain n residue 50 LYS Chi-restraints excluded: chain n residue 52 GLN Chi-restraints excluded: chain o residue 3 ILE Chi-restraints excluded: chain o residue 15 TYR Chi-restraints excluded: chain o residue 17 VAL Chi-restraints excluded: chain o residue 28 GLN Chi-restraints excluded: chain o residue 74 ASP Chi-restraints excluded: chain o residue 81 LEU Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 32 ARG Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain q residue 43 SER Chi-restraints excluded: chain q residue 48 THR Chi-restraints excluded: chain q residue 51 GLU Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain q residue 76 ARG Chi-restraints excluded: chain q residue 77 LEU Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 24 THR Chi-restraints excluded: chain r residue 50 THR Chi-restraints excluded: chain s residue 29 GLN Chi-restraints excluded: chain s residue 31 ILE Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain u residue 17 ARG Chi-restraints excluded: chain v residue 4 PHE Chi-restraints excluded: chain v residue 17 ILE Chi-restraints excluded: chain v residue 28 LEU Chi-restraints excluded: chain v residue 37 ASN Chi-restraints excluded: chain v residue 44 VAL Chi-restraints excluded: chain v residue 45 LYS Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 52 THR Chi-restraints excluded: chain v residue 57 THR Chi-restraints excluded: chain v residue 74 LEU Chi-restraints excluded: chain v residue 94 THR Chi-restraints excluded: chain v residue 151 LEU Chi-restraints excluded: chain v residue 184 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 923 optimal weight: 8.9990 chunk 107 optimal weight: 20.0000 chunk 545 optimal weight: 10.0000 chunk 699 optimal weight: 50.0000 chunk 541 optimal weight: 3.9990 chunk 806 optimal weight: 0.0170 chunk 534 optimal weight: 0.7980 chunk 954 optimal weight: 0.9990 chunk 597 optimal weight: 50.0000 chunk 581 optimal weight: 8.9990 chunk 440 optimal weight: 3.9990 overall best weight: 1.9624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 133 GLN C 199 GLN D 134 HIS E 174 GLN G 147 ASN H 3 GLN H 137 GLN J 70 ASN Q 95 ASN R 69 GLN S 39 ASN T 78 GLN ** U 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 25 ASN 3 31 HIS 3 43 GLN b 44 GLN ** c 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 61 ASN ** g 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 70 HIS l 109 HIS ** p 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 69 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6066 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.600 152951 Z= 0.300 Angle : 0.856 62.772 229118 Z= 0.412 Chirality : 0.050 2.156 29467 Planarity : 0.005 0.101 12075 Dihedral : 25.976 179.989 77016 Min Nonbonded Distance : 1.508 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.69 % Favored : 92.29 % Rotamer: Outliers : 8.00 % Allowed : 28.54 % Favored : 63.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.00 % 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: -2.04 (0.11), residues: 5487 helix: -0.59 (0.13), residues: 1563 sheet: -0.95 (0.16), residues: 981 loop : -1.96 (0.11), residues: 2943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 250 HIS 0.022 0.001 HIS S 44 PHE 0.031 0.001 PHE g 47 TYR 0.019 0.001 TYR s 61 ARG 0.016 0.001 ARG v 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10974 Ramachandran restraints generated. 5487 Oldfield, 0 Emsley, 5487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10974 Ramachandran restraints generated. 5487 Oldfield, 0 Emsley, 5487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 915 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 355 poor density : 560 time to evaluate : 5.949 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "VAL J 145 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 125 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.8065 (ptpp) REVERT: D 100 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7079 (mp0) REVERT: D 104 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7191 (mm-30) REVERT: E 200 LYS cc_start: 0.8561 (mmtm) cc_final: 0.8167 (mtmm) REVERT: F 17 MET cc_start: 0.3835 (mmm) cc_final: 0.3585 (mmp) REVERT: F 110 ARG cc_start: 0.4049 (OUTLIER) cc_final: 0.3690 (mpp80) REVERT: F 175 MET cc_start: 0.2855 (pp-130) cc_final: 0.2592 (tpp) REVERT: G 30 LYS cc_start: 0.4311 (OUTLIER) cc_final: 0.3851 (mptt) REVERT: G 87 LEU cc_start: 0.5281 (OUTLIER) cc_final: 0.4818 (pt) REVERT: G 120 ASN cc_start: 0.6045 (OUTLIER) cc_final: 0.5188 (m-40) REVERT: G 121 ILE cc_start: 0.6521 (OUTLIER) cc_final: 0.6292 (mp) REVERT: H 85 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8706 (tp) REVERT: I 4 GLN cc_start: 0.7959 (tt0) cc_final: 0.7501 (tt0) REVERT: I 5 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8095 (mm-30) REVERT: J 73 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.6930 (mm-30) REVERT: L 34 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7481 (tt0) REVERT: O 51 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.8293 (mtt-85) REVERT: O 108 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7990 (tt0) REVERT: T 7 ILE cc_start: 0.8285 (mp) cc_final: 0.8025 (mp) REVERT: T 21 LEU cc_start: 0.8790 (tt) cc_final: 0.8579 (tp) REVERT: T 57 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.6479 (tpt-90) REVERT: W 30 PHE cc_start: 0.8390 (OUTLIER) cc_final: 0.7620 (t80) REVERT: 4 20 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8084 (mppt) REVERT: b 11 GLU cc_start: 0.2688 (OUTLIER) cc_final: 0.1911 (pt0) REVERT: b 19 GLN cc_start: 0.1499 (OUTLIER) cc_final: 0.1121 (tm-30) REVERT: b 22 ARG cc_start: 0.2547 (mmm-85) cc_final: 0.1830 (mtm110) REVERT: b 35 ARG cc_start: 0.2751 (ttt90) cc_final: 0.1797 (mtp85) REVERT: b 51 ASP cc_start: 0.4607 (OUTLIER) cc_final: 0.4270 (p0) REVERT: b 59 GLN cc_start: 0.3676 (OUTLIER) cc_final: 0.3243 (mt0) REVERT: b 95 ARG cc_start: 0.1485 (ptt180) cc_final: 0.0728 (ttm170) REVERT: b 143 ARG cc_start: 0.1786 (ttm170) cc_final: 0.0970 (mmm-85) REVERT: b 168 LYS cc_start: 0.4500 (mttt) cc_final: 0.3012 (tttt) REVERT: b 169 GLU cc_start: 0.3476 (OUTLIER) cc_final: 0.2958 (mm-30) REVERT: b 170 ARG cc_start: 0.2337 (tpm170) cc_final: 0.2050 (tpm-80) REVERT: b 208 ARG cc_start: 0.3396 (mtp85) cc_final: 0.2705 (ptm-80) REVERT: b 213 LEU cc_start: 0.2701 (OUTLIER) cc_final: 0.2135 (tp) REVERT: c 57 GLU cc_start: 0.1327 (OUTLIER) cc_final: 0.0999 (tp30) REVERT: c 78 LYS cc_start: 0.3137 (OUTLIER) cc_final: 0.2649 (mtpp) REVERT: c 105 ILE cc_start: 0.0823 (OUTLIER) cc_final: 0.0466 (tp) REVERT: c 124 GLU cc_start: 0.1563 (mp0) cc_final: 0.1275 (mm-30) REVERT: c 163 ARG cc_start: 0.2734 (mtm110) cc_final: 0.1872 (mpt-90) REVERT: d 5 ARG cc_start: 0.2133 (mtm110) cc_final: 0.0548 (mmt-90) REVERT: d 10 LYS cc_start: 0.3021 (OUTLIER) cc_final: 0.1687 (ttmt) REVERT: d 26 LEU cc_start: 0.3759 (OUTLIER) cc_final: 0.3121 (pp) REVERT: d 49 LEU cc_start: 0.4909 (OUTLIER) cc_final: 0.4605 (tp) REVERT: d 63 MET cc_start: 0.2866 (OUTLIER) cc_final: 0.2575 (mtt) REVERT: d 78 LYS cc_start: 0.2703 (mtpt) cc_final: 0.1711 (tptp) REVERT: d 87 MET cc_start: 0.1790 (mmm) cc_final: 0.1000 (mpt) REVERT: d 134 LYS cc_start: 0.2505 (mptt) cc_final: 0.1211 (tptt) REVERT: d 153 GLU cc_start: 0.2083 (mm-30) cc_final: 0.1766 (tp30) REVERT: d 156 GLU cc_start: 0.1814 (OUTLIER) cc_final: 0.1422 (mm-30) REVERT: d 165 LEU cc_start: 0.1947 (OUTLIER) cc_final: 0.0743 (mt) REVERT: d 196 GLU cc_start: 0.2766 (pm20) cc_final: 0.2361 (pm20) REVERT: e 10 GLU cc_start: 0.2095 (OUTLIER) cc_final: 0.0981 (mm-30) REVERT: e 13 GLU cc_start: 0.2778 (OUTLIER) cc_final: 0.1600 (mm-30) REVERT: e 136 MET cc_start: 0.3637 (tpt) cc_final: 0.2720 (tpt) REVERT: f 90 MET cc_start: -0.0165 (pmt) cc_final: -0.0550 (mmt) REVERT: g 36 ARG cc_start: 0.3095 (tpp80) cc_final: 0.2823 (mmt180) REVERT: g 70 MET cc_start: 0.1095 (mmm) cc_final: 0.0532 (pmm) REVERT: g 94 GLU cc_start: 0.2502 (OUTLIER) cc_final: 0.2023 (mt-10) REVERT: h 3 MET cc_start: 0.3039 (OUTLIER) cc_final: 0.2194 (pmm) REVERT: h 53 GLU cc_start: 0.2892 (OUTLIER) cc_final: 0.1469 (pm20) REVERT: h 64 LEU cc_start: 0.2618 (mp) cc_final: 0.2379 (mt) REVERT: h 113 ILE cc_start: 0.3205 (OUTLIER) cc_final: 0.2343 (mp) REVERT: i 20 ARG cc_start: 0.2297 (pmt170) cc_final: 0.2046 (pmt170) REVERT: i 35 ARG cc_start: 0.2470 (ptm160) cc_final: 0.1813 (ttt-90) REVERT: i 46 LEU cc_start: 0.1780 (OUTLIER) cc_final: 0.1235 (tt) REVERT: i 66 LEU cc_start: 0.1260 (OUTLIER) cc_final: 0.0979 (pt) REVERT: i 112 MET cc_start: 0.3243 (OUTLIER) cc_final: 0.2557 (tpp) REVERT: i 