Starting phenix.real_space_refine on Fri Mar 1 02:32:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zep_6921/03_2024/5zep_6921.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zep_6921/03_2024/5zep_6921.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zep_6921/03_2024/5zep_6921.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zep_6921/03_2024/5zep_6921.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zep_6921/03_2024/5zep_6921.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zep_6921/03_2024/5zep_6921.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.017 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 4802 5.49 5 S 109 5.16 5 C 76675 2.51 5 N 28527 2.21 5 O 42338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "c ARG 11": "NH1" <-> "NH2" Residue "c ARG 21": "NH1" <-> "NH2" Residue "c ARG 39": "NH1" <-> "NH2" Residue "c ARG 58": "NH1" <-> "NH2" Residue "c ARG 60": "NH1" <-> "NH2" Residue "c ARG 64": "NH1" <-> "NH2" Residue "c ARG 71": "NH1" <-> "NH2" Residue "c ARG 78": "NH1" <-> "NH2" Residue "c ARG 79": "NH1" <-> "NH2" Residue "c ARG 87": "NH1" <-> "NH2" Residue "c GLU 109": "OE1" <-> "OE2" Residue "c ARG 126": "NH1" <-> "NH2" Residue "c PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 130": "NH1" <-> "NH2" Residue "c ARG 131": "NH1" <-> "NH2" Residue "c ARG 134": "NH1" <-> "NH2" Residue "c ARG 142": "NH1" <-> "NH2" Residue "c ARG 150": "NH1" <-> "NH2" Residue "c ARG 156": "NH1" <-> "NH2" Residue "c ARG 172": "NH1" <-> "NH2" Residue "c ARG 179": "NH1" <-> "NH2" Residue "c ARG 195": "NH1" <-> "NH2" Residue "e ARG 54": "NH1" <-> "NH2" Residue "e ARG 55": "NH1" <-> "NH2" Residue "e ARG 98": "NH1" <-> "NH2" Residue "e ARG 122": "NH1" <-> "NH2" Residue "e ARG 137": "NH1" <-> "NH2" Residue "e ARG 174": "NH1" <-> "NH2" Residue "e ARG 181": "NH1" <-> "NH2" Residue "e GLU 187": "OE1" <-> "OE2" Residue "e ARG 198": "NH1" <-> "NH2" Residue "g ARG 51": "NH1" <-> "NH2" Residue "g ARG 64": "NH1" <-> "NH2" Residue "g ARG 78": "NH1" <-> "NH2" Residue "g ARG 79": "NH1" <-> "NH2" Residue "g ARG 92": "NH1" <-> "NH2" Residue "g ARG 95": "NH1" <-> "NH2" Residue "g ARG 102": "NH1" <-> "NH2" Residue "g ARG 109": "NH1" <-> "NH2" Residue "g ARG 111": "NH1" <-> "NH2" Residue "g ARG 112": "NH1" <-> "NH2" Residue "g ARG 119": "NH1" <-> "NH2" Residue "g ARG 137": "NH1" <-> "NH2" Residue "g ARG 138": "NH1" <-> "NH2" Residue "g ARG 149": "NH1" <-> "NH2" Residue "h ARG 13": "NH1" <-> "NH2" Residue "h ARG 15": "NH1" <-> "NH2" Residue "h ARG 72": "NH1" <-> "NH2" Residue "h ARG 79": "NH1" <-> "NH2" Residue "h ARG 86": "NH1" <-> "NH2" Residue "h ARG 116": "NH1" <-> "NH2" Residue "h TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 31": "NH1" <-> "NH2" Residue "i ARG 38": "NH1" <-> "NH2" Residue "i ARG 40": "NH1" <-> "NH2" Residue "i ARG 53": "NH1" <-> "NH2" Residue "i ARG 77": "NH1" <-> "NH2" Residue "i ARG 100": "NH1" <-> "NH2" Residue "i ARG 105": "NH1" <-> "NH2" Residue "i ARG 115": "NH1" <-> "NH2" Residue "i ARG 126": "NH1" <-> "NH2" Residue "i TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 142": "NH1" <-> "NH2" Residue "i TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 150": "NH1" <-> "NH2" Residue "j ARG 7": "NH1" <-> "NH2" Residue "j ARG 31": "NH1" <-> "NH2" Residue "j ARG 62": "NH1" <-> "NH2" Residue "j ARG 68": "NH1" <-> "NH2" Residue "j ARG 72": "NH1" <-> "NH2" Residue "j ARG 89": "NH1" <-> "NH2" Residue "k ARG 65": "NH1" <-> "NH2" Residue "k ARG 81": "NH1" <-> "NH2" Residue "k ARG 102": "NH1" <-> "NH2" Residue "k ARG 107": "NH1" <-> "NH2" Residue "k ARG 131": "NH1" <-> "NH2" Residue "k ARG 135": "NH1" <-> "NH2" Residue "k ARG 137": "NH1" <-> "NH2" Residue "l ARG 9": "NH1" <-> "NH2" Residue "l ARG 30": "NH1" <-> "NH2" Residue "l ARG 31": "NH1" <-> "NH2" Residue "l TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 50": "NH1" <-> "NH2" Residue "l ARG 54": "NH1" <-> "NH2" Residue "l ARG 83": "NH1" <-> "NH2" Residue "l ARG 86": "NH1" <-> "NH2" Residue "l ARG 94": "NH1" <-> "NH2" Residue "l ARG 99": "NH1" <-> "NH2" Residue "l ARG 110": "NH1" <-> "NH2" Residue "l ARG 114": "NH1" <-> "NH2" Residue "l ARG 116": "NH1" <-> "NH2" Residue "o ARG 35": "NH1" <-> "NH2" Residue "o ARG 53": "NH1" <-> "NH2" Residue "o ARG 54": "NH1" <-> "NH2" Residue "o ARG 62": "NH1" <-> "NH2" Residue "o ARG 63": "NH1" <-> "NH2" Residue "o ARG 64": "NH1" <-> "NH2" Residue "o ARG 65": "NH1" <-> "NH2" Residue "o ARG 77": "NH1" <-> "NH2" Residue "o ARG 88": "NH1" <-> "NH2" Residue "q TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 20": "NH1" <-> "NH2" Residue "q ARG 43": "NH1" <-> "NH2" Residue "q ARG 73": "NH1" <-> "NH2" Residue "q ARG 80": "NH1" <-> "NH2" Residue "q ARG 87": "NH1" <-> "NH2" Residue "r ARG 39": "NH1" <-> "NH2" Residue "r ARG 49": "NH1" <-> "NH2" Residue "r ARG 52": "NH1" <-> "NH2" Residue "r ARG 72": "NH1" <-> "NH2" Residue "s ARG 36": "NH1" <-> "NH2" Residue "s ARG 37": "NH1" <-> "NH2" Residue "s ARG 55": "NH1" <-> "NH2" Residue "s ARG 78": "NH1" <-> "NH2" Residue "t ARG 12": "NH1" <-> "NH2" Residue "t ARG 16": "NH1" <-> "NH2" Residue "t ARG 20": "NH1" <-> "NH2" Residue "t ARG 29": "NH1" <-> "NH2" Residue "t ARG 33": "NH1" <-> "NH2" Residue "t ARG 36": "NH1" <-> "NH2" Residue "t ARG 56": "NH1" <-> "NH2" Residue "x ASP 44": "OD1" <-> "OD2" Residue "x ARG 47": "NH1" <-> "NH2" Residue "x TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 56": "NH1" <-> "NH2" Residue "x ARG 59": "NH1" <-> "NH2" Residue "x TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 75": "NH1" <-> "NH2" Residue "x ARG 78": "NH1" <-> "NH2" Residue "x ARG 80": "NH1" <-> "NH2" Residue "x ARG 91": "NH1" <-> "NH2" Residue "x ARG 93": "NH1" <-> "NH2" Residue "x ARG 98": "NH1" <-> "NH2" Residue "x GLU 100": "OE1" <-> "OE2" Residue "x PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 120": "NH1" <-> "NH2" Residue "x ARG 122": "NH1" <-> "NH2" Residue "x ARG 123": "NH1" <-> "NH2" Residue "x ASP 126": "OD1" <-> "OD2" Residue "x ARG 127": "NH1" <-> "NH2" Residue "C GLU 23": "OE1" <-> "OE2" Residue "C ARG 52": "NH1" <-> "NH2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ARG 183": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 211": "NH1" <-> "NH2" Residue "C ARG 258": "NH1" <-> "NH2" Residue "D PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 46": "NH1" <-> "NH2" Residue "E ARG 55": "NH1" <-> "NH2" Residue "E TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "E ARG 75": "NH1" <-> "NH2" Residue "E ARG 101": "NH1" <-> "NH2" Residue "E ARG 112": "NH1" <-> "NH2" Residue "E ARG 118": "NH1" <-> "NH2" Residue "E ARG 120": "NH1" <-> "NH2" Residue "E ARG 160": "NH1" <-> "NH2" Residue "F ARG 14": "NH1" <-> "NH2" Residue "F ARG 16": "NH1" <-> "NH2" Residue "F ASP 49": "OD1" <-> "OD2" Residue "F ARG 52": "NH1" <-> "NH2" Residue "F ARG 78": "NH1" <-> "NH2" Residue "F ARG 99": "NH1" <-> "NH2" Residue "F ARG 102": "NH1" <-> "NH2" Residue "F ASP 108": "OD1" <-> "OD2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 155": "NH1" <-> "NH2" Residue "F ARG 178": "NH1" <-> "NH2" Residue "F PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 99": "NH1" <-> "NH2" Residue "K PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 7": "NH1" <-> "NH2" Residue "L ARG 30": "NH1" <-> "NH2" Residue "L ARG 54": "NH1" <-> "NH2" Residue "L ARG 64": "NH1" <-> "NH2" Residue "L ARG 69": "NH1" <-> "NH2" Residue "L ARG 70": "NH1" <-> "NH2" Residue "L ARG 71": "NH1" <-> "NH2" Residue "L PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 94": "NH1" <-> "NH2" Residue "L ARG 104": "NH1" <-> "NH2" Residue "L ARG 107": "NH1" <-> "NH2" Residue "M PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 10": "NH1" <-> "NH2" Residue "N ARG 18": "NH1" <-> "NH2" Residue "N TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 45": "NH1" <-> "NH2" Residue "N ARG 51": "NH1" <-> "NH2" Residue "N ARG 56": "NH1" <-> "NH2" Residue "N ARG 60": "NH1" <-> "NH2" Residue "N ARG 101": "NH1" <-> "NH2" Residue "N ARG 120": "NH1" <-> "NH2" Residue "N ARG 134": "NH1" <-> "NH2" Residue "O ARG 33": "NH1" <-> "NH2" Residue "O ARG 42": "NH1" <-> "NH2" Residue "O ARG 45": "NH1" <-> "NH2" Residue "O TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 63": "NH1" <-> "NH2" Residue "O PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 90": "NH1" <-> "NH2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "R ARG 3": "NH1" <-> "NH2" Residue "T GLU 6": "OE1" <-> "OE2" Residue "T ARG 18": "NH1" <-> "NH2" Residue "T ARG 25": "NH1" <-> "NH2" Residue "T ARG 32": "NH1" <-> "NH2" Residue "T ARG 44": "NH1" <-> "NH2" Residue "T ASP 84": "OD1" <-> "OD2" Residue "T ARG 91": "NH1" <-> "NH2" Residue "T ARG 106": "NH1" <-> "NH2" Residue "U ASP 6": "OD1" <-> "OD2" Residue "U ARG 66": "NH1" <-> "NH2" Residue "U ARG 70": "NH1" <-> "NH2" Residue "U ARG 76": "NH1" <-> "NH2" Residue "U ARG 81": "NH1" <-> "NH2" Residue "U PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 30": "NH1" <-> "NH2" Residue "V ARG 40": "NH1" <-> "NH2" Residue "V ARG 82": "NH1" <-> "NH2" Residue "V TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 86": "NH1" <-> "NH2" Residue "V ARG 96": "NH1" <-> "NH2" Residue "W ARG 16": "NH1" <-> "NH2" Residue "W ARG 28": "NH1" <-> "NH2" Residue "W ARG 29": "NH1" <-> "NH2" Residue "W TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 52": "NH1" <-> "NH2" Residue "W ARG 59": "NH1" <-> "NH2" Residue "W ARG 89": "NH1" <-> "NH2" Residue "W ARG 90": "NH1" <-> "NH2" Residue "W GLU 104": "OE1" <-> "OE2" Residue "X ARG 14": "NH1" <-> "NH2" Residue "X ARG 20": "NH1" <-> "NH2" Residue "X ARG 25": "NH1" <-> "NH2" Residue "X ARG 39": "NH1" <-> "NH2" Residue "X ARG 41": "NH1" <-> "NH2" Residue "X ARG 53": "NH1" <-> "NH2" Residue "X ARG 75": "NH1" <-> "NH2" Residue "Z ARG 11": "NH1" <-> "NH2" Residue "Z ARG 23": "NH1" <-> "NH2" Residue "Z ARG 33": "NH1" <-> "NH2" Residue "Z ARG 45": "NH1" <-> "NH2" Residue "Z ARG 46": "NH1" <-> "NH2" Residue "Z ARG 62": "NH1" <-> "NH2" Residue "Z GLU 65": "OE1" <-> "OE2" Residue "v ARG 16": "NH1" <-> "NH2" Residue "v ARG 20": "NH1" <-> "NH2" Residue "v ARG 37": "NH1" <-> "NH2" Residue "v ARG 44": "NH1" <-> "NH2" Residue "y TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y GLU 62": "OE1" <-> "OE2" Residue "1 ARG 8": "NH1" <-> "NH2" Residue "1 ARG 21": "NH1" <-> "NH2" Residue "1 ARG 29": "NH1" <-> "NH2" Residue "1 ARG 30": "NH1" <-> "NH2" Residue "2 ARG 15": "NH1" <-> "NH2" Residue "2 ARG 24": "NH1" <-> "NH2" Residue "2 ARG 37": "NH1" <-> "NH2" Residue "2 ARG 43": "NH1" <-> "NH2" Residue "3 ARG 13": "NH1" <-> "NH2" Residue "3 ARG 15": "NH1" <-> "NH2" Residue "3 ARG 16": "NH1" <-> "NH2" Residue "3 ARG 24": "NH1" <-> "NH2" Residue "3 ARG 40": "NH1" <-> "NH2" Residue "3 ARG 42": "NH1" <-> "NH2" Residue "3 ARG 43": "NH1" <-> "NH2" Residue "3 ARG 47": "NH1" <-> "NH2" Residue "3 ARG 57": "NH1" <-> "NH2" Residue "4 ARG 15": "NH1" <-> "NH2" Residue "4 ARG 18": "NH1" <-> "NH2" Residue "4 ARG 22": "NH1" <-> "NH2" Residue "4 ARG 31": "NH1" <-> "NH2" Residue "4 ARG 35": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 152451 Number of models: 1 Model: "" Number of chains: 58 Chain: "a" Number of atoms: 32341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1506, 32341 Classifications: {'RNA': 1506} Modifications used: {'rna2p_pur': 112, 'rna2p_pyr': 85, 'rna3p_pur': 738, 'rna3p_pyr': 571} Link IDs: {'rna2p': 197, 'rna3p': 1308} Chain breaks: 1 Chain: "c" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1672 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 5, 'TRANS': 204} Chain: "e" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1433 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 8, 'TRANS': 189} Chain: "g" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1240 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 9, 'TRANS': 146} Chain: "h" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1003 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "i" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 994 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 8, 'TRANS': 117} Chain: "j" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 7, 'TRANS': 89} Chain: "k" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 871 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "l" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 958 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "o" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 709 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "q" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 730 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 5, 'TRANS': 86} Chain: "r" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 512 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "s" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 630 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "t" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 655 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "n" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 477 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "b" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1793 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "d" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1641 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 11, 'TRANS': 188} Chain: "f" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 771 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "m" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 935 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "p" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 891 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "u" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 280 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "w" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1643 Classifications: {'RNA': 77} Modifications used: {'p5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 34, 'rna3p_pyr': 34} Link IDs: {'rna2p': 9, 'rna3p': 67} Chain: "x" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 831 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain: "0" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1310 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 262} Link IDs: {'TRANS': 261} Chain breaks: 4 Unresolved non-hydrogen bonds: 524 Unresolved non-hydrogen angles: 786 Unresolved non-hydrogen dihedrals: 262 Planarities with less than four sites: {'UNK:plan-1': 262} Unresolved non-hydrogen planarities: 262 Chain: "C" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2097 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 19, 'TRANS': 253} Chain: "D" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1587 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 8, 'TRANS': 205} Chain: "E" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1553 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 11, 'TRANS': 195} Chain: "F" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1437 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 8, 'TRANS': 172} Chain: "G" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1348 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 11, 'TRANS': 164} Chain: "H" Number of atoms: 1018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1018 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 3, 'TRANS': 147} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 68 Chain: "I" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 918 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain: "J" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 990 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 8, 'TRANS': 124} Chain: "K" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1138 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 11, 'TRANS': 135} Chain: "L" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 930 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "M" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1078 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "N" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1074 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain: "O" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 919 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 6, 'TRANS': 110} Chain: "P" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 956 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "Q" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 907 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "R" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 988 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "S" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 768 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "T" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 873 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 8, 'TRANS': 105} Chain: "U" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 739 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "V" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 731 Classifications: {'peptide': 97} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 92} Chain: "W" Number of atoms: 1389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1389 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 9, 'TRANS': 176} Chain: "X" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 604 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "Y" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 470 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 4, 'TRANS': 58} Chain: "Z" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 527 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "v" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 483 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "y" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 510 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "z" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 423 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "1" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 416 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 4, 'TRANS': 45} Chain: "2" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 372 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "3" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 502 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "4" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 298 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "5" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 189 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "B" Number of atoms: 2501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2501 Classifications: {'RNA': 117} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 3, 'rna3p_pur': 60, 'rna3p_pyr': 51} Link IDs: {'rna2p': 6, 'rna3p': 110} Chain: "A" Number of atoms: 66623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3102, 66623 Classifications: {'RNA': 3102} Modifications used: {'rna2p_pur': 296, 'rna2p_pyr': 147, 'rna3p_pur': 1480, 'rna3p_pyr': 1179} Link IDs: {'rna2p': 443, 'rna3p': 2658} Chain breaks: 5 Time building chain proxies: 56.81, per 1000 atoms: 0.37 Number of scatterers: 152451 At special positions: 0 Unit cell: (277.76, 257.28, 259.84, 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 109 16.00 P 4802 15.00 O 42338 8.00 N 28527 7.00 C 76675 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS r 23 " - pdb=" SG CYS r 57 " distance=2.03 Simple disulfide: pdb=" SG CYS y 16 " - pdb=" SG CYS y 38 " distance=2.29 Simple disulfide: pdb=" SG CYS 1 18 " - pdb=" SG CYS 1 45 " distance=2.65 Simple disulfide: pdb=" SG CYS 4 11 " - pdb=" SG CYS 4 14 " distance=2.02 Simple disulfide: pdb=" SG CYS 4 14 " - pdb=" SG CYS 4 27 " distance=2.00 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 Atom "ATOM 84273 O4' G B 45 .*. O " rejected from bonding due to valence issues. Atom "ATOM 7331 O5' G a 350 .*. O " rejected from bonding due to valence issues. Atom "ATOM 20084 O4' A a 946 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 61.00 Conformation dependent library (CDL) restraints added in 6.8 seconds 12170 Ramachandran restraints generated. 6085 Oldfield, 0 Emsley, 6085 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11822 Finding SS restraints... Secondary structure from input PDB file: 193 helices and 80 sheets defined 35.5% alpha, 20.1% beta 1566 base pairs and 2587 stacking pairs defined. Time for finding SS restraints: 53.47 Creating SS restraints... Processing helix chain 'c' and resid 27 through 42 Processing helix chain 'c' and resid 43 through 50 Processing helix chain 'c' and resid 82 through 94 removed outlier: 3.869A pdb=" N ILE c 86 " --> pdb=" O GLU c 82 " (cutoff:3.500A) Processing helix chain 'c' and resid 107 through 110 Processing helix chain 'c' and resid 111 through 124 Processing helix chain 'c' and resid 128 through 143 removed outlier: 4.184A pdb=" N GLN c 138 " --> pdb=" O ARG c 134 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N SER c 139 " --> pdb=" O LYS c 135 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA c 140 " --> pdb=" O ALA c 136 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N MET c 141 " --> pdb=" O ILE c 137 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG c 142 " --> pdb=" O GLN c 138 " (cutoff:3.500A) Processing helix chain 'c' and resid 156 through 160 removed outlier: 3.527A pdb=" N GLY c 159 " --> pdb=" O ARG c 156 " (cutoff:3.500A) Processing helix chain 'e' and resid 80 through 95 Processing helix chain 'e' and resid 133 through 143 Processing helix chain 'e' and resid 158 through 171 Processing helix chain 'e' and resid 174 through 182 Processing helix chain 'e' and resid 191 through 214 removed outlier: 3.605A pdb=" N ALA e 214 " --> pdb=" O ARG e 210 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 removed outlier: 3.743A pdb=" N THR g 24 " --> pdb=" O SER g 20 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 55 Processing helix chain 'g' and resid 57 through 70 removed outlier: 3.572A pdb=" N THR g 61 " --> pdb=" O ASP g 57 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 110 Processing helix chain 'g' and resid 116 through 130 Processing helix chain 'g' and resid 132 through 148 removed outlier: 3.605A pdb=" N LYS g 136 " --> pdb=" O GLY g 132 " (cutoff:3.500A) Processing helix chain 'g' and resid 149 through 155 removed outlier: 3.739A pdb=" N HIS g 153 " --> pdb=" O ALA g 150 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR g 154 " --> pdb=" O PHE g 151 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG g 155 " --> pdb=" O ALA g 152 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 20 removed outlier: 3.730A pdb=" N ASP h 9 " --> pdb=" O ASP h 5 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 43 Processing helix chain 'h' and resid 97 through 101 Processing helix chain 'h' and resid 114 through 121 Processing helix chain 'i' and resid 54 through 59 Processing helix chain 'i' and resid 63 through 75 removed outlier: 3.576A pdb=" N LYS i 69 " --> pdb=" O GLN i 65 " (cutoff:3.500A) Proline residue: i 71 - end of helix removed outlier: 3.615A pdb=" N VAL i 75 " --> pdb=" O PRO i 71 " (cutoff:3.500A) Processing helix chain 'i' and resid 91 through 109 removed outlier: 3.748A pdb=" N GLN i 95 " --> pdb=" O GLY i 91 " (cutoff:3.500A) Processing helix chain 'i' and resid 111 through 113 No H-bonds generated for 'chain 'i' and resid 111 through 113' Processing helix chain 'i' and resid 114 through 122 removed outlier: 3.824A pdb=" N ALA i 121 " --> pdb=" O ALA i 117 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY i 122 " --> pdb=" O LEU i 118 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 Processing helix chain 'j' and resid 80 through 90 removed outlier: 4.136A pdb=" N ALA j 86 " --> pdb=" O LYS j 82 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU j 87 " --> pdb=" O THR j 83 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N MET j 88 " --> pdb=" O VAL j 84 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE j 90 " --> pdb=" O ALA j 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 56 through 60 removed outlier: 3.559A pdb=" N GLY k 60 " --> pdb=" O SER k 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 56 through 60' Processing helix chain 'k' and resid 62 through 67 removed outlier: 3.769A pdb=" N ARG k 65 " --> pdb=" O LYS k 62 " (cutoff:3.500A) Processing helix chain 'k' and resid 68 through 85 Processing helix chain 'k' and resid 102 through 112 Processing helix chain 'l' and resid 4 through 10 Processing helix chain 'o' and resid 6 through 16 removed outlier: 3.657A pdb=" N ILE o 11 " --> pdb=" O GLN o 7 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 46 Processing helix chain 'o' and resid 51 through 74 Processing helix chain 'o' and resid 74 through 86 Processing helix chain 'r' and resid 34 through 40 removed outlier: 3.697A pdb=" N LEU r 38 " --> pdb=" O ASP r 34 " (cutoff:3.500A) Processing helix chain 'r' and resid 50 through 55 Processing helix chain 'r' and resid 57 through 74 Processing helix chain 's' and resid 12 through 25 Processing helix chain 's' and resid 41 through 45 removed outlier: 3.598A pdb=" N PHE s 44 " --> pdb=" O ILE s 41 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE s 45 " --> pdb=" O PRO s 42 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 41 through 45' Processing helix chain 's' and resid 63 through 67 removed outlier: 3.827A pdb=" N VAL s 67 " --> pdb=" O GLU s 64 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 75 removed outlier: 3.625A pdb=" N GLU s 73 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE s 74 " --> pdb=" O LEU s 71 " (cutoff:3.500A) Processing helix chain 't' and resid 7 through 40 Processing helix chain 't' and resid 43 through 64 Processing helix chain 't' and resid 68 through 86 removed outlier: 4.212A pdb=" N LYS t 85 " --> pdb=" O LEU t 81 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU t 86 " --> pdb=" O ALA t 82 " (cutoff:3.500A) Processing helix chain 'n' and resid 3 through 10 Processing helix chain 'n' and resid 16 through 20 removed outlier: 3.779A pdb=" N ALA n 20 " --> pdb=" O ALA n 17 " (cutoff:3.500A) Processing helix chain 'n' and resid 40 through 50 Processing helix chain 'b' and resid 5 through 12 removed outlier: 3.729A pdb=" N LEU b 9 " --> pdb=" O THR b 5 " (cutoff:3.500A) Processing helix chain 'b' and resid 24 through 28 Processing helix chain 'b' and resid 42 through 62 removed outlier: 3.695A pdb=" N THR b 46 " --> pdb=" O ASP b 42 " (cutoff:3.500A) Processing helix chain 'b' and resid 76 through 87 Processing helix chain 'b' and resid 106 through 120 removed outlier: 3.821A pdb=" N ARG b 110 " --> pdb=" O THR b 106 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU b 111 " --> pdb=" O VAL b 107 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 148 removed outlier: 3.515A pdb=" N LEU b 148 " --> pdb=" O LEU b 144 " (cutoff:3.500A) Processing helix chain 'b' and resid 150 through 155 removed outlier: 3.844A pdb=" N GLN b 155 " --> pdb=" O ILE b 151 " (cutoff:3.500A) Processing helix chain 'b' and resid 169 through 179 Processing helix chain 'b' and resid 192 through 196 removed outlier: 3.670A pdb=" N VAL b 195 " --> pdb=" O ASP b 192 " (cutoff:3.500A) Processing helix chain 'b' and resid 206 through 228 removed outlier: 4.132A pdb=" N ALA b 227 " --> pdb=" O GLU b 223 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG b 228 " --> pdb=" O GLY b 224 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 15 Processing helix chain 'd' and resid 24 through 29 Processing helix chain 'd' and resid 44 through 61 removed outlier: 3.884A pdb=" N GLN d 48 " --> pdb=" O SER d 44 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS d 53 " --> pdb=" O GLN d 49 " (cutoff:3.500A) Processing helix chain 'd' and resid 63 through 77 Processing helix chain 'd' and resid 80 through 91 Processing helix chain 'd' and resid 92 through 100 Processing helix chain 'd' and resid 105 through 115 Processing helix chain 'd' and resid 141 through 146 removed outlier: 3.817A pdb=" N ASN d 146 " --> pdb=" O GLU d 142 " (cutoff:3.500A) Processing helix chain 'd' and resid 147 through 156 Processing helix chain 'd' and resid 182 through 187 removed outlier: 