114 GLU cc_start: 0.2613 (OUTLIER) cc_final: 0.2115 (tm-30) REVERT: j 11 LYS cc_start: 0.4078 (OUTLIER) cc_final: 0.2993 (tppp) REVERT: j 66 GLU cc_start: 0.0776 (OUTLIER) cc_final: -0.0885 (pp20) REVERT: j 88 MET cc_start: 0.3614 (mpt) cc_final: 0.2591 (ttm) REVERT: k 101 GLN cc_start: 0.2399 (OUTLIER) cc_final: 0.1474 (pm20) REVERT: l 9 ARG cc_start: 0.1951 (ttp-170) cc_final: 0.0733 (tmm-80) REVERT: l 33 LYS cc_start: 0.5996 (mppt) cc_final: 0.5571 (mmtm) REVERT: l 67 ARG cc_start: 0.4382 (OUTLIER) cc_final: 0.3783 (tpp80) REVERT: l 99 ARG cc_start: 0.3379 (OUTLIER) cc_final: 0.3050 (ttm-80) REVERT: m 63 TYR cc_start: 0.2396 (OUTLIER) cc_final: 0.2093 (p90) REVERT: m 110 LYS cc_start: 0.3824 (OUTLIER) cc_final: 0.2692 (mtpt) REVERT: n 6 MET cc_start: 0.1655 (mpp) cc_final: 0.0638 (tpt) REVERT: n 52 GLN cc_start: 0.3426 (OUTLIER) cc_final: 0.2267 (tp-100) REVERT: o 3 ILE cc_start: 0.2347 (OUTLIER) cc_final: 0.1735 (tp) REVERT: o 15 TYR cc_start: 0.2460 (OUTLIER) cc_final: 0.1011 (m-10) REVERT: o 28 GLN cc_start: 0.2185 (OUTLIER) cc_final: 0.1747 (pt0) REVERT: o 59 MET cc_start: 0.3177 (OUTLIER) cc_final: 0.2944 (ptt) REVERT: o 74 ASP cc_start: 0.1832 (OUTLIER) cc_final: 0.0321 (m-30) REVERT: q 38 LYS cc_start: 0.4600 (tttp) cc_final: 0.4278 (ttpt) REVERT: r 70 MET cc_start: 0.1894 (mmt) cc_final: 0.0493 (ptt) REVERT: t 73 ARG cc_start: 0.2005 (OUTLIER) cc_final: 0.1491 (ttp-170) REVERT: u 12 LEU cc_start: 0.0506 (OUTLIER) cc_final: 0.0170 (mt) REVERT: u 17 ARG cc_start: 0.2071 (OUTLIER) cc_final: 0.1460 (mtt180) REVERT: v 4 PHE cc_start: -0.0775 (OUTLIER) cc_final: -0.1151 (m-10) REVERT: v 37 ASN cc_start: 0.1000 (OUTLIER) cc_final: 0.0676 (m-40) REVERT: v 45 LYS cc_start: 0.1119 (OUTLIER) cc_final: -0.0784 (tmtt) REVERT: v 144 MET cc_start: 0.1186 (pmt) cc_final: 0.0573 (mmt) outliers start: 355 outliers final: 212 residues processed: 853 average time/residue: 2.1233 time to fit residues: 2558.4463 Evaluate side-chains 813 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 541 time to evaluate : 5.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 193 LYS Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 3 ASN Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 110 ARG Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 120 ASN Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 118 LYS Chi-restraints excluded: chain I residue 5 GLU Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 59 LYS Chi-restraints excluded: chain I residue 116 SER Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 73 GLU Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 34 GLU Chi-restraints excluded: chain L residue 45 GLU Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain M residue 6 ASP Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 84 GLU Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 16 LYS Chi-restraints excluded: chain O residue 51 ARG Chi-restraints excluded: chain O residue 74 MET Chi-restraints excluded: chain O residue 90 ILE Chi-restraints excluded: chain O residue 103 GLU Chi-restraints excluded: chain O residue 108 GLN Chi-restraints excluded: chain P residue 26 ASP Chi-restraints excluded: chain P residue 63 ASN Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 14 GLU Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain S residue 3 ILE Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 57 ARG Chi-restraints excluded: chain U residue 72 ASP Chi-restraints excluded: chain U residue 75 VAL Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain W residue 14 ILE Chi-restraints excluded: chain W residue 25 LEU Chi-restraints excluded: chain W residue 30 PHE Chi-restraints excluded: chain W residue 63 GLU Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain Y residue 5 ILE Chi-restraints excluded: chain Z residue 7 ARG Chi-restraints excluded: chain Z residue 8 THR Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 30 CYS Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 2 residue 31 VAL Chi-restraints excluded: chain 3 residue 14 VAL Chi-restraints excluded: chain 4 residue 7 VAL Chi-restraints excluded: chain 4 residue 20 LYS Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 11 GLU Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 18 HIS Chi-restraints excluded: chain b residue 19 GLN Chi-restraints excluded: chain b residue 51 ASP Chi-restraints excluded: chain b residue 59 GLN Chi-restraints excluded: chain b residue 60 VAL Chi-restraints excluded: chain b residue 89 GLN Chi-restraints excluded: chain b residue 101 LEU Chi-restraints excluded: chain b residue 105 LYS Chi-restraints excluded: chain b residue 116 GLU Chi-restraints excluded: chain b residue 169 GLU Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain c residue 78 LYS Chi-restraints excluded: chain c residue 94 THR Chi-restraints excluded: chain c residue 105 ILE Chi-restraints excluded: chain c residue 113 ARG Chi-restraints excluded: chain c residue 115 VAL Chi-restraints excluded: chain c residue 118 ASN Chi-restraints excluded: chain c residue 160 ASP Chi-restraints excluded: chain c residue 167 TYR Chi-restraints excluded: chain c residue 183 TYR Chi-restraints excluded: chain c residue 197 VAL Chi-restraints excluded: chain d residue 4 PHE Chi-restraints excluded: chain d residue 10 LYS Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 49 LEU Chi-restraints excluded: chain d residue 63 MET Chi-restraints excluded: chain d residue 71 THR Chi-restraints excluded: chain d residue 114 VAL Chi-restraints excluded: chain d residue 156 GLU Chi-restraints excluded: chain d residue 165 LEU Chi-restraints excluded: chain e residue 10 GLU Chi-restraints excluded: chain e residue 13 GLU Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 72 VAL Chi-restraints excluded: chain e residue 106 ILE Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain e residue 141 ILE Chi-restraints excluded: chain e residue 163 GLU Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 14 ILE Chi-restraints excluded: chain f residue 20 LYS Chi-restraints excluded: chain f residue 38 LEU Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 68 ASP Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 87 ILE Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 64 GLU Chi-restraints excluded: chain g residue 94 GLU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain h residue 3 MET Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 24 LYS Chi-restraints excluded: chain h residue 26 GLU Chi-restraints excluded: chain h residue 47 LYS Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 70 ASP Chi-restraints excluded: chain h residue 112 VAL Chi-restraints excluded: chain h residue 113 ILE Chi-restraints excluded: chain i residue 37 VAL Chi-restraints excluded: chain i residue 40 TYR Chi-restraints excluded: chain i residue 46 LEU Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 66 LEU Chi-restraints excluded: chain i residue 112 MET Chi-restraints excluded: chain i residue 114 GLU Chi-restraints excluded: chain i residue 129 PHE Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 11 LYS Chi-restraints excluded: chain j residue 66 GLU Chi-restraints excluded: chain k residue 100 LEU Chi-restraints excluded: chain k residue 101 GLN Chi-restraints excluded: chain l residue 42 GLN Chi-restraints excluded: chain l residue 47 CYS Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 62 LEU Chi-restraints excluded: chain l residue 67 ARG Chi-restraints excluded: chain l residue 73 ASN Chi-restraints excluded: chain l residue 99 ARG Chi-restraints excluded: chain l residue 100 VAL Chi-restraints excluded: chain l residue 115 LEU Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain m residue 57 ARG Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 63 TYR Chi-restraints excluded: chain m residue 79 ARG Chi-restraints excluded: chain m residue 108 THR Chi-restraints excluded: chain m residue 110 LYS Chi-restraints excluded: chain n residue 4 THR Chi-restraints excluded: chain n residue 31 HIS Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 38 LYS Chi-restraints excluded: chain n residue 52 GLN Chi-restraints excluded: chain o residue 3 ILE Chi-restraints excluded: chain o residue 15 TYR Chi-restraints excluded: chain o residue 17 VAL Chi-restraints excluded: chain o residue 28 GLN Chi-restraints excluded: chain o residue 59 MET Chi-restraints excluded: chain o residue 74 ASP Chi-restraints excluded: chain o residue 81 LEU Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 32 ARG Chi-restraints excluded: chain q residue 51 GLU Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain q residue 76 ARG Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 24 THR Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 50 THR Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 31 ILE Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain t residue 73 ARG Chi-restraints excluded: chain u residue 12 LEU Chi-restraints excluded: chain u residue 17 ARG Chi-restraints excluded: chain v residue 4 PHE Chi-restraints excluded: chain v residue 17 ILE Chi-restraints excluded: chain v residue 28 LEU Chi-restraints excluded: chain v residue 37 ASN Chi-restraints excluded: chain v residue 44 VAL Chi-restraints excluded: chain v residue 45 LYS Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 52 THR Chi-restraints excluded: chain v residue 57 THR Chi-restraints excluded: chain v residue 74 LEU Chi-restraints excluded: chain v residue 94 THR Chi-restraints excluded: chain v residue 151 LEU Chi-restraints excluded: chain v residue 184 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 590 optimal weight: 8.9990 chunk 381 optimal weight: 6.9990 chunk 569 optimal weight: 10.0000 chunk 287 optimal weight: 4.9990 chunk 187 optimal weight: 30.0000 chunk 184 optimal weight: 6.9990 chunk 606 optimal weight: 40.0000 chunk 650 optimal weight: 40.0000 chunk 471 optimal weight: 10.0000 chunk 88 optimal weight: 7.9990 chunk 750 optimal weight: 4.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 133 GLN C 199 GLN E 174 GLN G 23 HIS H 3 GLN M 43 GLN ** O 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 95 ASN S 39 ASN ** S 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 78 GLN 1 25 ASN 3 31 HIS ** b 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 33 HIS ** c 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 109 HIS o 9 ASN ** p 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 69 HIS t 24 GLN t 62 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6241 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.599 152951 Z= 0.544 Angle : 1.235 62.856 229118 Z= 0.582 Chirality : 0.064 2.163 29467 Planarity : 0.007 0.086 12075 Dihedral : 26.270 179.838 76988 Min Nonbonded Distance : 1.507 Molprobity Statistics. All-atom Clashscore : 22.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.59 % Favored : 90.38 % Rotamer: Outliers : 8.15 % Allowed : 28.47 % Favored : 63.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.07 % 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: -2.23 (0.11), residues: 5487 helix: -0.85 (0.13), residues: 1554 sheet: -1.00 (0.16), residues: 974 loop : -2.03 (0.11), residues: 2959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP C 250 HIS 0.023 0.002 HIS S 44 PHE 0.034 0.003 PHE g 47 TYR 0.029 0.003 TYR O 32 ARG 0.013 0.001 ARG O 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10974 Ramachandran restraints generated. 5487 Oldfield, 0 Emsley, 5487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10974 Ramachandran restraints generated. 5487 Oldfield, 0 Emsley, 5487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 894 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 362 poor density : 532 time to evaluate : 5.969 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 3 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8378 (mt) REVERT: C 125 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8093 (ptpp) REVERT: C 207 LYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8466 (ptmm) REVERT: D 100 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7138 (mp0) REVERT: D 159 ASP cc_start: 0.7217 (OUTLIER) cc_final: 0.6877 (m-30) REVERT: E 200 LYS cc_start: 0.8592 (mmtm) cc_final: 0.8200 (mtmm) REVERT: F 17 MET cc_start: 0.3852 (mmm) cc_final: 0.3612 (mmp) REVERT: F 110 ARG cc_start: 0.4135 (OUTLIER) cc_final: 0.3815 (mpp80) REVERT: G 30 LYS cc_start: 0.4346 (OUTLIER) cc_final: 0.3840 (mttt) REVERT: G 87 LEU cc_start: 0.5955 (OUTLIER) cc_final: 0.5574 (pt) REVERT: G 121 ILE cc_start: 0.6587 (OUTLIER) cc_final: 0.6362 (mp) REVERT: H 85 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8837 (tp) REVERT: I 4 GLN cc_start: 0.8106 (tt0) cc_final: 0.7734 (tt0) REVERT: I 5 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8280 (mp0) REVERT: J 73 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7024 (mm-30) REVERT: L 31 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.7018 (tt0) REVERT: O 16 LYS cc_start: 0.8462 (ptpp) cc_final: 0.8229 (ptpt) REVERT: O 59 LYS cc_start: 0.8584 (ttpt) cc_final: 0.8306 (ttmm) REVERT: O 108 GLN cc_start: 0.8352 (tt0) cc_final: 0.8111 (tt0) REVERT: T 7 ILE cc_start: 0.8307 (mp) cc_final: 0.8039 (mp) REVERT: T 57 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.6468 (tpt-90) REVERT: W 30 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.8035 (m-80) REVERT: X 17 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.7098 (tp30) REVERT: 2 15 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.7763 (mptm) REVERT: 3 59 LYS cc_start: 0.8323 (ttpp) cc_final: 0.7727 (ttmm) REVERT: 4 20 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8166 (mppt) REVERT: b 19 GLN cc_start: 0.1220 (OUTLIER) cc_final: 0.0976 (tm-30) REVERT: b 22 ARG cc_start: 0.2683 (OUTLIER) cc_final: 0.1860 (mtm110) REVERT: b 51 ASP cc_start: 0.4572 (OUTLIER) cc_final: 0.4199 (p0) REVERT: b 59 GLN cc_start: 0.3697 (OUTLIER) cc_final: 0.3217 (mm110) REVERT: b 143 ARG cc_start: 0.1866 (ttm170) cc_final: 0.1032 (mmm-85) REVERT: b 168 LYS cc_start: 0.4380 (mttt) cc_final: 0.2964 (tttt) REVERT: b 169 GLU cc_start: 0.3686 (OUTLIER) cc_final: 0.3280 (mm-30) REVERT: b 177 ARG cc_start: 0.2430 (mmt180) cc_final: 0.1375 (mmm160) REVERT: b 208 ARG cc_start: 0.3445 (mtp85) cc_final: 0.2800 (ptm-80) REVERT: b 213 LEU cc_start: 0.2867 (OUTLIER) cc_final: 0.2203 (tp) REVERT: c 57 GLU cc_start: 0.1471 (OUTLIER) cc_final: 0.0941 (tp30) REVERT: c 78 LYS cc_start: 0.3121 (OUTLIER) cc_final: 0.2724 (mtpp) REVERT: c 105 ILE cc_start: 0.1175 (OUTLIER) cc_final: 0.0866 (tp) REVERT: c 163 ARG cc_start: 0.2899 (mtm110) cc_final: 0.1983 (mpt-90) REVERT: d 5 ARG cc_start: 0.2124 (mtm110) cc_final: 0.0569 (mmm-85) REVERT: d 26 LEU cc_start: 0.3710 (OUTLIER) cc_final: 0.3092 (pp) REVERT: d 49 LEU cc_start: 0.4941 (OUTLIER) cc_final: 0.4662 (tp) REVERT: d 63 MET cc_start: 0.3356 (pp-130) cc_final: 0.2799 (mtt) REVERT: d 87 MET cc_start: 0.1571 (mmm) cc_final: 0.0946 (mpt) REVERT: d 124 LYS cc_start: 0.1963 (tptp) cc_final: 0.1537 (tptt) REVERT: d 134 LYS cc_start: 0.2425 (mptt) cc_final: 0.1037 (tptt) REVERT: d 139 ILE cc_start: 0.2070 (OUTLIER) cc_final: 0.1389 (mp) REVERT: d 153 GLU cc_start: 0.2302 (mm-30) cc_final: 0.1914 (tp30) REVERT: d 156 GLU cc_start: 0.2204 (OUTLIER) cc_final: 0.1535 (mt-10) REVERT: d 196 GLU cc_start: 0.2998 (pm20) cc_final: 0.2511 (pm20) REVERT: e 10 GLU cc_start: 0.2330 (OUTLIER) cc_final: 0.1491 (mm-30) REVERT: e 13 GLU cc_start: 0.2317 (OUTLIER) cc_final: 0.1290 (mm-30) REVERT: e 136 MET cc_start: 0.3088 (tpt) cc_final: 0.2479 (tpt) REVERT: e 163 GLU cc_start: 0.1859 (OUTLIER) cc_final: 0.1057 (pt0) REVERT: f 90 MET cc_start: 0.0215 (pmt) cc_final: -0.0587 (mpp) REVERT: g 70 MET cc_start: 0.1324 (mmm) cc_final: 0.0467 (pmm) REVERT: g 94 GLU cc_start: 0.2416 (OUTLIER) cc_final: 0.2047 (mt-10) REVERT: h 3 MET cc_start: 0.3214 (OUTLIER) cc_final: 0.2562 (pmm) REVERT: h 53 GLU cc_start: 0.2943 (OUTLIER) cc_final: 0.1597 (pm20) REVERT: h 78 LYS cc_start: 0.2804 (tmtm) cc_final: 0.2524 (ttmm) REVERT: h 96 LYS cc_start: 0.2940 (tppp) cc_final: 0.1451 (mmmm) REVERT: i 20 ARG cc_start: 0.2374 (pmt170) cc_final: 0.1058 (pmt-80) REVERT: i 35 ARG cc_start: 0.2571 (ptm160) cc_final: 0.1873 (ttt180) REVERT: i 46 LEU cc_start: 0.1920 (OUTLIER) cc_final: 0.1422 (tt) REVERT: i 66 LEU cc_start: 0.1346 (OUTLIER) cc_final: 0.0935 (pt) REVERT: i 114 GLU cc_start: 0.2630 (OUTLIER) cc_final: 0.2004 (tm-30) REVERT: j 11 LYS cc_start: 0.3719 (OUTLIER) cc_final: 0.2671 (tppp) REVERT: j 31 ARG cc_start: 0.2911 (OUTLIER) cc_final: 0.1154 (ppt170) REVERT: j 88 MET cc_start: 0.3415 (mpt) cc_final: 0.2546 (ttm) REVERT: l 9 ARG cc_start: 0.2374 (ttp-170) cc_final: 0.1098 (tmm-80) REVERT: l 63 ARG cc_start: 0.3374 (OUTLIER) cc_final: 0.3172 (mmt-90) REVERT: l 67 ARG cc_start: 0.4484 (OUTLIER) cc_final: 0.3901 (tpp80) REVERT: l 95 VAL cc_start: 0.4354 (OUTLIER) cc_final: 0.4077 (p) REVERT: l 99 ARG cc_start: 0.3594 (OUTLIER) cc_final: 0.3350 (ttm-80) REVERT: m 63 TYR cc_start: 0.2501 (OUTLIER) cc_final: 0.2263 (p90) REVERT: m 77 ILE cc_start: 0.2406 (OUTLIER) cc_final: 0.2148 (pt) REVERT: m 110 LYS