3.782A pdb=" N ILE d 186 " --> pdb=" O GLU d 182 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ASP d 187 " --> pdb=" O ARG d 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 182 through 187' Processing helix chain 'd' and resid 192 through 200 removed outlier: 3.688A pdb=" N VAL d 196 " --> pdb=" O GLU d 192 " (cutoff:3.500A) Processing helix chain 'f' and resid 15 through 34 removed outlier: 3.863A pdb=" N VAL f 19 " --> pdb=" O ASP f 15 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ALA f 20 " --> pdb=" O GLU f 16 " (cutoff:3.500A) Proline residue: f 21 - end of helix removed outlier: 4.625A pdb=" N VAL f 29 " --> pdb=" O THR f 25 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ILE f 30 " --> pdb=" O PHE f 26 " (cutoff:3.500A) Processing helix chain 'f' and resid 70 through 82 removed outlier: 3.878A pdb=" N ASN f 80 " --> pdb=" O ASP f 76 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU f 81 " --> pdb=" O ARG f 77 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN f 82 " --> pdb=" O GLN f 78 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 19 Processing helix chain 'm' and resid 26 through 38 removed outlier: 3.783A pdb=" N ALA m 35 " --> pdb=" O ASN m 31 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY m 38 " --> pdb=" O LEU m 34 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 63 Processing helix chain 'm' and resid 66 through 84 Processing helix chain 'm' and resid 86 through 95 Processing helix chain 'm' and resid 107 through 112 removed outlier: 3.778A pdb=" N LYS m 111 " --> pdb=" O ALA m 107 " (cutoff:3.500A) Processing helix chain 'p' and resid 52 through 62 Processing helix chain 'p' and resid 67 through 78 Processing helix chain 'p' and resid 78 through 85 Processing helix chain 'p' and resid 101 through 114 Processing helix chain 'u' and resid 3 through 24 removed outlier: 4.685A pdb=" N LYS u 7 " --> pdb=" O SER u 3 " (cutoff:3.500A) Processing helix chain 'u' and resid 24 through 33 Processing helix chain 'x' and resid 43 through 61 removed outlier: 3.868A pdb=" N LEU x 57 " --> pdb=" O LYS x 53 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE x 60 " --> pdb=" O ARG x 56 " (cutoff:3.500A) Processing helix chain 'x' and resid 105 through 124 removed outlier: 3.632A pdb=" N ALA x 109 " --> pdb=" O SER x 105 " (cutoff:3.500A) Processing helix chain '0' and resid 2 through 19 removed outlier: 4.253A pdb=" N UNK 0 12 " --> pdb=" O UNK 0 8 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N UNK 0 13 " --> pdb=" O UNK 0 9 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N UNK 0 16 " --> pdb=" O UNK 0 12 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N UNK 0 17 " --> pdb=" O UNK 0 13 " (cutoff:3.500A) Processing helix chain '0' and resid 136 through 139 Processing helix chain '0' and resid 232 through 234 No H-bonds generated for 'chain '0' and resid 232 through 234' Processing helix chain '0' and resid 332 through 334 No H-bonds generated for 'chain '0' and resid 332 through 334' Processing helix chain '0' and resid 432 through 434 No H-bonds generated for 'chain '0' and resid 432 through 434' Processing helix chain 'C' and resid 210 through 215 removed outlier: 3.905A pdb=" N LYS C 215 " --> pdb=" O ARG C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 226 removed outlier: 3.633A pdb=" N VAL C 225 " --> pdb=" O ARG C 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 73 Processing helix chain 'D' and resid 88 through 93 Processing helix chain 'D' and resid 102 through 106 removed outlier: 3.712A pdb=" N ILE D 105 " --> pdb=" O THR D 102 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE D 106 " --> pdb=" O ALA D 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 102 through 106' Processing helix chain 'D' and resid 125 through 130 Processing helix chain 'E' and resid 23 through 27 removed outlier: 3.954A pdb=" N ASP E 26 " --> pdb=" O GLU E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 43 Processing helix chain 'E' and resid 103 through 121 Processing helix chain 'E' and resid 139 through 148 Processing helix chain 'E' and resid 162 through 170 removed outlier: 3.890A pdb=" N ALA E 166 " --> pdb=" O ASP E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 183 removed outlier: 3.723A pdb=" N LEU E 183 " --> pdb=" O PRO E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 191 Processing helix chain 'E' and resid 198 through 209 Processing helix chain 'F' and resid 9 through 16 Processing helix chain 'F' and resid 17 through 27 Processing helix chain 'F' and resid 55 through 65 removed outlier: 3.701A pdb=" N GLY F 59 " --> pdb=" O LYS F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 113 Processing helix chain 'F' and resid 113 through 118 removed outlier: 4.021A pdb=" N ARG F 117 " --> pdb=" O ILE F 113 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE F 118 " --> pdb=" O ALA F 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 113 through 118' Processing helix chain 'F' and resid 170 through 180 Processing helix chain 'G' and resid 59 through 82 removed outlier: 4.227A pdb=" N GLY G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU G 68 " --> pdb=" O SER G 64 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL G 80 " --> pdb=" O LEU G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 151 Processing helix chain 'H' and resid 22 through 29 Processing helix chain 'H' and resid 29 through 34 removed outlier: 3.768A pdb=" N ARG H 33 " --> pdb=" O TYR H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 58 Processing helix chain 'H' and resid 62 through 73 removed outlier: 3.934A pdb=" N ALA H 71 " --> pdb=" O GLU H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 107 Processing helix chain 'H' and resid 113 through 117 Processing helix chain 'I' and resid 2 through 19 Processing helix chain 'I' and resid 32 through 43 Processing helix chain 'I' and resid 53 through 61 Processing helix chain 'I' and resid 66 through 70 removed outlier: 3.805A pdb=" N ASP I 70 " --> pdb=" O GLU I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 100 removed outlier: 4.565A pdb=" N ALA I 89 " --> pdb=" O GLU I 85 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA I 90 " --> pdb=" O ALA I 86 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS I 91 " --> pdb=" O VAL I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 124 Processing helix chain 'J' and resid 25 through 31 removed outlier: 3.937A pdb=" N ALA J 29 " --> pdb=" O PRO J 25 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU J 30 " --> pdb=" O VAL J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 49 Processing helix chain 'J' and resid 76 through 81 Processing helix chain 'J' and resid 103 through 114 removed outlier: 3.632A pdb=" N VAL J 107 " --> pdb=" O THR J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 138 removed outlier: 3.943A pdb=" N ALA J 126 " --> pdb=" O ASP J 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 27 through 38 Processing helix chain 'K' and resid 58 through 62 removed outlier: 3.943A pdb=" N ILE K 62 " --> pdb=" O ALA K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 72 Processing helix chain 'K' and resid 96 through 109 removed outlier: 4.043A pdb=" N VAL K 100 " --> pdb=" O HIS K 96 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL K 101 " --> pdb=" O PRO K 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 118 Processing helix chain 'L' and resid 111 through 118 Processing helix chain 'M' and resid 39 through 44 Processing helix chain 'M' and resid 56 through 61 removed outlier: 3.683A pdb=" N LEU M 61 " --> pdb=" O ILE M 57 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 87 Processing helix chain 'M' and resid 94 through 101 Processing helix chain 'M' and resid 130 through 140 removed outlier: 3.620A pdb=" N ALA M 140 " --> pdb=" O ALA M 136 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 58 removed outlier: 3.614A pdb=" N ILE N 47 " --> pdb=" O THR N 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 123 Processing helix chain 'O' and resid 15 through 32 Processing helix chain 'O' and resid 38 through 58 removed outlier: 3.913A pdb=" N ALA O 43 " --> pdb=" O PRO O 39 " (cutoff:3.500A) Proline residue: O 46 - end of helix Processing helix chain 'O' and resid 62 through 67 Processing helix chain 'O' and resid 72 through 88 Proline residue: O 85 - end of helix Processing helix chain 'P' and resid 9 through 24 Processing helix chain 'P' and resid 25 through 28 Processing helix chain 'P' and resid 67 through 72 Processing helix chain 'P' and resid 76 through 95 Processing helix chain 'P' and resid 111 through 123 Processing helix chain 'Q' and resid 4 through 12 removed outlier: 4.836A pdb=" N ALA Q 10 " --> pdb=" O PHE Q 6 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER Q 11 " --> pdb=" O VAL Q 7 " (cutoff:3.500A) Processing helix chain 'Q' and resid 52 through 55 removed outlier: 4.033A pdb=" N SER Q 55 " --> pdb=" O GLY Q 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 52 through 55' Processing helix chain 'Q' and resid 96 through 101 removed outlier: 3.663A pdb=" N LEU Q 99 " --> pdb=" O LEU Q 96 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG Q 100 " --> pdb=" O TYR Q 97 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU Q 101 " --> pdb=" O TYR Q 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 96 through 101' Processing helix chain 'Q' and resid 103 through 108 Processing helix chain 'R' and resid 6 through 21 removed outlier: 4.461A pdb=" N LYS R 13 " --> pdb=" O ASN R 9 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 31 removed outlier: 4.106A pdb=" N ARG R 30 " --> pdb=" O GLY R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 71 removed outlier: 3.681A pdb=" N ARG R 51 " --> pdb=" O TYR R 47 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS R 54 " --> pdb=" O ARG R 50 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLY R 55 " --> pdb=" O ARG R 51 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG R 58 " --> pdb=" O LYS R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 86 Processing helix chain 'R' and resid 91 through 101 Processing helix chain 'R' and resid 102 through 117 removed outlier: 3.845A pdb=" N PHE R 106 " --> pdb=" O ASP R 102 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU R 117 " --> pdb=" O ALA R 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 51 through 57 Processing helix chain 'T' and resid 20 through 32 removed outlier: 4.092A pdb=" N VAL T 27 " --> pdb=" O LYS T 23 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU T 30 " --> pdb=" O ARG T 26 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL T 31 " --> pdb=" O VAL T 27 " (cutoff:3.500A) Processing helix chain 'T' and resid 36 through 40 Processing helix chain 'T' and resid 50 through 68 removed outlier: 3.922A pdb=" N VAL T 54 " --> pdb=" O ALA T 50 " (cutoff:3.500A) Processing helix chain 'U' and resid 17 through 26 removed outlier: 3.756A pdb=" N TYR U 21 " --> pdb=" O SER U 17 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP U 26 " --> pdb=" O GLY U 22 " (cutoff:3.500A) Processing helix chain 'U' and resid 38 through 50 Processing helix chain 'V' and resid 89 through 92 Processing helix chain 'W' and resid 20 through 30 removed outlier: 3.632A pdb=" N ASP W 30 " --> pdb=" O GLN W 26 " (cutoff:3.500A) Processing helix chain 'W' and resid 51 through 61 Processing helix chain 'W' and resid 160 through 162 No H-bonds generated for 'chain 'W' and resid 160 through 162' Processing helix chain 'W' and resid 186 through 191 Processing helix chain 'Y' and resid 53 through 58 Processing helix chain 'Z' and resid 14 through 39 Processing helix chain 'Z' and resid 44 through 66 Processing helix chain 'v' and resid 16 through 27 Processing helix chain 'v' and resid 41 through 50 Processing helix chain 'y' and resid 42 through 54 removed outlier: 3.523A pdb=" N LYS y 48 " --> pdb=" O PHE y 44 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER y 54 " --> pdb=" O LYS y 50 " (cutoff:3.500A) Processing helix chain 'y' and resid 56 through 65 Processing helix chain 'z' and resid 9 through 18 Processing helix chain 'z' and resid 43 through 49 Processing helix chain '2' and resid 12 through 20 Processing helix chain '2' and resid 20 through 25 Processing helix chain '2' and resid 27 through 40 Processing helix chain '3' and resid 7 through 14 Processing helix chain '3' and resid 37 through 44 Processing helix chain '3' and resid 51 through 63 removed outlier: 4.118A pdb=" N LYS 3 60 " --> pdb=" O SER 3 56 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU 3 61 " --> pdb=" O ARG 3 57 " (cutoff:3.500A) Processing helix chain '5' and resid 3 through 11 Processing helix chain '5' and resid 12 through 14 No H-bonds generated for 'chain '5' and resid 12 through 14' Processing sheet with id=AA1, first strand: chain 'c' and resid 20 through 21 Processing sheet with id=AA2, first strand: chain 'c' and resid 166 through 169 Processing sheet with id=AA3, first strand: chain 'e' and resid 37 through 50 removed outlier: 6.869A pdb=" N LEU e 61 " --> pdb=" O VAL e 41 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE e 43 " --> pdb=" O THR e 59 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR e 59 " --> pdb=" O ILE e 43 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ARG e 45 " --> pdb=" O SER e 57 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N SER e 57 " --> pdb=" O ARG e 45 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N SER e 47 " --> pdb=" O ARG e 55 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ARG e 55 " --> pdb=" O SER e 47 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL e 49 " --> pdb=" O GLY e 53 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLY e 53 " --> pdb=" O VAL e 49 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL e 64 " --> pdb=" O GLY e 72 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N MET e 70 " --> pdb=" O ASP e 66 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'e' and resid 110 through 114 Processing sheet with id=AA5, first strand: chain 'g' and resid 73 through 76 Processing sheet with id=AA6, first strand: chain 'h' and resid 24 through 28 removed outlier: 3.742A pdb=" N ASP h 48 " --> pdb=" O GLN h 63 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'h' and resid 103 through 104 Processing sheet with id=AA8, first strand: chain 'i' and resid 27 through 31 removed outlier: 3.672A pdb=" N ARG i 40 " --> pdb=" O TYR i 84 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N TYR i 84 " --> pdb=" O ARG i 40 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ASN i 49 " --> pdb=" O ALA i 85 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N LEU i 87 " --> pdb=" O ASN i 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'j' and resid 97 through 101 removed outlier: 4.120A pdb=" N SER j 35 " --> pdb=" O LEU j 77 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'j' and resid 40 through 46 removed outlier: 4.088A pdb=" N LYS j 71 " --> pdb=" O LEU j 42 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N THR j 44 " --> pdb=" O THR j 69 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N THR j 69 " --> pdb=" O THR j 44 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS j 46 " --> pdb=" O MET j 67 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N MET j 67 " --> pdb=" O LYS j 46 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'n' and resid 56 through 58 Processing sheet with id=AB3, first strand: chain 'k' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'l' and resid 39 through 40 removed outlier: 4.538A pdb=" N TYR l 95 " --> pdb=" O THR l 64 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG l 54 " --> pdb=" O THR l 35 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'q' and resid 52 through 62 removed outlier: 3.589A pdb=" N LYS q 44 " --> pdb=" O ILE q 53 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'q' and resid 77 through 78 Processing sheet with id=AB7, first strand: chain 's' and resid 31 through 33 removed outlier: 6.384A pdb=" N ILE s 31 " --> pdb=" O ALA s 50 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N HIS s 52 " --> pdb=" O ILE s 31 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N THR s 33 " --> pdb=" O HIS s 52 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'b' and resid 31 through 35 removed outlier: 6.698A pdb=" N ILE b 40 " --> pdb=" O PHE b 32 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ASP b 34 " --> pdb=" O ILE b 38 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE b 38 " --> pdb=" O ASP b 34 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'b' and resid 91 through 92 removed outlier: 8.023A pdb=" N VAL b 92 " --> pdb=" O VAL b 67 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N PHE b 69 " --> pdb=" O VAL b 92 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LEU b 68 " --> pdb=" O TRP b 162 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL b 183 " --> pdb=" O TYR b 198 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE b 200 " --> pdb=" O VAL b 183 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ALA b 185 " --> pdb=" O ILE b 200 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'd' and resid 123 through 124 Processing sheet with id=AC2, first strand: chain 'f' and resid 39 through 40 removed outlier: 5.833A pdb=" N TYR f 60 " --> pdb=" O GLY f 44 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLY f 44 " --> pdb=" O TYR f 60 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'f' and resid 39 through 40 removed outlier: 6.758A pdb=" N MET f 7 " --> pdb=" O THR f 88 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N THR f 88 " --> pdb=" O MET f 7 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE f 9 " --> pdb=" O LEU f 86 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'p' and resid 35 through 36 removed outlier: 7.081A pdb=" N VAL p 3 " --> pdb=" O GLN p 65 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'p' and resid 38 through 40 Processing sheet with id=AC6, first strand: chain 'x' and resid 32 through 37 Processing sheet with id=AC7, first strand: chain '0' and resid 109 through 118 removed outlier: 6.046A pdb=" N UNK 0 123 " --> pdb=" O UNK 0 115 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N UNK 0 117 " --> pdb=" O UNK 0 121 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N UNK 0 121 " --> pdb=" O UNK 0 117 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N UNK 0 166 " --> pdb=" O UNK 0 153 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N UNK 0 153 " --> pdb=" O UNK 0 166 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain '0' and resid 205 through 214 removed outlier: 6.858A pdb=" N UNK 0 220 " --> pdb=" O UNK 0 212 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N UNK 0 214 " --> pdb=" O UNK 0 218 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N UNK 0 218 " --> pdb=" O UNK 0 214 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N UNK 0 253 " --> pdb=" O UNK 0 226 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N UNK 0 230 " --> pdb=" O UNK 0 255 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N UNK 0 205 " --> pdb=" O UNK 0 246 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '0' and resid 305 through 310 removed outlier: 3.563A pdb=" N UNK 0 305 " --> pdb=" O UNK 0 346 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '0' and resid 313 through 314 removed outlier: 3.575A pdb=" N UNK 0 313 " --> pdb=" O UNK 0 320 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '0' and resid 405 through 414 removed outlier: 5.817A pdb=" N UNK 0 411 " --> pdb=" O UNK 0 422 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N UNK 0 422 " --> pdb=" O UNK 0 411 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N UNK 0 413 " --> pdb=" O UNK 0 420 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N UNK 0 426 " --> pdb=" O UNK 0 453 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N UNK 0 455 " --> pdb=" O UNK 0 426 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N UNK 0 428 " --> pdb=" O UNK 0 455 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N UNK 0 405 " --> pdb=" O UNK 0 446 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 4 through 5 Processing sheet with id=AD4, first strand: chain 'C' and resid 102 through 105 removed outlier: 4.082A pdb=" N HIS C 81 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N HIS C 96 " --> pdb=" O VAL C 79 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N VAL C 79 " --> pdb=" O HIS C 96 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 130 through 132 removed outlier: 5.800A pdb=" N LEU C 165 " --> pdb=" O ARG C 176 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ARG C 176 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLY C 167 " --> pdb=" O ALA C 174 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA C 174 " --> pdb=" O GLY C 167 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N TYR C 172 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ARG C 184 " --> pdb=" O ILE C 268 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ILE C 268 " --> pdb=" O ARG C 184 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 174 through 180 removed outlier: 5.812A pdb=" N VAL D 112 " --> pdb=" O ASN D 179 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR D 117 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LEU D 205 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY D 204 " --> pdb=" O LYS D 10 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL D 28 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N MET D 13 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL D 26 " --> pdb=" O MET D 13 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLN D 15 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL D 24 " --> pdb=" O GLN D 15 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL D 191 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N VAL D 185 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU D 193 " --> pdb=" O HIS D 183 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 80 through 85 removed outlier: 3.647A pdb=" N ARG D 38 " --> pdb=" O GLN D 51 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA D 53 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N VAL D 36 " --> pdb=" O ALA D 53 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 123 through 124 Processing sheet with id=AD9, first strand: chain 'E' and resid 16 through 18 removed outlier: 3.547A pdb=" N GLY E 16 " --> pdb=" O VAL E 7 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ALA E 126 " --> pdb=" O ASP E 6 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 73 through 76 removed outlier: 4.159A pdb=" N GLY F 93 " --> pdb=" O ARG F 75 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ALA F 94 " --> pdb=" O MET F 45 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL F 96 " --> pdb=" O VAL F 43 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL F 164 " --> pdb=" O VAL F 39 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL F 41 " --> pdb=" O THR F 162 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N THR F 162 " --> pdb=" O VAL F 41 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL F 43 " --> pdb=" O ASP F 160 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ASP F 160 " --> pdb=" O VAL F 43 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 9 through 10 Processing sheet with id=AE3, first strand: chain 'G' and resid 16 through 20 removed outlier: 3.847A pdb=" N GLY G 31 " --> pdb=" O GLY G 28 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 122 through 128 removed outlier: 6.813A pdb=" N LYS G 131 " --> pdb=" O GLU G 127 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 96 through 100 removed outlier: 3.541A pdb=" N GLU G 105 " --> pdb=" O GLN G 98 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN G 103 " --> pdb=" O LYS G 100 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 18 through 20 removed outlier: 3.553A pdb=" N ILE H 37 " --> pdb=" O ILE H 4 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 78 through 81 removed outlier: 6.320A pdb=" N VAL H 78 " --> pdb=" O ASN H 147 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N VAL H 149 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N LEU H 80 " --> pdb=" O VAL H 149 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY H 128 " --> pdb=" O VAL H 148 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 47 through 51 removed outlier: 6.957A pdb=" N THR I 23 " --> pdb=" O GLY I 108 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY I 108 " --> pdb=" O THR I 23 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL I 25 " --> pdb=" O LYS I 106 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 12 through 15 removed outlier: 3.827A pdb=" N LEU J 13 " --> pdb=" O VAL J 58 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 101 through 102 removed outlier: 3.544A pdb=" N VAL J 102 " --> pdb=" O THR J 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'K' and resid 54 through 56 Processing sheet with id=AF3, first strand: chain 'K' and resid 73 through 77 removed outlier: 3.527A pdb=" N ARG K 87 " --> pdb=" O ALA K 74 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ARG K 76 " --> pdb=" O ARG K 85 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG K 85 " --> pdb=" O ARG K 76 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 6 through 9 removed outlier: 3.979A pdb=" N SER L 6 " --> pdb=" O CYS L 21 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASP L 45 " --> pdb=" O LYS L 17 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE L 19 " --> pdb=" O VAL L 43 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL L 43 " --> pdb=" O ILE L 19 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N CYS L 21 " --> pdb=" O ALA L 41 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ALA L 41 " --> pdb=" O CYS L 21 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ARG L 23 " --> pdb=" O ILE L 39 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ILE L 39 " --> pdb=" O ARG L 23 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP L 37 " --> pdb=" O VAL L 62 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS L 59 " --> pdb=" O ILE L 87 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 76 through 79 removed outlier: 6.658A pdb=" N THR Q 59 " --> pdb=" O ILE Q 47 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N GLU Q 63 " --> pdb=" O LYS Q 43 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N LYS Q 43 " --> pdb=" O GLU Q 63 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASN Q 26 " --> pdb=" O VAL Q 85 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N VAL Q 85 " --> pdb=" O ASN Q 26 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N HIS Q 28 " --> pdb=" O ILE Q 83 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE Q 83 " --> pdb=" O HIS Q 28 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N LYS Q 30 " --> pdb=" O ASP Q 81 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ASP Q 81 " --> pdb=" O LYS Q 30 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 76 through 79 removed outlier: 5.622A pdb=" N GLN M 76 " --> pdb=" O LYS M 111 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LEU M 113 " --> pdb=" O GLN M 76 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N VAL M 78 " --> pdb=" O LEU M 113 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 91 through 93 Processing sheet with id=AF8, first strand: chain 'N' and resid 64 through 66 removed outlier: 6.572A pdb=" N ILE N 34 " --> pdb=" O LEU N 103 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLU N 105 " --> pdb=" O TYR N 32 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N TYR N 32 " --> pdb=" O GLU N 105 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'N' and resid 72 through 75 removed outlier: 3.637A pdb=" N LEU N 74 " --> pdb=" O TRP N 92 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TRP N 92 " --> pdb=" O LEU N 74 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'O' and resid 35 through 37 removed outlier: 4.526A pdb=" N MET O 110 " --> pdb=" O VAL O 100 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'P' and resid 58 through 64 removed outlier: 6.378A pdb=" N LEU P 51 " --> pdb=" O LEU P 60 