cc_start: 0.3762 (OUTLIER) cc_final: 0.2551 (mtpt) REVERT: n 6 MET cc_start: 0.1795 (mpp) cc_final: 0.0738 (tpt) REVERT: n 52 GLN cc_start: 0.3437 (OUTLIER) cc_final: 0.2166 (tp-100) REVERT: o 3 ILE cc_start: 0.2228 (OUTLIER) cc_final: 0.1620 (tp) REVERT: o 15 TYR cc_start: 0.2807 (OUTLIER) cc_final: 0.1318 (m-10) REVERT: o 28 GLN cc_start: 0.2519 (OUTLIER) cc_final: 0.1451 (mm-40) REVERT: o 74 ASP cc_start: 0.2166 (OUTLIER) cc_final: 0.0503 (m-30) REVERT: p 59 LYS cc_start: 0.3760 (OUTLIER) cc_final: 0.3225 (ptpp) REVERT: p 80 ILE cc_start: 0.2422 (OUTLIER) cc_final: 0.2152 (mt) REVERT: q 38 LYS cc_start: 0.4462 (tttp) cc_final: 0.3981 (tmmt) REVERT: r 70 MET cc_start: 0.1526 (mmt) cc_final: 0.0188 (ptt) REVERT: s 66 MET cc_start: 0.3206 (ppp) cc_final: 0.2958 (ppp) REVERT: t 73 ARG cc_start: 0.1955 (OUTLIER) cc_final: 0.1011 (ttp-170) REVERT: u 12 LEU cc_start: 0.0854 (OUTLIER) cc_final: 0.0563 (mt) REVERT: u 17 ARG cc_start: 0.2201 (OUTLIER) cc_final: 0.1689 (mtt-85) REVERT: v 4 PHE cc_start: -0.0938 (OUTLIER) cc_final: -0.1287 (m-10) REVERT: v 45 LYS cc_start: 0.1182 (OUTLIER) cc_final: -0.1008 (tmtt) outliers start: 362 outliers final: 236 residues processed: 840 average time/residue: 2.1524 time to fit residues: 2561.8991 Evaluate side-chains 820 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 297 poor density : 523 time to evaluate : 5.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 3 ASN Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 24 SER Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 110 ARG Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 120 ASN Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 118 LYS Chi-restraints excluded: chain I residue 5 GLU Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 59 LYS Chi-restraints excluded: chain I residue 116 SER Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 73 GLU Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 40 SER Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 31 GLU Chi-restraints excluded: chain L residue 34 GLU Chi-restraints excluded: chain L residue 45 GLU Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain M residue 6 ASP Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 84 GLU Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 74 MET Chi-restraints excluded: chain O residue 90 ILE Chi-restraints excluded: chain P residue 26 ASP Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 63 ASN Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 14 GLU Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain S residue 3 ILE Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 57 ARG Chi-restraints excluded: chain U residue 72 ASP Chi-restraints excluded: chain U residue 75 VAL Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain W residue 14 ILE Chi-restraints excluded: chain W residue 25 LEU Chi-restraints excluded: chain W residue 30 PHE Chi-restraints excluded: chain W residue 63 GLU Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain Y residue 5 ILE Chi-restraints excluded: chain Z residue 7 ARG Chi-restraints excluded: chain Z residue 8 THR Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 30 CYS Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 2 residue 14 SER Chi-restraints excluded: chain 2 residue 15 LYS Chi-restraints excluded: chain 2 residue 31 VAL Chi-restraints excluded: chain 3 residue 14 VAL Chi-restraints excluded: chain 4 residue 2 LYS Chi-restraints excluded: chain 4 residue 7 VAL Chi-restraints excluded: chain 4 residue 18 LYS Chi-restraints excluded: chain 4 residue 20 LYS Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 19 GLN Chi-restraints excluded: chain b residue 22 ARG Chi-restraints excluded: chain b residue 51 ASP Chi-restraints excluded: chain b residue 59 GLN Chi-restraints excluded: chain b residue 60 VAL Chi-restraints excluded: chain b residue 73 LYS Chi-restraints excluded: chain b residue 89 GLN Chi-restraints excluded: chain b residue 101 LEU Chi-restraints excluded: chain b residue 105 LYS Chi-restraints excluded: chain b residue 116 GLU Chi-restraints excluded: chain b residue 169 GLU Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain c residue 78 LYS Chi-restraints excluded: chain c residue 94 THR Chi-restraints excluded: chain c residue 102 VAL Chi-restraints excluded: chain c residue 105 ILE Chi-restraints excluded: chain c residue 113 ARG Chi-restraints excluded: chain c residue 115 VAL Chi-restraints excluded: chain c residue 167 TYR Chi-restraints excluded: chain c residue 183 TYR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 197 VAL Chi-restraints excluded: chain d residue 10 LYS Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 49 LEU Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 71 THR Chi-restraints excluded: chain d residue 107 ARG Chi-restraints excluded: chain d residue 139 ILE Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 156 GLU Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain e residue 10 GLU Chi-restraints excluded: chain e residue 13 GLU Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 72 VAL Chi-restraints excluded: chain e residue 91 SER Chi-restraints excluded: chain e residue 106 ILE Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain e residue 141 ILE Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 163 GLU Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 14 ILE Chi-restraints excluded: chain f residue 20 LYS Chi-restraints excluded: chain f residue 38 LEU Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 68 ASP Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 87 ILE Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 64 GLU Chi-restraints excluded: chain g residue 94 GLU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain h residue 3 MET Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 26 GLU Chi-restraints excluded: chain h residue 47 LYS Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 112 VAL Chi-restraints excluded: chain h residue 113 ILE Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 37 VAL Chi-restraints excluded: chain i residue 40 TYR Chi-restraints excluded: chain i residue 46 LEU Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 66 LEU Chi-restraints excluded: chain i residue 112 MET Chi-restraints excluded: chain i residue 114 GLU Chi-restraints excluded: chain i residue 129 PHE Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 11 LYS Chi-restraints excluded: chain j residue 31 ARG Chi-restraints excluded: chain j residue 66 GLU Chi-restraints excluded: chain k residue 43 SER Chi-restraints excluded: chain k residue 53 LYS Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 94 GLU Chi-restraints excluded: chain k residue 100 LEU Chi-restraints excluded: chain k residue 101 GLN Chi-restraints excluded: chain l residue 42 GLN Chi-restraints excluded: chain l residue 47 CYS Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 62 LEU Chi-restraints excluded: chain l residue 63 ARG Chi-restraints excluded: chain l residue 67 ARG Chi-restraints excluded: chain l residue 73 ASN Chi-restraints excluded: chain l residue 95 VAL Chi-restraints excluded: chain l residue 99 ARG Chi-restraints excluded: chain l residue 100 VAL Chi-restraints excluded: chain l residue 115 LEU Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain m residue 57 ARG Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 63 TYR Chi-restraints excluded: chain m residue 77 ILE Chi-restraints excluded: chain m residue 79 ARG Chi-restraints excluded: chain m residue 108 THR Chi-restraints excluded: chain m residue 110 LYS Chi-restraints excluded: chain n residue 4 THR Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 38 LYS Chi-restraints excluded: chain n residue 52 GLN Chi-restraints excluded: chain n residue 56 VAL Chi-restraints excluded: chain o residue 3 ILE Chi-restraints excluded: chain o residue 15 TYR Chi-restraints excluded: chain o residue 17 VAL Chi-restraints excluded: chain o residue 28 GLN Chi-restraints excluded: chain o residue 74 ASP Chi-restraints excluded: chain o residue 81 LEU Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 32 ARG Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 59 LYS Chi-restraints excluded: chain p residue 80 ILE Chi-restraints excluded: chain q residue 51 GLU Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain q residue 76 ARG Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 24 THR Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 50 THR Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 31 ILE Chi-restraints excluded: chain s residue 44 PHE Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain t residue 73 ARG Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 12 LEU Chi-restraints excluded: chain u residue 17 ARG Chi-restraints excluded: chain u residue 33 ARG Chi-restraints excluded: chain v residue 4 PHE Chi-restraints excluded: chain v residue 17 ILE Chi-restraints excluded: chain v residue 28 LEU Chi-restraints excluded: chain v residue 44 VAL Chi-restraints excluded: chain v residue 45 LYS Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 52 THR Chi-restraints excluded: chain v residue 57 THR Chi-restraints excluded: chain v residue 74 LEU Chi-restraints excluded: chain v residue 89 VAL Chi-restraints excluded: chain v residue 94 THR Chi-restraints excluded: chain v residue 151 LEU Chi-restraints excluded: chain v residue 184 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 868 optimal weight: 2.9990 chunk 914 optimal weight: 1.9990 chunk 834 optimal weight: 1.9990 chunk 889 optimal weight: 50.0000 chunk 913 optimal weight: 10.0000 chunk 535 optimal weight: 5.9990 chunk 387 optimal weight: 8.9990 chunk 698 optimal weight: 50.0000 chunk 272 optimal weight: 1.9990 chunk 803 optimal weight: 9.9990 chunk 840 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 133 GLN C 199 GLN E 174 GLN H 3 GLN H 11 ASN H 137 GLN ** O 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 95 ASN R 69 GLN S 39 ASN ** S 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 25 ASN 3 31 HIS c 118 ASN ** c 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6137 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.600 152951 Z= 0.345 Angle : 0.940 62.754 229118 Z= 0.450 Chirality : 0.053 2.154 29467 Planarity : 0.006 0.096 12075 Dihedral : 26.041 179.903 76981 Min Nonbonded Distance : 1.507 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.00 % Favored : 91.98 % Rotamer: Outliers : 7.18 % Allowed : 29.73 % Favored : 63.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.11), residues: 5487 helix: -0.66 (0.13), residues: 1563 sheet: -0.96 (0.16), residues: 999 loop : -1.95 (0.11), residues: 2925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 250 HIS 0.020 0.002 HIS S 44 PHE 0.034 0.002 PHE g 47 TYR 0.020 0.002 TYR l 130 ARG 0.009 0.001 ARG o 53 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10974 Ramachandran restraints generated. 5487 Oldfield, 0 Emsley, 5487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10974 Ramachandran restraints generated. 5487 Oldfield, 0 Emsley, 5487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 319 poor density : 534 time to evaluate : 6.055 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 125 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.8022 (ptpp) REVERT: C 207 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8413 (ptmm) REVERT: D 100 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7093 (mp0) REVERT: E 200 LYS cc_start: 0.8573 (mmtm) cc_final: 0.8185 (mtmm) REVERT: F 22 TYR cc_start: 0.4854 (m-80) cc_final: 0.4640 (m-80) REVERT: F 110 ARG cc_start: 0.4091 (OUTLIER) cc_final: 0.3880 (mpp80) REVERT: G 30 LYS cc_start: 0.4352 (OUTLIER) cc_final: 0.4040 (mptt) REVERT: G 87 LEU cc_start: 0.5583 (OUTLIER) cc_final: 0.5120 (pt) REVERT: G 121 ILE cc_start: 0.6623 (OUTLIER) cc_final: 0.6389 (mp) REVERT: H 85 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8752 (tp) REVERT: I 4 GLN cc_start: 0.7958 (tt0) cc_final: 0.7538 (tt0) REVERT: I 5 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8082 (mm-30) REVERT: I 18 GLU cc_start: 0.7744 (tt0) cc_final: 0.7543 (tt0) REVERT: J 73 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.6973 (mm-30) REVERT: K 42 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8739 (mm) REVERT: O 108 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7968 (tt0) REVERT: T 7 ILE cc_start: 0.8283 (mp) cc_final: 0.8023 (mp) REVERT: T 57 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.6466 (tpt-90) REVERT: W 30 PHE cc_start: 0.8388 (OUTLIER) cc_final: 0.7593 (t80) REVERT: 2 15 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.7831 (mptm) REVERT: 4 20 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8025 (mppt) REVERT: b 19 GLN cc_start: 0.1428 (OUTLIER) cc_final: 0.1133 (tm-30) REVERT: b 22 ARG cc_start: 0.2534 (OUTLIER) cc_final: 0.1593 (mtm110) REVERT: b 51 ASP cc_start: 0.4739 (OUTLIER) cc_final: 0.4364 (p0) REVERT: b 143 ARG cc_start: 0.1756 (ttm170) cc_final: 0.0994 (mmm-85) REVERT: b 168 LYS cc_start: 0.4362 (mttt) cc_final: 0.2994 (tttt) REVERT: b 169 GLU cc_start: 0.3739 (OUTLIER) cc_final: 0.3336 (mm-30) REVERT: b 177 ARG cc_start: 0.2521 (mmt180) cc_final: 0.1404 (mmm160) REVERT: b 187 VAL cc_start: 0.2309 (t) cc_final: 0.1766 (t) REVERT: b 208 ARG cc_start: 0.3466 (mtp85) cc_final: 0.2745 (ptm-80) REVERT: b 213 LEU cc_start: 0.2746 (OUTLIER) cc_final: 0.2130 (tp) REVERT: c 57 GLU cc_start: 0.1414 (OUTLIER) cc_final: 0.0955 (tp30) REVERT: c 78 LYS cc_start: 0.3168 (OUTLIER) cc_final: 0.2690 (mtpp) REVERT: c 105 ILE cc_start: 0.1037 (OUTLIER) cc_final: 0.0797 (tp) REVERT: c 124 GLU cc_start: 0.1493 (mp0) cc_final: 0.1135 (mm-30) REVERT: c 163 ARG cc_start: 0.2822 (mtm110) cc_final: 0.1966 (mpt-90) REVERT: d 5 ARG cc_start: 0.2126 (mtm110) cc_final: 0.0544 (mmt-90) REVERT: d 10 LYS cc_start: 0.2793 (OUTLIER) cc_final: 0.1311 (ttmt) REVERT: d 26 LEU cc_start: 0.3988 (OUTLIER) cc_final: 0.3347 (pp) REVERT: d 49 LEU cc_start: 0.4886 (OUTLIER) cc_final: 0.4593 (tp) REVERT: d 63 MET cc_start: 0.3022 (OUTLIER) cc_final: 0.2575 (mtt) REVERT: d 78 LYS cc_start: 0.2800 (mtpt) cc_final: 0.1659 (tptp) REVERT: d 87 MET cc_start: 0.1503 (mmm) cc_final: 0.0752 (mpt) REVERT: d 124 LYS cc_start: 0.1857 (tptp) cc_final: 0.1431 (tptt) REVERT: d 134 LYS cc_start: 0.2269 (mptt) cc_final: 0.1036 (tptt) REVERT: d 156 GLU cc_start: 0.2122 (OUTLIER) cc_final: 0.1621 (mm-30) REVERT: d 196 GLU cc_start: 0.2853 (pm20) cc_final: 0.2414 (pm20) REVERT: e 10 GLU cc_start: 0.1991 (OUTLIER) cc_final: 0.1147 (mm-30) REVERT: e 13 GLU cc_start: 0.2401 (OUTLIER) cc_final: 0.1422 (mm-30) REVERT: e 136 MET cc_start: 0.3209 (tpt) cc_final: 0.2628 (tpt) REVERT: f 90 MET cc_start: 0.0232 (pmt) cc_final: -0.0549 (mpp) REVERT: g 31 MET cc_start: 0.1549 (tmt) cc_final: -0.0376 (ptp) REVERT: g 94 GLU cc_start: 0.2484 (OUTLIER) cc_final: 0.2132 (mt-10) REVERT: h 3 MET cc_start: 0.2960 (OUTLIER) cc_final: 0.2404 (pmm) REVERT: h 53 GLU cc_start: 0.2793 (OUTLIER) cc_final: 0.1575 (pm20) REVERT: h 78 LYS cc_start: 0.2940 (tmtm) cc_final: 0.2630 (tttm) REVERT: h 113 ILE cc_start: 0.3188 (OUTLIER) cc_final: 0.2305 (mp) REVERT: i 35 ARG cc_start: 0.2617 (ptm160) cc_final: 0.2102 (ttt-90) REVERT: i 46 LEU cc_start: 0.1996 (OUTLIER) cc_final: 0.1506 (tt) REVERT: i 66 LEU cc_start: 0.1172 (OUTLIER) cc_final: 0.0835 (pt) REVERT: i 114 GLU cc_start: 0.2641 (OUTLIER) cc_final: 0.2125 (tm-30) REVERT: j 11 LYS cc_start: 0.4322 (OUTLIER) cc_final: 0.2914 (tppp) REVERT: j 31 ARG cc_start: 0.3155 (OUTLIER) cc_final: 0.1143 (ppt170) REVERT: j 88 MET cc_start: 0.3457 (mpt) cc_final: 0.2492 (ttm) REVERT: k 65 MET cc_start: 0.2474 (pmm) cc_final: 0.1908 (mmt) REVERT: l 9 ARG cc_start: 0.2190 (ttp-170) cc_final: 0.0893 (tmm-80) REVERT: l 33 LYS cc_start: 0.5936 (mppt) cc_final: 0.5503 (mmtm) REVERT: l 67 ARG cc_start: 0.4496 (OUTLIER) cc_final: 0.3921 (tpp80) REVERT: m 63 TYR cc_start: 0.2427 (OUTLIER) cc_final: 0.2089 (p90) REVERT: m 77 ILE cc_start: 0.2199 (OUTLIER) cc_final: 0.1995 (pt) REVERT: m 110 LYS cc_start: 0.3849 (OUTLIER) cc_final: 0.2717 (mtpt) REVERT: n 6 MET cc_start: 0.1855 (mpp) cc_final: 0.0814 (tpt) REVERT: n 52 GLN cc_start: 0.3373 (OUTLIER) cc_final: 0.2182 (tp-100) REVERT: o 3 ILE cc_start: 0.2358 (OUTLIER) cc_final: 0.1994 (tt) REVERT: o 15 TYR cc_start: 0.2770 (OUTLIER) cc_final: 0.1210 (m-10) REVERT: o 28 GLN cc_start: 0.2383 (OUTLIER) cc_final: 0.1942 (pt0) REVERT: o 59 MET cc_start: 0.3349 (ptt) cc_final: 0.3097 (ptm) REVERT: o 74 ASP cc_start: 0.2095 (OUTLIER) cc_final: 0.0391 (m-30) REVERT: p 80 ILE cc_start: 0.2156 (OUTLIER) cc_final: 0.1877 (mt) REVERT: q 38 LYS cc_start: 0.4637 (tttp) cc_final: 0.4302 (ttpt) REVERT: r 45 LEU cc_start: 0.3092 (OUTLIER) cc_final: 0.2030 (pp) REVERT: r 70 MET cc_start: 0.1487 (mmt) cc_final: 0.0164 (ptt) REVERT: t 12 LYS cc_start: 0.5901 (tmmt) cc_final: 0.5556 (tmmt) REVERT: t 73 ARG cc_start: 0.1702 (OUTLIER) cc_final: 0.1213 (ttp-170) REVERT: u 12 LEU cc_start: 0.0849 (OUTLIER) cc_final: 0.0577 (mt) REVERT: u 17 ARG cc_start: 0.2144 (OUTLIER) cc_final: 0.1674 (mtt-85) REVERT: v 4 PHE cc_start: -0.0832 (OUTLIER) cc_final: -0.1185 (m-10) REVERT: v 45 LYS cc_start: 0.1420 (OUTLIER) cc_final: -0.0874 (tmtt) outliers start: 319 outliers final: 216 residues processed: 804 average time/residue: 2.2096 time to fit residues: 2510.8194 Evaluate side-chains 798 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 526 time to evaluate : 5.