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ALA P 62 " --> pdb=" O VAL P 49 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL P 49 " --> pdb=" O ALA P 62 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N SER P 64 " --> pdb=" O ILE P 47 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE P 47 " --> pdb=" O SER P 64 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'S' and resid 12 through 17 removed outlier: 3.728A pdb=" N ASN S 47 " --> pdb=" O ASP S 44 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'S' and resid 21 through 25 removed outlier: 3.664A pdb=" N GLU S 66 " --> pdb=" O VAL S 96 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LYS S 98 " --> pdb=" O VAL S 64 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N VAL S 64 " --> pdb=" O LYS S 98 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N THR S 100 " --> pdb=" O ALA S 62 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ALA S 62 " --> pdb=" O THR S 100 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'S' and resid 73 through 79 removed outlier: 3.542A pdb=" N LYS S 79 " --> pdb=" O TYR S 84 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TYR S 84 " --> pdb=" O LYS S 79 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'T' and resid 9 through 17 removed outlier: 5.745A pdb=" N SER T 108 " --> pdb=" O TYR T 16 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS T 34 " --> pdb=" O VAL T 78 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'T' and resid 9 through 17 removed outlier: 5.745A pdb=" N SER T 108 " --> pdb=" O TYR T 16 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N HIS T 109 " --> pdb=" O GLU T 85 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N GLU T 85 " --> pdb=" O HIS T 109 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'U' and resid 11 through 14 removed outlier: 3.528A pdb=" N ALA U 13 " --> pdb=" O VAL U 32 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS U 80 " --> pdb=" O VAL U 33 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N THR U 79 " --> pdb=" O ASN U 61 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ASN U 61 " --> pdb=" O THR U 79 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ARG U 81 " --> pdb=" O THR U 59 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N THR U 59 " --> pdb=" O ARG U 81 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE U 83 " --> pdb=" O VAL U 57 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N VAL U 57 " --> pdb=" O ILE U 83 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LYS U 85 " --> pdb=" O ASP U 55 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'V' and resid 66 through 67 removed outlier: 3.634A pdb=" N VAL V 25 " --> pdb=" O LEU V 34 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N THR V 8 " --> pdb=" O VAL V 74 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'V' and resid 40 through 43 Processing sheet with id=AH2, first strand: chain 'V' and resid 84 through 88 removed outlier: 3.827A pdb=" N ASP V 88 " --> pdb=" O LYS V 93 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS V 93 " --> pdb=" O ASP V 88 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'W' and resid 10 through 15 removed outlier: 8.255A pdb=" N THR W 12 " --> pdb=" O ASN W 50 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ASN W 50 " --> pdb=" O THR W 12 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN W 14 " --> pdb=" O GLU W 48 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU W 48 " --> pdb=" O ASN W 14 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP W 96 " --> pdb=" O LYS W 81 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN W 76 " --> pdb=" O LEU W 69 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'W' and resid 110 through 111 Processing sheet with id=AH5, first strand: chain 'W' and resid 114 through 115 removed outlier: 3.545A pdb=" N GLU W 115 " --> pdb=" O VAL W 146 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'W' and resid 123 through 126 Processing sheet with id=AH7, first strand: chain 'W' and resid 133 through 134 Processing sheet with id=AH8, first strand: chain 'X' and resid 22 through 23 removed outlier: 6.603A pdb=" N LEU X 59 " --> pdb=" O LEU X 37 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'X' and resid 30 through 31 removed outlier: 6.522A pdb=" N HIS X 46 " --> pdb=" O VAL X 78 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N ILE X 80 " --> pdb=" O HIS X 46 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'Y' and resid 13 through 18 removed outlier: 3.547A pdb=" N ARG Y 27 " --> pdb=" O GLY Y 15 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR Y 25 " --> pdb=" O SER Y 17 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Y' and resid 33 through 39 Processing sheet with id=AI3, first strand: chain 'v' and resid 34 through 36 Processing sheet with id=AI4, first strand: chain 'y' and resid 21 through 26 Processing sheet with id=AI5, first strand: chain 'z' and resid 28 through 32 Processing sheet with id=AI6, first strand: chain '1' and resid 22 through 26 Processing sheet with id=AI7, first strand: chain '3' and resid 15 through 17 removed outlier: 3.530A pdb=" N LYS 3 21 " --> pdb=" O THR 3 17 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain '4' and resid 15 through 18 1999 hydrogen bonds defined for protein. 5664 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3984 hydrogen bonds 6272 hydrogen bond angles 0 basepair planarities 1566 basepair parallelities 2587 stacking parallelities Total time for adding SS restraints: 249.78 Time building geometry restraints manager: 66.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.54: 155311 1.54 - 1.90: 10160 1.90 - 2.25: 0 2.25 - 2.60: 0 2.60 - 2.96: 1 Bond restraints: 165472 Sorted by residual: bond pdb=" C VAL V 47 " pdb=" N SER V 56 " ideal model delta sigma weight residual 1.329 2.959 -1.630 1.40e-02 5.10e+03 1.36e+04 bond pdb=" C ILE W 7 " pdb=" N PRO W 8 " ideal model delta sigma weight residual 1.335 1.389 -0.054 8.70e-03 1.32e+04 3.92e+01 bond pdb=" C GLY O 84 " pdb=" N PRO O 85 " ideal model delta sigma weight residual 1.335 1.419 -0.084 1.36e-02 5.41e+03 3.80e+01 bond pdb=" C ARG T 117 " pdb=" N PRO T 118 " ideal model delta sigma weight residual 1.329 1.398 -0.069 1.18e-02 7.18e+03 3.43e+01 bond pdb=" C ARG O 45 " pdb=" N PRO O 46 " ideal model delta sigma weight residual 1.336 1.403 -0.068 1.23e-02 6.61e+03 3.03e+01 ... (remaining 165467 not shown) Histogram of bond angle deviations from ideal: 71.54 - 86.43: 2 86.43 - 101.32: 2208 101.32 - 116.21: 142743 116.21 - 131.09: 100977 131.09 - 145.98: 1529 Bond angle restraints: 247459 Sorted by residual: angle pdb=" O VAL V 47 " pdb=" C VAL V 47 " pdb=" N SER V 56 " ideal model delta sigma weight residual 121.87 94.22 27.65 9.70e-01 1.06e+00 8.12e+02 angle pdb=" C VAL V 47 " pdb=" N SER V 56 " pdb=" CA SER V 56 " ideal model delta sigma weight residual 121.70 71.54 50.16 1.80e+00 3.09e-01 7.77e+02 angle pdb=" N GLY W 62 " pdb=" CA GLY W 62 " pdb=" C GLY W 62 " ideal model delta sigma weight residual 111.93 133.81 -21.88 1.15e+00 7.56e-01 3.62e+02 angle pdb=" CA VAL V 47 " pdb=" C VAL V 47 " pdb=" N SER V 56 " ideal model delta sigma weight residual 117.15 138.42 -21.27 1.14e+00 7.69e-01 3.48e+02 angle pdb=" N LEU h 94 " pdb=" CA LEU h 94 " pdb=" C LEU h 94 " ideal model delta sigma weight residual 109.04 85.11 23.93 1.52e+00 4.33e-01 2.48e+02 ... (remaining 247454 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 93102 35.93 - 71.86: 11967 71.86 - 107.78: 1360 107.78 - 143.71: 38 143.71 - 179.64: 59 Dihedral angle restraints: 106526 sinusoidal: 88171 harmonic: 18355 Sorted by residual: dihedral pdb=" CA THR D 156 " pdb=" C THR D 156 " pdb=" N PRO D 157 " pdb=" CA PRO D 157 " ideal model delta harmonic sigma weight residual 180.00 92.83 87.17 0 5.00e+00 4.00e-02 3.04e+02 dihedral pdb=" CA UNK 0 337 " pdb=" C UNK 0 337 " pdb=" N UNK 0 338 " pdb=" CA UNK 0 338 " ideal model delta harmonic sigma weight residual 180.00 97.01 82.99 0 5.00e+00 4.00e-02 2.75e+02 dihedral pdb=" CA ARG g 76 " pdb=" C ARG g 76 " pdb=" N SER g 77 " pdb=" CA SER g 77 " ideal model delta harmonic sigma weight residual -180.00 -98.22 -81.78 0 5.00e+00 4.00e-02 2.68e+02 ... (remaining 106523 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.157: 31001 0.157 - 0.313: 605 0.313 - 0.470: 36 0.470 - 0.626: 6 0.626 - 0.783: 1 Chirality restraints: 31649 Sorted by residual: chirality pdb=" CA PRO T 118 " pdb=" N PRO T 118 " pdb=" C PRO T 118 " pdb=" CB PRO T 118 " both_signs ideal model delta sigma weight residual False 2.72 1.94 0.78 2.00e-01 2.50e+01 1.53e+01 chirality pdb=" C3' U a1482 " pdb=" C4' U a1482 " pdb=" O3' U a1482 " pdb=" C2' U a1482 " both_signs ideal model delta sigma weight residual False -2.74 -2.13 -0.62 2.00e-01 2.50e+01 9.60e+00 chirality pdb=" CB VAL d 188 " pdb=" CA VAL d 188 " pdb=" CG1 VAL d 188 " pdb=" CG2 VAL d 188 " both_signs ideal model delta sigma weight residual False -2.63 -2.07 -0.56 2.00e-01 2.50e+01 7.82e+00 ... (remaining 31646 not shown) Planarity restraints: 13589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR x 65 " 0.242 2.00e-02 2.50e+03 1.34e-01 3.61e+02 pdb=" CG TYR x 65 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TYR x 65 " -0.123 2.00e-02 2.50e+03 pdb=" CD2 TYR x 65 " -0.103 2.00e-02 2.50e+03 pdb=" CE1 TYR x 65 " -0.064 2.00e-02 2.50e+03 pdb=" CE2 TYR x 65 " -0.088 2.00e-02 2.50e+03 pdb=" CZ TYR x 65 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR x 65 " 0.210 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL V 47 " -0.086 2.00e-02 2.50e+03 1.11e-01 1.23e+02 pdb=" C VAL V 47 " 0.190 2.00e-02 2.50e+03 pdb=" O VAL V 47 " -0.067 2.00e-02 2.50e+03 pdb=" N SER V 56 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE x 110 " 0.087 2.00e-02 2.50e+03 5.33e-02 4.96e+01 pdb=" CG PHE x 110 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 PHE x 110 " -0.055 2.00e-02 2.50e+03 pdb=" CD2 PHE x 110 " -0.050 2.00e-02 2.50e+03 pdb=" CE1 PHE x 110 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE x 110 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE x 110 " 0.051 2.00e-02 2.50e+03 ... (remaining 13586 not shown) Histogram of nonbonded interaction distances: 1.09 - 1.85: 186 1.85 - 2.61: 4869 2.61 - 3.38: 177512 3.38 - 4.14: 496697 4.14 - 4.90: 706122 Nonbonded interactions: 1385386 Sorted by model distance: nonbonded pdb=" O2' G a1097 " pdb=" NH1 ARG i 126 " model vdw 1.089 2.520 nonbonded pdb=" OP1 G a 998 " pdb=" NE2 HIS s 14 " model vdw 1.090 2.520 nonbonded pdb=" CZ PHE O 86 " pdb=" O ARG O 117 " model vdw 1.115 3.340 nonbonded pdb=" C2 A a 940 " pdb=" NE ARG s 55 " model vdw 1.123 3.420 nonbonded pdb=" CB UNK 0 116 " pdb=" CB UNK 0 340 " model vdw 1.138 3.840 ... (remaining 1385381 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.33 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: 3.040 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: 0.110 Extract box with map and model: 13.280 Check model and map are aligned: 1.620 Set scattering table: 1.040 Process input model: 523.140 Find NCS groups from input model: 3.060 Set up NCS constraints: 0.400 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 548.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5165 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.630 165472 Z= 0.602 Angle : 1.182 50.163 247459 Z= 0.622 Chirality : 0.058 0.783 31649 Planarity : 0.008 0.145 13589 Dihedral : 24.039 179.638 94689 Min Nonbonded Distance : 1.089 Molprobity Statistics. All-atom Clashscore : 21.16 Ramachandran Plot: Outliers : 1.27 % Allowed : 8.46 % Favored : 90.27 % Rotamer: Outliers : 3.06 % Allowed : 6.12 % Favored : 90.82 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.75 % 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: -3.96 (0.09), residues: 6085 helix: -2.88 (0.09), residues: 1969 sheet: -1.96 (0.14), residues: 1093 loop : -2.69 (0.09), residues: 3023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.005 TRP N 92 HIS 0.026 0.003 HIS T 109 PHE 0.087 0.005 PHE x 110 TYR 0.242 0.005 TYR x 65 ARG 0.031 0.002 ARG X 75 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12170 Ramachandran restraints generated. 6085 Oldfield, 0 Emsley, 6085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12170 Ramachandran restraints generated. 6085 Oldfield, 0 Emsley, 6085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2656 residues out of total 5058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 2502 time to evaluate : 5.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 182 ARG cc_start: 0.3609 (OUTLIER) cc_final: 0.3261 (mtm180) REVERT: l 87 VAL cc_start: 0.3914 (t) cc_final: 0.3711 (p) REVERT: b 207 ILE cc_start: 0.8496 (tt) cc_final: 0.8127 (tt) REVERT: d 11 LYS cc_start: 0.7213 (mttt) cc_final: 0.6924 (mttt) REVERT: p 100 PRO cc_start: 0.7027 (Cg_exo) cc_final: 0.6741 (Cg_endo) REVERT: u 18 ARG cc_start: 0.6437 (mmt180) cc_final: 0.5805 (mmt90) REVERT: x 73 HIS cc_start: 0.0918 (OUTLIER) cc_final: -0.1566 (m-70) REVERT: C 104 TYR cc_start: 0.5941 (m-80) cc_final: 0.4986 (m-10) REVERT: E 150 GLU cc_start: 0.1513 (OUTLIER) cc_final: 0.0941 (mt-10) REVERT: I 110 MET cc_start: 0.7278 (mtp) cc_final: 0.7022 (ppp) REVERT: K 76 ARG cc_start: 0.5442 (OUTLIER) cc_final: 0.5205 (ptp90) REVERT: U 10 ILE cc_start: 0.4473 (OUTLIER) cc_final: 0.3877 (mt) outliers start: 154 outliers final: 42 residues processed: 2585 average time/residue: 1.4810 time to fit residues: 6304.9639 Evaluate side-chains 1472 residues out of total 5058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 1425 time to evaluate : 6.