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 193 LYS Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 3 ASN Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 110 ARG Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 118 LYS Chi-restraints excluded: chain H residue 137 GLN Chi-restraints excluded: chain I residue 5 GLU Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 59 LYS Chi-restraints excluded: chain I residue 116 SER Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 73 GLU Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 34 GLU Chi-restraints excluded: chain L residue 45 GLU Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain M residue 6 ASP Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 84 GLU Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 74 MET Chi-restraints excluded: chain O residue 90 ILE Chi-restraints excluded: chain O residue 108 GLN Chi-restraints excluded: chain P residue 26 ASP Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 63 ASN Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 14 GLU Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain S residue 3 ILE Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 57 ARG Chi-restraints excluded: chain U residue 72 ASP Chi-restraints excluded: chain U residue 75 VAL Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain W residue 14 ILE Chi-restraints excluded: chain W residue 25 LEU Chi-restraints excluded: chain W residue 30 PHE Chi-restraints excluded: chain W residue 63 GLU Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain Y residue 5 ILE Chi-restraints excluded: chain Z residue 7 ARG Chi-restraints excluded: chain Z residue 8 THR Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 30 CYS Chi-restraints excluded: chain Z residue 42 VAL Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 2 residue 14 SER Chi-restraints excluded: chain 2 residue 15 LYS Chi-restraints excluded: chain 2 residue 31 VAL Chi-restraints excluded: chain 3 residue 14 VAL Chi-restraints excluded: chain 4 residue 2 LYS Chi-restraints excluded: chain 4 residue 7 VAL Chi-restraints excluded: chain 4 residue 20 LYS Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 19 GLN Chi-restraints excluded: chain b residue 22 ARG Chi-restraints excluded: chain b residue 51 ASP Chi-restraints excluded: chain b residue 60 VAL Chi-restraints excluded: chain b residue 89 GLN Chi-restraints excluded: chain b residue 101 LEU Chi-restraints excluded: chain b residue 105 LYS Chi-restraints excluded: chain b residue 116 GLU Chi-restraints excluded: chain b residue 169 GLU Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain c residue 78 LYS Chi-restraints excluded: chain c residue 94 THR Chi-restraints excluded: chain c residue 105 ILE Chi-restraints excluded: chain c residue 113 ARG Chi-restraints excluded: chain c residue 115 VAL Chi-restraints excluded: chain c residue 118 ASN Chi-restraints excluded: chain c residue 167 TYR Chi-restraints excluded: chain c residue 197 VAL Chi-restraints excluded: chain d residue 10 LYS Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 49 LEU Chi-restraints excluded: chain d residue 63 MET Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 71 THR Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 156 GLU Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain e residue 10 GLU Chi-restraints excluded: chain e residue 13 GLU Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 72 VAL Chi-restraints excluded: chain e residue 106 ILE Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain e residue 141 ILE Chi-restraints excluded: chain e residue 163 GLU Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 14 ILE Chi-restraints excluded: chain f residue 20 LYS Chi-restraints excluded: chain f residue 38 LEU Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 68 ASP Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 87 ILE Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 64 GLU Chi-restraints excluded: chain g residue 94 GLU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain h residue 3 MET Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 24 LYS Chi-restraints excluded: chain h residue 26 GLU Chi-restraints excluded: chain h residue 47 LYS Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 70 ASP Chi-restraints excluded: chain h residue 112 VAL Chi-restraints excluded: chain h residue 113 ILE Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 40 TYR Chi-restraints excluded: chain i residue 46 LEU Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 66 LEU Chi-restraints excluded: chain i residue 112 MET Chi-restraints excluded: chain i residue 114 GLU Chi-restraints excluded: chain i residue 129 PHE Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 11 LYS Chi-restraints excluded: chain j residue 31 ARG Chi-restraints excluded: chain j residue 66 GLU Chi-restraints excluded: chain k residue 53 LYS Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 100 LEU Chi-restraints excluded: chain k residue 101 GLN Chi-restraints excluded: chain l residue 42 GLN Chi-restraints excluded: chain l residue 47 CYS Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 62 LEU Chi-restraints excluded: chain l residue 67 ARG Chi-restraints excluded: chain l residue 73 ASN Chi-restraints excluded: chain l residue 100 VAL Chi-restraints excluded: chain l residue 115 LEU Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain m residue 57 ARG Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 63 TYR Chi-restraints excluded: chain m residue 77 ILE Chi-restraints excluded: chain m residue 108 THR Chi-restraints excluded: chain m residue 110 LYS Chi-restraints excluded: chain n residue 4 THR Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 38 LYS Chi-restraints excluded: chain n residue 52 GLN Chi-restraints excluded: chain n residue 56 VAL Chi-restraints excluded: chain o residue 3 ILE Chi-restraints excluded: chain o residue 15 TYR Chi-restraints excluded: chain o residue 28 GLN Chi-restraints excluded: chain o residue 74 ASP Chi-restraints excluded: chain o residue 81 LEU Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 32 ARG Chi-restraints excluded: chain p residue 80 ILE Chi-restraints excluded: chain q residue 51 GLU Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain q residue 76 ARG Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 24 THR Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 50 THR Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 31 ILE Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain t residue 73 ARG Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 12 LEU Chi-restraints excluded: chain u residue 17 ARG Chi-restraints excluded: chain u residue 33 ARG Chi-restraints excluded: chain v residue 4 PHE Chi-restraints excluded: chain v residue 17 ILE Chi-restraints excluded: chain v residue 28 LEU Chi-restraints excluded: chain v residue 44 VAL Chi-restraints excluded: chain v residue 45 LYS Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 52 THR Chi-restraints excluded: chain v residue 57 THR Chi-restraints excluded: chain v residue 74 LEU Chi-restraints excluded: chain v residue 94 THR Chi-restraints excluded: chain v residue 151 LEU Chi-restraints excluded: chain v residue 184 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 886 optimal weight: 6.9990 chunk 583 optimal weight: 9.9990 chunk 940 optimal weight: 10.0000 chunk 573 optimal weight: 40.0000 chunk 446 optimal weight: 8.9990 chunk 653 optimal weight: 40.0000 chunk 986 optimal weight: 20.0000 chunk 907 optimal weight: 30.0000 chunk 785 optimal weight: 20.0000 chunk 81 optimal weight: 5.9990 chunk 606 optimal weight: 40.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 133 GLN C 199 GLN E 174 GLN F 63 GLN H 3 GLN H 11 ASN O 81 ASN Q 95 ASN R 69 GLN S 39 ASN ** S 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 25 ASN 3 31 HIS ** b 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 16 ASN ** k 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 88 GLN ** p 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6299 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.598 152951 Z= 0.667 Angle : 1.413 62.830 229118 Z= 0.658 Chirality : 0.071 2.161 29467 Planarity : 0.008 0.098 12075 Dihedral : 26.389 179.840 76975 Min Nonbonded Distance : 1.508 Molprobity Statistics. All-atom Clashscore : 23.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.33 % Favored : 89.63 % Rotamer: Outliers : 6.98 % Allowed : 29.95 % Favored : 63.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.07 % 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: -2.38 (0.11), residues: 5487 helix: -0.99 (0.13), residues: 1553 sheet: -1.02 (0.16), residues: 951 loop : -2.13 (0.11), residues: 2983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.004 TRP K 93 HIS 0.021 0.003 HIS S 44 PHE 0.036 0.003 PHE g 47 TYR 0.033 0.003 TYR O 32 ARG 0.017 0.001 ARG 2 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10974 Ramachandran restraints generated. 5487 Oldfield, 0 Emsley, 5487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10974 Ramachandran restraints generated. 5487 Oldfield, 0 Emsley, 5487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 310 poor density : 526 time to evaluate : 6.057 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN N 113 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU X 58 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 3 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8474 (mt) REVERT: C 125 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8019 (ptpp) REVERT: C 207 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8490 (ptmm) REVERT: D 100 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7153 (mp0) REVERT: E 200 LYS cc_start: 0.8602 (mmtm) cc_final: 0.8199 (mtmm) REVERT: F 110 ARG cc_start: 0.4282 (OUTLIER) cc_final: 0.3970 (mpp80) REVERT: G 30 LYS cc_start: 0.4470 (OUTLIER) cc_final: 0.3899 (mttt) REVERT: G 43 PHE cc_start: 0.3788 (OUTLIER) cc_final: 0.3542 (p90) REVERT: G 87 LEU cc_start: 0.6071 (OUTLIER) cc_final: 0.5833 (pt) REVERT: G 121 ILE cc_start: 0.6599 (OUTLIER) cc_final: 0.6379 (mp) REVERT: H 85 ILE cc_start: 0.9113 (OUTLIER) cc_final: 0.8814 (tp) REVERT: I 18 GLU cc_start: 0.7834 (tt0) cc_final: 0.7574 (tt0) REVERT: K 42 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8834 (mm) REVERT: K 116 GLU cc_start: 0.7884 (tp30) cc_final: 0.7362 (tp30) REVERT: L 31 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.7025 (tt0) REVERT: O 16 LYS cc_start: 0.8530 (ptpp) cc_final: 0.8307 (ptpt) REVERT: O 19 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8272 (tptt) REVERT: O 59 LYS cc_start: 0.8616 (ttpt) cc_final: 0.8344 (ttmm) REVERT: S 56 ILE cc_start: 0.6760 (OUTLIER) cc_final: 0.6441 (pp) REVERT: T 7 ILE cc_start: 0.8293 (mp) cc_final: 0.8044 (mp) REVERT: T 57 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.6435 (tpt-90) REVERT: W 30 PHE cc_start: 0.8495 (OUTLIER) cc_final: 0.8082 (m-80) REVERT: 2 15 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.7786 (mptm) REVERT: 3 59 LYS cc_start: 0.8338 (ttpp) cc_final: 0.7728 (ttmm) REVERT: 4 20 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8168 (mppt) REVERT: b 19 GLN cc_start: 0.1567 (OUTLIER) cc_final: 0.1277 (tt0) REVERT: b 22 ARG cc_start: 0.2510 (OUTLIER) cc_final: 0.1606 (mtm110) REVERT: b 51 ASP cc_start: 0.4720 (OUTLIER) cc_final: 0.4376 (p0) REVERT: b 143 ARG cc_start: 0.1885 (ttm170) cc_final: 0.1056 (mmm-85) REVERT: b 168 LYS cc_start: 0.4271 (mttt) cc_final: 0.2794 (tttt) REVERT: b 169 GLU cc_start: 0.3805 (OUTLIER) cc_final: 0.3368 (mm-30) REVERT: b 187 VAL cc_start: 0.2402 (t) cc_final: 0.1894 (t) REVERT: b 213 LEU cc_start: 0.2749 (OUTLIER) cc_final: 0.2073 (tp) REVERT: c 57 GLU cc_start: 0.1436 (OUTLIER) cc_final: 0.0770 (mm-30) REVERT: c 78 LYS cc_start: 0.3179 (OUTLIER) cc_final: 0.2755 (mtpp) REVERT: c 105 ILE cc_start: 0.0961 (OUTLIER) cc_final: 0.0757 (pp) REVERT: c 163 ARG cc_start: 0.2784 (mtm110) cc_final: 0.1997 (mpt-90) REVERT: d 5 ARG cc_start: 0.2070 (mtm110) cc_final: 0.1135 (mpt180) REVERT: d 26 LEU cc_start: 0.3941 (OUTLIER) cc_final: 0.3306 (pp) REVERT: d 49 LEU cc_start: 0.4814 (OUTLIER) cc_final: 0.4516 (tp) REVERT: d 63 MET cc_start: 0.3168 (OUTLIER) cc_final: 0.2641 (mtt) REVERT: d 77 LYS cc_start: 0.4076 (tttt) cc_final: 0.3727 (tttt) REVERT: d 78 LYS cc_start: 0.2671 (mtpt) cc_final: 0.1599 (tptp) REVERT: d 87 MET cc_start: 0.1294 (mmm) cc_final: 0.0676 (mpt) REVERT: d 124 LYS cc_start: 0.1804 (tptp) cc_final: 0.1427 (tptt) REVERT: d 156 GLU cc_start: 0.2213 (OUTLIER) cc_final: 0.1752 (pt0) REVERT: d 196 GLU cc_start: 0.3085 (pm20) cc_final: 0.2570 (pm20) REVERT: e 10 GLU cc_start: 0.2438 (OUTLIER) cc_final: 0.1311 (mm-30) REVERT: e 136 MET cc_start: 0.3094 (tpt) cc_final: 0.2467 (tpt) REVERT: f 14 ILE cc_start: 0.1699 (OUTLIER) cc_final: 0.1339 (tp) REVERT: f 90 MET cc_start: 0.0522 (pmt) cc_final: -0.0275 (mmt) REVERT: g 94 GLU cc_start: 0.2318 (OUTLIER) cc_final: 0.1916 (mt-10) REVERT: h 3 MET cc_start: 0.3311 (OUTLIER) cc_final: 0.2540 (pmm) REVERT: h 53 GLU cc_start: 0.3221 (OUTLIER) cc_final: 0.2055 (pm20) REVERT: h 78 LYS cc_start: 0.2851 (tmtm) cc_final: 0.2569 (ttmm) REVERT: i 20 ARG cc_start: 0.2450 (pmt170) cc_final: 0.1952 (pmt-80) REVERT: i 35 ARG cc_start: 0.2496 (ptm160) cc_final: 0.1815 (ttt180) REVERT: i 46 LEU cc_start: 0.1897 (OUTLIER) cc_final: 0.1411 (tt) REVERT: j 11 LYS cc_start: 0.3886 (OUTLIER) cc_final: 0.2705 (tppp) REVERT: j 31 ARG cc_start: 0.2925 (OUTLIER) cc_final: 0.1162 (ppt170) REVERT: j 88 MET cc_start: 0.3494 (mpt) cc_final: 0.2428 (ttm) REVERT: k 65 MET cc_start: 0.2383 (pmm) cc_final: 0.1874 (mmt) REVERT: l 9 ARG cc_start: 0.2283 (ttp-170) cc_final: 0.0983 (tmm-80) REVERT: l 33 LYS cc_start: 0.6078 (mppt) cc_final: 0.5627 (mppt) REVERT: l 67 ARG cc_start: 0.4506 (OUTLIER) cc_final: 0.3864 (tpp80) REVERT: m 63 TYR cc_start: 0.2583 (OUTLIER) cc_final: 0.2307 (p90) REVERT: m 77 ILE cc_start: 0.3204 (OUTLIER) cc_final: 0.2893 (pt) REVERT: m 110 LYS cc_start: 0.3798 (OUTLIER) cc_final: 0.2762 (mtpt) REVERT: n 6 MET cc_start: 0.1858 (mpp) cc_final: 0.0790 (tpt) REVERT: n 52 GLN cc_start: 0.3370 (OUTLIER) cc_final: 0.2103 (tp-100) REVERT: o 3 ILE cc_start: 0.2256 (OUTLIER) cc_final: 0.1903 (tt) REVERT: o 15 TYR cc_start: 0.2891 (OUTLIER) cc_final: 0.1365 (m-10) REVERT: o 59 MET cc_start: 0.3359 (ptt) cc_final: 0.3128 (ptm) REVERT: o 74 ASP cc_start: 0.2393 (OUTLIER) cc_final: 0.0616 (m-30) REVERT: p 59 LYS cc_start: 0.3779 (OUTLIER) cc_final: 0.3175 (ptpp) REVERT: p 80 ILE cc_start: 0.2042 (OUTLIER) cc_final: 0.1800 (pt) REVERT: q 38 LYS cc_start: 0.4458 (tttp) cc_final: 0.3972 (tmmt) REVERT: r 45 LEU cc_start: 0.2553 (OUTLIER) cc_final: 0.1456 (pt) REVERT: r 70 MET cc_start: 0.1608 (mmt) cc_final: 0.0187 (ptt) REVERT: t 73 ARG cc_start: 0.1804 (OUTLIER) cc_final: 0.0909 (ttp-170) REVERT: u 12 LEU cc_start: 0.0922 (OUTLIER) cc_final: 0.0620 (mt) REVERT: u 17 ARG cc_start: 0.2199 (OUTLIER) cc_final: 0.1175 (mtm180) REVERT: v 4 PHE cc_start: -0.0905 (OUTLIER) cc_final: -0.1285 (m-10) REVERT: v 45 LYS cc_start: 0.1501 (OUTLIER) cc_final: -0.0829 (tmtt) outliers start: 310 outliers final: 219 residues processed: 793 average time/residue: 2.2105 time to fit residues: 2478.7534 Evaluate side-chains 796 residues out of total 4751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 523 time to evaluate : 5.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 3 ASN Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 110 ARG Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 97 GLN Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 118 LYS Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 59 LYS Chi-restraints excluded: chain I residue 116 SER Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 42 ILE Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 31 GLU Chi-restraints excluded: chain L residue 34 GLU Chi-restraints excluded: chain L residue 45 GLU Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain M residue 6 ASP Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 59 LYS Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 84 GLU Chi-restraints excluded: chain O residue 4 VAL Chi-restraints excluded: chain O residue 19 LYS Chi-restraints excluded: chain O residue 90 ILE Chi-restraints excluded: chain O residue 109 LEU Chi-restraints excluded: chain P residue 26 ASP Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 63 ASN Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 14 GLU Chi-restraints excluded: chain R residue 28 ASP Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain S residue 3 ILE Chi-restraints excluded: chain S residue 23 VAL Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 36 