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 143 GLN Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain e residue 182 ARG Chi-restraints excluded: chain i residue 41 LEU Chi-restraints excluded: chain i residue 81 PHE Chi-restraints excluded: chain i residue 84 TYR Chi-restraints excluded: chain r residue 74 VAL Chi-restraints excluded: chain s residue 29 GLN Chi-restraints excluded: chain t residue 8 ILE Chi-restraints excluded: chain u residue 8 ARG Chi-restraints excluded: chain u residue 10 LYS Chi-restraints excluded: chain u residue 11 ARG Chi-restraints excluded: chain x residue 60 PHE Chi-restraints excluded: chain x residue 73 HIS Chi-restraints excluded: chain x residue 77 ARG Chi-restraints excluded: chain x residue 78 ARG Chi-restraints excluded: chain x residue 87 GLU Chi-restraints excluded: chain x residue 89 THR Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 258 ARG Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 34 GLN Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain K residue 75 TYR Chi-restraints excluded: chain K residue 76 ARG Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain N residue 92 TRP Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain S residue 103 LYS Chi-restraints excluded: chain U residue 10 ILE Chi-restraints excluded: chain U residue 68 ARG Chi-restraints excluded: chain V residue 10 LEU Chi-restraints excluded: chain W residue 6 ASN Chi-restraints excluded: chain W residue 7 ILE Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain W residue 129 ASN Chi-restraints excluded: chain Z residue 5 THR Chi-restraints excluded: chain y residue 44 PHE Chi-restraints excluded: chain y residue 60 ARG Chi-restraints excluded: chain 1 residue 22 ASN Chi-restraints excluded: chain 1 residue 42 CYS Chi-restraints excluded: chain 2 residue 27 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1102 random chunks: chunk 930 optimal weight: 10.0000 chunk 835 optimal weight: 30.0000 chunk 463 optimal weight: 5.9990 chunk 285 optimal weight: 8.9990 chunk 563 optimal weight: 4.9990 chunk 446 optimal weight: 7.9990 chunk 863 optimal weight: 10.0000 chunk 334 optimal weight: 3.9990 chunk 525 optimal weight: 8.9990 chunk 642 optimal weight: 4.9990 chunk 1000 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 107 ASN c 125 ASN c 138 GLN g 25 GLN ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 63 GLN h 117 GLN j 47 ASN k 31 HIS ** k 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 46 ASN o 7 GLN o 28 GLN o 50 HIS s 29 GLN s 47 HIS ** s 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 167 ASN ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 63 ASN x 76 ASN x 79 GLN ** x 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 HIS C 130 ASN C 135 ASN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 ASN ** D 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 ASN E 35 HIS E 121 ASN E 151 ASN E 202 ASN F 83 GLN ** F 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 ASN ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 HIS H 147 ASN J 33 HIS J 106 GLN J 119 ASN K 58 ASN K 111 HIS K 130 HIS K 132 HIS K 135 GLN L 4 GLN M 127 ASN N 35 GLN ** O 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 ASN O 77 HIS ** P 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 9 ASN R 41 HIS ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 92 GLN ** T 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 68 ASN ** U 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 58 ASN U 61 ASN W 46 HIS W 91 ASN ** W 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 12 ASN ** X 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 44 HIS X 46 HIS X 79 ASN ** v 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 20 HIS ** z 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 19 GLN z 36 GLN ** 1 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 48 HIS ** 1 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 11 ASN 3 31 HIS ** 3 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 63 ASN 5 17 ASN Total number of N/Q/H flips: 64 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5499 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.131 165472 Z= 0.260 Angle : 0.779 18.242 247459 Z= 0.396 Chirality : 0.040 0.381 31649 Planarity : 0.007 0.176 13589 Dihedral : 24.907 179.945 82819 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 22.86 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.90 % Favored : 92.66 % Rotamer: Outliers : 6.54 % Allowed : 22.02 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.74 % Twisted General : 0.29 % 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: 6087 helix: -1.29 (0.10), residues: 2046 sheet: -1.38 (0.15), residues: 1124 loop : -2.23 (0.10), residues: 2917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP c 201 HIS 0.016 0.002 HIS u 17 PHE 0.032 0.003 PHE O 86 TYR 0.034 0.003 TYR h 130 ARG 0.025 0.001 ARG F 99 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12174 Ramachandran restraints generated. 6087 Oldfield, 0 Emsley, 6087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12174 Ramachandran restraints generated. 6087 Oldfield, 0 Emsley, 6087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1956 residues out of total 5058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 329 poor density : 1627 time to evaluate : 6.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: i 47 GLN cc_start: 0.5101 (pp30) cc_final: 0.4721 (pp30) REVERT: s 28 LYS cc_start: 0.5715 (mmtt) cc_final: 0.4741 (mmtt) REVERT: b 29 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.7255 (ptp90) REVERT: b 153 ASP cc_start: 0.8816 (m-30) cc_final: 0.8064 (t70) REVERT: d 11 LYS cc_start: 0.7242 (mttt) cc_final: 0.7016 (mttt) REVERT: p 37 ILE cc_start: 0.7582 (OUTLIER) cc_final: 0.7316 (tp) REVERT: x 73 HIS cc_start: 0.1226 (OUTLIER) cc_final: -0.1031 (m90) REVERT: D 11 LEU cc_start: 0.6758 (tp) cc_final: 0.6427 (tt) REVERT: E 150 GLU cc_start: 0.1544 (OUTLIER) cc_final: -0.0541 (pp20) REVERT: H 125 LYS cc_start: 0.7676 (tptp) cc_final: 0.7353 (pttt) REVERT: M 72 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.6113 (tpt90) REVERT: N 45 ARG cc_start: 0.4604 (mmp-170) cc_final: 0.3876 (mmp-170) REVERT: S 65 LEU cc_start: 0.8040 (tt) cc_final: 0.7493 (mp) REVERT: T 81 VAL cc_start: 0.6959 (OUTLIER) cc_final: 0.6653 (m) REVERT: X 38 VAL cc_start: 0.5339 (p) cc_final: 0.4843 (p) outliers start: 329 outliers final: 168 residues processed: 1793 average time/residue: 1.4622 time to fit residues: 4386.1625 Evaluate side-chains 1498 residues out of total 5058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 1324 time to evaluate : 6.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 89 ASP Chi-restraints excluded: chain c residue 141 MET Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain e residue 61 LEU Chi-restraints excluded: chain e residue 79 LYS Chi-restraints excluded: chain e residue 101 LEU Chi-restraints excluded: chain e residue 119 VAL Chi-restraints excluded: chain e residue 159 ILE Chi-restraints excluded: chain e residue 182 ARG Chi-restraints excluded: chain g residue 31 LEU Chi-restraints excluded: chain g residue 48 GLU Chi-restraints excluded: chain g residue 62 LEU Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain h residue 94 LEU Chi-restraints excluded: chain h residue 112 LEU Chi-restraints excluded: chain i residue 61 ASN Chi-restraints excluded: chain i residue 84 TYR Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 9 ARG Chi-restraints excluded: chain j residue 15 HIS Chi-restraints excluded: chain k residue 67 SER Chi-restraints excluded: chain k residue 74 LEU Chi-restraints excluded: chain l residue 21 THR Chi-restraints excluded: chain l residue 80 VAL Chi-restraints excluded: chain l residue 97 ILE Chi-restraints excluded: chain o residue 19 ASP Chi-restraints excluded: chain o residue 45 VAL Chi-restraints excluded: chain o residue 73 VAL Chi-restraints excluded: chain q residue 53 ILE Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 74 VAL Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain s residue 41 ILE Chi-restraints excluded: chain s residue 55 ARG Chi-restraints excluded: chain t residue 8 ILE Chi-restraints excluded: chain n residue 56 VAL Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain b residue 29 ARG Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 93 ASN Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain b residue 105 SER Chi-restraints excluded: chain b residue 133 GLU Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain d residue 188 VAL Chi-restraints excluded: chain f residue 15 ASP Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 93 THR Chi-restraints excluded: chain m residue 8 ASP Chi-restraints excluded: chain m residue 40 ASP Chi-restraints excluded: chain p residue 3 VAL Chi-restraints excluded: chain p residue 10 LEU Chi-restraints excluded: chain p residue 20 ILE Chi-restraints excluded: chain p residue 34 ILE Chi-restraints excluded: chain p residue 37 ILE Chi-restraints excluded: chain p residue 51 ILE Chi-restraints excluded: chain p residue 73 LEU Chi-restraints excluded: chain p residue 92 THR Chi-restraints excluded: chain u residue 3 SER Chi-restraints excluded: chain u residue 8 ARG Chi-restraints excluded: chain u residue 10 LYS Chi-restraints excluded: chain x residue 36 LYS Chi-restraints excluded: chain x residue 73 HIS Chi-restraints excluded: chain x residue 79 GLN Chi-restraints excluded: chain x residue 107 TYR Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 258 ARG Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain H residue 90 LYS Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 75 TYR Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain L residue 13 ASN Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain M residue 72 ARG Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 108 SER Chi-restraints excluded: chain N residue 25 THR Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 92 TRP Chi-restraints excluded: chain N residue 94 VAL Chi-restraints excluded: chain N residue 131 ILE Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 91 ASN Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain P residue 10 ILE Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 99 THR Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 33 GLU Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain Q residue 82 HIS Chi-restraints excluded: chain Q residue 83 ILE Chi-restraints excluded: chain Q residue 86 LEU Chi-restraints excluded: chain Q residue 88 ARG Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain R residue 94 ASN Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain S residue 9 THR Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 47 ASN Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 85 HIS Chi-restraints excluded: chain S residue 103 LYS Chi-restraints excluded: chain T residue 7 PHE Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 69 GLU Chi-restraints excluded: chain T residue 78 VAL Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 92 ILE Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain U residue 37 SER Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain U residue 56 SER Chi-restraints excluded: chain U residue 84 VAL Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 13 SER Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 86 ARG Chi-restraints excluded: chain V residue 95 VAL Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain W residue 117 ASP Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 37 LEU Chi-restraints excluded: chain Y residue 18 VAL Chi-restraints excluded: chain Z residue 5 THR Chi-restraints excluded: chain Z residue 14 THR Chi-restraints excluded: chain v residue 22 SER Chi-restraints excluded: chain v residue 23 LEU Chi-restraints excluded: chain v residue 28 LEU Chi-restraints excluded: chain v residue 51 HIS Chi-restraints excluded: chain y residue 34 VAL Chi-restraints excluded: chain z residue 7 ARG Chi-restraints excluded: chain z residue 15 SER Chi-restraints excluded: chain 1 residue 12 THR Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 3 residue 33 LEU Chi-restraints excluded: chain 3 residue 44 LEU Chi-restraints excluded: chain 3 residue 51 SER Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain 4 residue 20 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1102 random chunks: chunk 556 optimal weight: 50.0000 chunk 310 optimal weight: 6.9990 chunk 832 optimal weight: 20.0000 chunk 681 optimal weight: 6.9990 chunk 276 optimal weight: 8.9990 chunk 1002 optimal weight: 20.0000 chunk 1083 optimal weight: 20.0000 chunk 892 optimal weight: 20.0000 chunk 994 optimal weight: 10.0000 chunk 341 optimal weight: 30.0000 chunk 804 optimal weight: 20.0000 overall best weight: 10.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 101 ASN g 28 ASN ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 86 HIS k 58 HIS ** k 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 70 ASN ** n 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 170 HIS d 49 GLN ** d 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 96 HIS m 88 GLN ** p 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 HIS D 183 HIS E 176 HIS F 28 ASN ** F 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 ASN ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 ASN J 45 ASN K 132 HIS L 4 GLN N 35 GLN ** N 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 22 HIS ** P 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 122 ASN S 67 HIS S 93 GLN ** T 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 58 ASN V 67 HIS ** W 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 12 ASN X 29 GLN Z 52 GLN ** v 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5827 moved from start: 0.4910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 165472 Z= 0.364 Angle : 0.806 18.861 247459 Z= 0.408 Chirality : 0.041 0.400 31649 Planarity : 0.007 0.152 13589 Dihedral : 25.131 179.915 82750 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 31.55 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.31 % Favored : 92.38 % Rotamer: Outliers : 7.51 % Allowed : 23.25 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.11 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.10), residues: 6087 helix: -0.72 (0.11), residues: 2062 sheet: -1.23 (0.15), residues: 1051 loop : -1.96 (0.11), residues: 2974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP v 17 HIS 0.014 0.002 HIS E 125 PHE 0.036 0.003 PHE t 35 TYR 0.035 0.003 TYR h 130 ARG 0.026 0.001 ARG v 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12174 Ramachandran restraints generated. 6087 Oldfield, 0 Emsley, 6087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12174 Ramachandran restraints generated. 6087 Oldfield, 0 Emsley, 6087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1815 residues out of total 5058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 378 poor density : 1437 time to evaluate : 6.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 19 LYS cc_start: 0.4863 (OUTLIER) cc_final: 0.4590 (pttm) REVERT: j 88 MET cc_start: 0.6083 (pmm) cc_final: 0.5796 (pmm) REVERT: b 153 ASP cc_start: 0.8849 (m-30) cc_final: 0.8009 (t70) REVERT: m 17 ILE cc_start: 0.4730 (OUTLIER) cc_final: 0.4357 (mp) REVERT: x 73 HIS cc_start: 0.1642 (OUTLIER) cc_final: -0.0875 (m90) REVERT: H 1 MET cc_start: 0.5522 (OUTLIER) cc_final: 0.5191 (ppp) REVERT: H 118 GLN cc_start: 0.6761 (OUTLIER) cc_final: 0.6512 (tp40) REVERT: H 125 LYS cc_start: 0.7604 (tptp) cc_final: 0.7212 (pttt) REVERT: Q 80 ILE cc_start: 0.7595 (mm) cc_final: 0.7318 (mm) REVERT: S 65 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7388 (tp) outliers start: 378 outliers final: 237 residues processed: 1633 average time/residue: 1.4640 time to fit residues: 4072.5726 Evaluate side-chains 1459 residues out of total 5058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 1216 time to evaluate : 6.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 19 LYS Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain e residue 61 LEU Chi-restraints excluded: chain e residue 63 ILE Chi-restraints excluded: chain e residue 79 LYS Chi-restraints excluded: chain e residue 101 LEU Chi-restraints excluded: chain g residue 31 LEU Chi-restraints excluded: chain g residue 33 GLU Chi-restraints excluded: chain g residue 62 LEU Chi-restraints excluded: chain g residue 142 HIS Chi-restraints excluded: chain h residue 19 SER Chi-restraints excluded: chain h residue 38 GLU Chi-restraints excluded: chain h residue 52 GLU Chi-restraints excluded: chain h residue 82 LYS Chi-restraints excluded: chain i residue 61 ASN Chi-restraints excluded: chain i residue 79 ASP Chi-restraints excluded: chain i residue 84 TYR Chi-restraints excluded: chain i residue 110 VAL Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 9 ARG Chi-restraints excluded: chain j residue 15 HIS Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 51 VAL Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 67 SER Chi-restraints excluded: chain k residue 74 LEU Chi-restraints excluded: chain l residue 21 THR Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 101 SER Chi-restraints excluded: chain o residue 40 THR Chi-restraints excluded: chain o residue 45 VAL Chi-restraints excluded: chain o residue 73 VAL Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 60 LYS Chi-restraints excluded: chain q residue 74 VAL Chi-restraints excluded: chain q residue 75 SER Chi-restraints excluded: chain q residue 80 ARG Chi-restraints excluded: chain r residue 30 ILE Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 74 VAL Chi-restraints excluded: chain s residue 16 LEU Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain s residue 41 ILE Chi-restraints excluded: chain s residue 55 ARG Chi-restraints excluded: chain t residue 15 GLU Chi-restraints excluded: chain t residue 83 LEU Chi-restraints excluded: chain n residue 6 LEU Chi-restraints excluded: chain n residue 24 CYS Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain b residue 29 ARG Chi-restraints excluded: chain b residue 42 ASP Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 93 ASN Chi-restraints excluded: chain b residue 133 GLU Chi-restraints excluded: chain b residue 161 VAL Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain b residue 196 VAL Chi-restraints excluded: chain b residue 200 ILE Chi-restraints excluded: chain d residue 9 THR Chi-restraints excluded: chain d residue 49 GLN Chi-restraints excluded: chain d residue 50 LEU Chi-restraints excluded: chain d residue 186 ILE Chi-restraints excluded: chain d residue 188 VAL Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain f residue 7 MET Chi-restraints excluded: chain f residue 15 ASP Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 62 VAL Chi-restraints excluded: chain f residue 72 VAL Chi-restraints excluded: chain f residue 74 GLU Chi-restraints excluded: chain f residue 93 THR Chi-restraints excluded: chain m residue 17 ILE Chi-restraints excluded: chain m residue 40 ASP Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain p residue 3 VAL Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 10 LEU Chi-restraints excluded: chain p residue 51 ILE Chi-restraints excluded: chain p residue 73 LEU Chi-restraints excluded: chain p residue 92 THR Chi-restraints excluded: chain u residue 3 SER Chi-restraints excluded: chain u residue 6 LYS Chi-restraints excluded: chain x residue 73 HIS Chi-restraints excluded: chain x residue 79 GLN Chi-restraints excluded: chain x residue 107 TYR Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 174 ARG Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 103 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 90 LYS Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain H residue 121 LYS Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain L residue 13 ASN Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 72 ARG Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain N residue 25 THR Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 116 ASP Chi-restraints excluded: chain N residue 131 ILE Chi-restraints excluded: chain O residue 15 SER Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 54 HIS Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 91 ASN Chi-restraints excluded: chain O residue 101 GLU Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain O residue 116 VAL Chi-restraints excluded: chain P residue 10 ILE Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 99 THR Chi-restraints excluded: chain Q residue 14 ASP Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain Q residue 82 HIS Chi-restraints excluded: chain Q residue 86 LEU Chi-restraints excluded: chain Q residue 88 ARG Chi-restraints excluded: chain Q residue 109 ILE Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain R residue 94 ASN Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain S residue 9 THR Chi-restraints excluded: chain S residue 27 LEU Chi-restraints excluded: chain S residue 47 ASN Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 65 LEU Chi-restraints excluded: chain S residue 85 HIS Chi-restraints excluded: chain S residue 103 LYS Chi-restraints excluded: chain T residue 7 PHE Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 31 VAL Chi-restraints excluded: chain T residue 38 GLU Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 48 GLN Chi-restraints excluded: chain T residue 92 ILE Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 15 VAL Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 37 SER Chi-restraints excluded: chain U residue 39 LYS Chi-restraints excluded: chain U residue 41 GLN Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain U residue 56 SER Chi-restraints excluded: chain U residue 84 VAL Chi-restraints excluded: chain V residue 5 LYS Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 95 VAL Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain W residue 117 ASP Chi-restraints excluded: chain X residue 37 LEU Chi-restraints excluded: chain X residue 57 ASP Chi-restraints excluded: chain X residue 58 THR Chi-restraints excluded: chain X residue 67 VAL Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 49 ILE Chi-restraints excluded: chain Z residue 5 THR Chi-restraints excluded: chain v residue 28 LEU Chi-restraints excluded: chain v residue 51 HIS Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain y residue 24 THR Chi-restraints excluded: chain y residue 34 VAL Chi-restraints excluded: chain y residue 44 PHE Chi-restraints excluded: chain z residue 7 ARG Chi-restraints excluded: chain 1 residue 12 THR Chi-restraints excluded: chain 1 residue 13 LEU Chi-restraints excluded: chain 1 residue 44 ASN Chi-restraints excluded: chain 3 residue 25 GLN Chi-restraints excluded: chain 3 residue 33 LEU Chi-restraints excluded: chain 3 residue 44 LEU Chi-restraints excluded: chain 3 residue 50 VAL Chi-restraints excluded: chain 4 residue 3 VAL Chi-restraints excluded: chain 4 residue 19 ARG Chi-restraints excluded: chain 4 residue 20 HIS Chi-restraints excluded: chain 4 residue 25 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1102 random chunks: chunk 990 optimal weight: 10.0000 chunk 753 optimal weight: 7.9990 chunk 520 optimal weight: 5.9990 chunk 110 optimal weight: 40.0000 chunk 478 optimal weight: 30.0000 chunk 673 optimal weight: 20.0000 chunk 1006 optimal weight: 20.0000 chunk 1065 optimal weight: 20.0000 chunk 525 optimal weight: 20.0000 chunk 953 optimal weight: 40.0000 chunk 287 optimal weight: 0.0870 overall best weight: 8.8170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 86 GLN g 142 HIS h 121 GLN ** i 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 46 HIS ** s 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 134 GLN ** f 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 81 GLN ** x 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 15 GLN D 34 ASN E 68 GLN F 83 GLN ** F 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS G 103 ASN ** H 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 ASN I 100 ASN J 32 GLN ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 58 ASN N 39 HIS ** N 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 54 HIS ** O 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 107 ASN ** P 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 93 GLN ** T 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 26 GLN ** W 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 35 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5873 moved from start: 0.5834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.141 165472 Z= 0.296 Angle : 0.719 16.974 247459 Z= 0.365 Chirality : 0.038 0.372 31649 Planarity : 0.006 0.143 13589 Dihedral : 25.186 179.982 82721 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 26.89 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.23 % Favored : 92.48 % Rotamer: Outliers : 7.15 % Allowed : 24.64 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.48 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.10), residues: 6087 helix: -0.31 (0.11), residues: 2022 sheet: -1.18 (0.15), residues: 1122 loop : -1.93 (0.11), residues: 2943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP N 92 HIS 0.018 0.002 HIS N 39 PHE 0.037 0.003 PHE t 35 TYR 0.034 0.003 TYR h 130 ARG 0.020 0.001 ARG C 256 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12174 Ramachandran restraints generated. 6087 Oldfield, 0 Emsley, 6087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12174 Ramachandran restraints generated. 6087 Oldfield, 0 Emsley, 6087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1749 residues out of total 5058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 360 poor density : 1389 time to evaluate : 6.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 1 MET cc_start: 0.1307 (ptt) cc_final: 0.0648 (ptt) REVERT: g 33 GLU cc_start: 0.6188 (OUTLIER) cc_final: 0.5848 (pp20) REVERT: h 33 LYS cc_start: 0.4230 (OUTLIER) cc_final: 0.3661 (ptmm) REVERT: r 45 ARG cc_start: 0.5140 (tpm170) cc_final: 0.4812 (tpm170) REVERT: s 25 LYS cc_start: 0.8244 (pptt) cc_final: 0.8036 (pptt) REVERT: s 28 LYS cc_start: 0.5246 (mmtt) cc_final: 0.4961 (mmmm) REVERT: n 24 CYS cc_start: 0.6188 (OUTLIER) cc_final: 0.5367 (p) REVERT: n 52 GLU cc_start: 0.5334 (tm-30) cc_final: 0.4909 (tm-30) REVERT: b 153 ASP cc_start: 0.8922 (m-30) cc_final: 0.7993 (t0) REVERT: d 199 TYR cc_start: 0.7167 (m-80) cc_final: 0.6959 (m-80) REVERT: u 11 ARG cc_start: 0.5586 (OUTLIER) cc_final: 0.5138 (ttt180) REVERT: u 24 THR cc_start: 0.8232 (p) cc_final: 0.7960 (p) REVERT: C 259 LYS cc_start: 0.5985 (OUTLIER) cc_final: 0.5743 (mtmm) REVERT: G 82 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7521 (mp0) REVERT: J 137 MET cc_start: 0.7731 (mmt) cc_final: 0.7039 (mmm) REVERT: Z 16 ASP cc_start: 0.2075 (OUTLIER) cc_final: 0.1685 (p0) outliers start: 360 outliers final: 225 residues processed: 1583 average time/residue: 1.3736 time to fit residues: 3697.4139 Evaluate side-chains 1444 residues out of total 5058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 1213 time to evaluate : 6.