THR Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 57 ARG Chi-restraints excluded: chain U residue 72 ASP Chi-restraints excluded: chain U residue 75 VAL Chi-restraints excluded: chain W residue 14 ILE Chi-restraints excluded: chain W residue 25 LEU Chi-restraints excluded: chain W residue 30 PHE Chi-restraints excluded: chain W residue 63 GLU Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain Y residue 5 ILE Chi-restraints excluded: chain Z residue 7 ARG Chi-restraints excluded: chain Z residue 8 THR Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 30 CYS Chi-restraints excluded: chain Z residue 42 VAL Chi-restraints excluded: chain 1 residue 19 THR Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 2 residue 15 LYS Chi-restraints excluded: chain 2 residue 31 VAL Chi-restraints excluded: chain 3 residue 14 VAL Chi-restraints excluded: chain 4 residue 2 LYS Chi-restraints excluded: chain 4 residue 7 VAL Chi-restraints excluded: chain 4 residue 20 LYS Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 19 GLN Chi-restraints excluded: chain b residue 22 ARG Chi-restraints excluded: chain b residue 51 ASP Chi-restraints excluded: chain b residue 60 VAL Chi-restraints excluded: chain b residue 101 LEU Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain b residue 105 LYS Chi-restraints excluded: chain b residue 116 GLU Chi-restraints excluded: chain b residue 169 GLU Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 57 GLU Chi-restraints excluded: chain c residue 78 LYS Chi-restraints excluded: chain c residue 94 THR Chi-restraints excluded: chain c residue 102 VAL Chi-restraints excluded: chain c residue 105 ILE Chi-restraints excluded: chain c residue 113 ARG Chi-restraints excluded: chain c residue 115 VAL Chi-restraints excluded: chain c residue 167 TYR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 197 VAL Chi-restraints excluded: chain d residue 10 LYS Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 49 LEU Chi-restraints excluded: chain d residue 63 MET Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 71 THR Chi-restraints excluded: chain d residue 107 ARG Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 156 GLU Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain e residue 10 GLU Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 56 VAL Chi-restraints excluded: chain e residue 72 VAL Chi-restraints excluded: chain e residue 106 ILE Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain e residue 141 ILE Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 163 GLU Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 14 ILE Chi-restraints excluded: chain f residue 20 LYS Chi-restraints excluded: chain f residue 38 LEU Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 68 ASP Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 87 ILE Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 64 GLU Chi-restraints excluded: chain g residue 94 GLU Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain h residue 3 MET Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 26 GLU Chi-restraints excluded: chain h residue 47 LYS Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 112 VAL Chi-restraints excluded: chain h residue 113 ILE Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 40 TYR Chi-restraints excluded: chain i residue 46 LEU Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 112 MET Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 11 LYS Chi-restraints excluded: chain j residue 31 ARG Chi-restraints excluded: chain j residue 64 GLN Chi-restraints excluded: chain j residue 66 GLU Chi-restraints excluded: chain k residue 43 SER Chi-restraints excluded: chain k residue 53 LYS Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 101 GLN Chi-restraints excluded: chain k residue 121 CYS Chi-restraints excluded: chain l residue 42 GLN Chi-restraints excluded: chain l residue 47 CYS Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 62 LEU Chi-restraints excluded: chain l residue 67 ARG Chi-restraints excluded: chain l residue 73 ASN Chi-restraints excluded: chain l residue 100 VAL Chi-restraints excluded: chain l residue 107 ARG Chi-restraints excluded: chain l residue 115 LEU Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain m residue 57 ARG Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 63 TYR Chi-restraints excluded: chain m residue 77 ILE Chi-restraints excluded: chain m residue 108 THR Chi-restraints excluded: chain m residue 110 LYS Chi-restraints excluded: chain n residue 4 THR Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 38 LYS Chi-restraints excluded: chain n residue 52 GLN Chi-restraints excluded: chain n residue 56 VAL Chi-restraints excluded: chain o residue 3 ILE Chi-restraints excluded: chain o residue 15 TYR Chi-restraints excluded: chain o residue 17 VAL Chi-restraints excluded: chain o residue 74 ASP Chi-restraints excluded: chain o residue 81 LEU Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 32 ARG Chi-restraints excluded: chain p residue 59 LYS Chi-restraints excluded: chain p residue 80 ILE Chi-restraints excluded: chain q residue 51 GLU Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain q residue 76 ARG Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 24 THR Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 50 THR Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 31 ILE Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain t residue 73 ARG Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 12 LEU Chi-restraints excluded: chain u residue 17 ARG Chi-restraints excluded: chain v residue 4 PHE Chi-restraints excluded: chain v residue 17 ILE Chi-restraints excluded: chain v residue 28 LEU Chi-restraints excluded: chain v residue 44 VAL Chi-restraints excluded: chain v residue 45 LYS Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 52 THR Chi-restraints excluded: chain v residue 57 THR Chi-restraints excluded: chain v residue 74 LEU Chi-restraints excluded: chain v residue 94 THR Chi-restraints excluded: chain v residue 151 LEU Chi-restraints excluded: chain v residue 184 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 990 random chunks: chunk 481 optimal weight: 0.9990 chunk 623 optimal weight: 40.0000 chunk 836 optimal weight: 7.9990 chunk 240 optimal weight: 0.6980 chunk 724 optimal weight: 40.0000 chunk 115 optimal weight: 3.9990 chunk 218 optimal weight: 40.0000 chunk 786 optimal weight: 0.1980 chunk 329 optimal weight: 0.7980 chunk 807 optimal weight: 8.9990 chunk 99 optimal weight: 0.5980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 133 GLN C 199 GLN E 174 GLN ** F 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN M 43 GLN Q 65 ASN Q 95 ASN R 69 GLN S 39 ASN ** U 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 25 ASN 3 31 HIS 3 43 GLN b 15 HIS ** c 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 82 HIS ** d 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 27 ASN ** g 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 16 ASN ** k 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 28 GLN ** p 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 97 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4892 r_free = 0.4892 target = 0.276464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.253797 restraints weight = 153251.919| |-----------------------------------------------------------------------------| r_work (start): 0.4698 rms_B_bonded: 0.28 r_work: 0.4547 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.4511 rms_B_bonded: 2.17 restraints_weight: 0.2500 r_work (final): 0.4511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6091 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.600 152951 Z= 0.264 Angle : 0.820 62.672 229118 Z= 0.393 Chirality : 0.049 2.142 29467 Planarity : 0.005 0.102 12075 Dihedral : 25.942 179.329 76969 Min Nonbonded Distance : 1.508 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.07 % Favored : 92.91 % Rotamer: Outliers : 5.32 % Allowed : 31.73 % Favored : 62.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.52 % Twisted General : 0.00 % 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: -1.98 (0.11), residues: 5487 helix: -0.51 (0.13), residues: 1559 sheet: -0.90 (0.16), residues: 1006 loop : -1.95 (0.11), residues: 2922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP O 61 HIS 0.016 0.001 HIS S 44 PHE 0.033 0.001 PHE g 47 TYR 0.024 0.001 TYR s 61 ARG 0.017 0.001 ARG b 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 42606.68 seconds wall clock time: 749 minutes 29.74 seconds (44969.74 seconds total)