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 59 THR Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 101 ASN Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain e residue 63 ILE Chi-restraints excluded: chain e residue 79 LYS Chi-restraints excluded: chain e residue 101 LEU Chi-restraints excluded: chain g residue 33 GLU Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 62 LEU Chi-restraints excluded: chain g residue 142 HIS Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 19 SER Chi-restraints excluded: chain h residue 33 LYS Chi-restraints excluded: chain h residue 126 GLU Chi-restraints excluded: chain i residue 26 ILE Chi-restraints excluded: chain i residue 42 VAL Chi-restraints excluded: chain i residue 47 GLN Chi-restraints excluded: chain i residue 56 GLU Chi-restraints excluded: chain i residue 61 ASN Chi-restraints excluded: chain i residue 79 ASP Chi-restraints excluded: chain i residue 84 TYR Chi-restraints excluded: chain i residue 110 VAL Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 15 HIS Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain k residue 91 VAL Chi-restraints excluded: chain k residue 92 ASP Chi-restraints excluded: chain l residue 21 THR Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 74 LEU Chi-restraints excluded: chain l residue 97 ILE Chi-restraints excluded: chain o residue 45 VAL Chi-restraints excluded: chain o residue 49 ASP Chi-restraints excluded: chain q residue 24 ILE Chi-restraints excluded: chain q residue 43 ARG Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain r residue 35 THR Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 74 VAL Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain s residue 55 ARG Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 73 GLU Chi-restraints excluded: chain t residue 15 GLU Chi-restraints excluded: chain t residue 37 GLU Chi-restraints excluded: chain n residue 24 CYS Chi-restraints excluded: chain n residue 25 ASN Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 59 SER Chi-restraints excluded: chain b residue 42 ASP Chi-restraints excluded: chain b residue 51 ASP Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 93 ASN Chi-restraints excluded: chain b residue 133 GLU Chi-restraints excluded: chain b residue 161 VAL Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain b residue 196 VAL Chi-restraints excluded: chain b residue 200 ILE Chi-restraints excluded: chain d residue 50 LEU Chi-restraints excluded: chain d residue 186 ILE Chi-restraints excluded: chain d residue 188 VAL Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain f residue 7 MET Chi-restraints excluded: chain f residue 15 ASP Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 46 ARG Chi-restraints excluded: chain f residue 62 VAL Chi-restraints excluded: chain f residue 72 VAL Chi-restraints excluded: chain f residue 74 GLU Chi-restraints excluded: chain f residue 93 THR Chi-restraints excluded: chain m residue 8 ASP Chi-restraints excluded: chain m residue 40 ASP Chi-restraints excluded: chain m residue 90 LEU Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 10 LEU Chi-restraints excluded: chain p residue 73 LEU Chi-restraints excluded: chain u residue 3 SER Chi-restraints excluded: chain u residue 11 ARG Chi-restraints excluded: chain x residue 107 TYR Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 262 LYS Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 172 ASN Chi-restraints excluded: chain D residue 174 ARG Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain I residue 96 PHE Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 55 ILE Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain L residue 13 ASN Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 72 ARG Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain N residue 25 THR Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 67 ASN Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 131 ILE Chi-restraints excluded: chain O residue 18 SER Chi-restraints excluded: chain O residue 35 LYS Chi-restraints excluded: chain O residue 54 HIS Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 99 LYS Chi-restraints excluded: chain O residue 101 GLU Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain O residue 116 VAL Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 99 THR Chi-restraints excluded: chain Q residue 14 ASP Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain Q residue 82 HIS Chi-restraints excluded: chain Q residue 88 ARG Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain R residue 94 ASN Chi-restraints excluded: chain S residue 14 TYR Chi-restraints excluded: chain S residue 27 LEU Chi-restraints excluded: chain S residue 47 ASN Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 65 LEU Chi-restraints excluded: chain S residue 103 LYS Chi-restraints excluded: chain T residue 7 PHE Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 31 VAL Chi-restraints excluded: chain T residue 38 GLU Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 77 VAL Chi-restraints excluded: chain T residue 78 VAL Chi-restraints excluded: chain T residue 92 ILE Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 15 VAL Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 37 SER Chi-restraints excluded: chain U residue 38 ASN Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain U residue 56 SER Chi-restraints excluded: chain U residue 84 VAL Chi-restraints excluded: chain U residue 95 LEU Chi-restraints excluded: chain V residue 5 LYS Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 43 LYS Chi-restraints excluded: chain V residue 86 ARG Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 80 THR Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain W residue 117 ASP Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 31 VAL Chi-restraints excluded: chain X residue 37 LEU Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 58 THR Chi-restraints excluded: chain X residue 67 VAL Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Z residue 5 THR Chi-restraints excluded: chain Z residue 14 THR Chi-restraints excluded: chain Z residue 16 ASP Chi-restraints excluded: chain v residue 23 LEU Chi-restraints excluded: chain v residue 51 HIS Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain y residue 24 THR Chi-restraints excluded: chain y residue 34 VAL Chi-restraints excluded: chain y residue 44 PHE Chi-restraints excluded: chain y residue 61 PHE Chi-restraints excluded: chain 1 residue 13 LEU Chi-restraints excluded: chain 1 residue 15 CYS Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 3 residue 33 LEU Chi-restraints excluded: chain 3 residue 44 LEU Chi-restraints excluded: chain 3 residue 51 SER Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain 4 residue 20 HIS Chi-restraints excluded: chain 4 residue 23 VAL Chi-restraints excluded: chain 4 residue 24 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1102 random chunks: chunk 887 optimal weight: 20.0000 chunk 604 optimal weight: 1.9990 chunk 15 optimal weight: 30.0000 chunk 793 optimal weight: 20.0000 chunk 439 optimal weight: 5.9990 chunk 908 optimal weight: 50.0000 chunk 736 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 543 optimal weight: 7.9990 chunk 956 optimal weight: 20.0000 chunk 268 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 125 ASN e 95 ASN ** e 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 142 HIS ** i 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 14 HIS ** s 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 8 HIS ** b 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 HIS ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 ASN ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 67 ASN ** U 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 67 HIS W 26 GLN ** Y 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 19 GLN ** 1 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 51 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5901 moved from start: 0.6317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 165472 Z= 0.264 Angle : 0.694 20.311 247459 Z= 0.350 Chirality : 0.037 0.345 31649 Planarity : 0.006 0.200 13589 Dihedral : 25.149 179.794 82719 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 27.82 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.33 % Favored : 92.41 % Rotamer: Outliers : 6.42 % Allowed : 27.84 % Favored : 65.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.48 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.10), residues: 6087 helix: -0.12 (0.11), residues: 2011 sheet: -1.14 (0.15), residues: 1121 loop : -1.83 (0.11), residues: 2955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP N 92 HIS 0.030 0.002 HIS g 142 PHE 0.037 0.002 PHE U 50 TYR 0.030 0.002 TYR h 130 ARG 0.021 0.001 ARG y 25 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12174 Ramachandran restraints generated. 6087 Oldfield, 0 Emsley, 6087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12174 Ramachandran restraints generated. 6087 Oldfield, 0 Emsley, 6087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1637 residues out of total 5058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 323 poor density : 1314 time to evaluate : 6.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 1 MET cc_start: 0.0846 (ptt) cc_final: 0.0535 (ptt) REVERT: g 33 GLU cc_start: 0.6265 (OUTLIER) cc_final: 0.6004 (pp20) REVERT: t 30 THR cc_start: 0.4836 (m) cc_final: 0.4622 (m) REVERT: n 24 CYS cc_start: 0.6143 (OUTLIER) cc_final: 0.5381 (p) REVERT: m 75 GLN cc_start: 0.7672 (tm-30) cc_final: 0.7441 (tm-30) REVERT: G 82 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7766 (mp0) REVERT: H 1 MET cc_start: 0.6713 (ppp) cc_final: 0.5853 (ppp) REVERT: H 125 LYS cc_start: 0.6705 (pttt) cc_final: 0.6401 (pttt) REVERT: J 137 MET cc_start: 0.7879 (mmt) cc_final: 0.6998 (mmt) REVERT: K 60 ASP cc_start: 0.4414 (p0) cc_final: 0.4213 (p0) REVERT: O 99 LYS cc_start: 0.6455 (OUTLIER) cc_final: 0.6214 (mttm) REVERT: S 27 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7463 (tp) REVERT: W 38 TYR cc_start: 0.3337 (OUTLIER) cc_final: 0.1930 (m-80) REVERT: y 9 TYR cc_start: 0.7421 (t80) cc_final: 0.6972 (t80) outliers start: 323 outliers final: 224 residues processed: 1497 average time/residue: 1.3814 time to fit residues: 3521.3975 Evaluate side-chains 1426 residues out of total 5058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 1197 time to evaluate : 6.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 101 ASN Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain e residue 63 ILE Chi-restraints excluded: chain e residue 79 LYS Chi-restraints excluded: chain e residue 95 ASN Chi-restraints excluded: chain e residue 101 LEU Chi-restraints excluded: chain g residue 33 GLU Chi-restraints excluded: chain g residue 62 LEU Chi-restraints excluded: chain g residue 85 TYR Chi-restraints excluded: chain h residue 19 SER Chi-restraints excluded: chain h residue 33 LYS Chi-restraints excluded: chain h residue 38 GLU Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain i residue 47 GLN Chi-restraints excluded: chain i residue 56 GLU Chi-restraints excluded: chain i residue 61 ASN Chi-restraints excluded: chain i residue 79 ASP Chi-restraints excluded: chain i residue 84 TYR Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 15 HIS Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 67 SER Chi-restraints excluded: chain k residue 92 ASP Chi-restraints excluded: chain k residue 95 VAL Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 127 HIS Chi-restraints excluded: chain l residue 21 THR Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 74 LEU Chi-restraints excluded: chain l residue 97 ILE Chi-restraints excluded: chain o residue 36 ILE Chi-restraints excluded: chain o residue 45 VAL Chi-restraints excluded: chain o residue 49 ASP Chi-restraints excluded: chain q residue 43 ARG Chi-restraints excluded: chain q residue 53 ILE Chi-restraints excluded: chain q residue 63 ASP Chi-restraints excluded: chain q residue 74 VAL Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain r residue 35 THR Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 74 VAL Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain s residue 47 HIS Chi-restraints excluded: chain s residue 55 ARG Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 15 GLU Chi-restraints excluded: chain n residue 24 CYS Chi-restraints excluded: chain n residue 25 ASN Chi-restraints excluded: chain n residue 59 SER Chi-restraints excluded: chain b residue 42 ASP Chi-restraints excluded: chain b residue 51 ASP Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 70 VAL Chi-restraints excluded: chain b residue 93 ASN Chi-restraints excluded: chain b residue 100 MET Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain b residue 133 GLU Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain b residue 196 VAL Chi-restraints excluded: chain b residue 200 ILE Chi-restraints excluded: chain d residue 50 LEU Chi-restraints excluded: chain d residue 156 THR Chi-restraints excluded: chain d residue 186 ILE Chi-restraints excluded: chain d residue 188 VAL Chi-restraints excluded: chain f residue 8 VAL Chi-restraints excluded: chain f residue 15 ASP Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 62 VAL Chi-restraints excluded: chain f residue 68 GLU Chi-restraints excluded: chain f residue 74 GLU Chi-restraints excluded: chain f residue 93 THR Chi-restraints excluded: chain m residue 40 ASP Chi-restraints excluded: chain m residue 90 LEU Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 10 LEU Chi-restraints excluded: chain p residue 51 ILE Chi-restraints excluded: chain p residue 73 LEU Chi-restraints excluded: chain p residue 92 THR Chi-restraints excluded: chain u residue 3 SER Chi-restraints excluded: chain u residue 6 LYS Chi-restraints excluded: chain x residue 73 HIS Chi-restraints excluded: chain x residue 107 TYR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain C residue 262 LYS Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 161 PHE Chi-restraints excluded: chain D residue 172 ASN Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain H residue 29 TYR Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain I residue 96 PHE Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain L residue 13 ASN Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain N residue 25 THR Chi-restraints excluded: chain N residue 131 ILE Chi-restraints excluded: chain O residue 35 LYS Chi-restraints excluded: chain O residue 47 TYR Chi-restraints excluded: chain O residue 54 HIS Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 99 LYS Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain O residue 116 VAL Chi-restraints excluded: chain P residue 10 ILE Chi-restraints excluded: chain P residue 28 LYS Chi-restraints excluded: chain P residue 99 THR Chi-restraints excluded: chain Q residue 11 SER Chi-restraints excluded: chain Q residue 14 ASP Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain Q residue 82 HIS Chi-restraints excluded: chain Q residue 88 ARG Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain R residue 91 ASP Chi-restraints excluded: chain R residue 94 ASN Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 98 LEU Chi-restraints excluded: chain S residue 14 TYR Chi-restraints excluded: chain S residue 27 LEU Chi-restraints excluded: chain S residue 47 ASN Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 65 LEU Chi-restraints excluded: chain S residue 96 VAL Chi-restraints excluded: chain S residue 103 LYS Chi-restraints excluded: chain T residue 7 PHE Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 31 VAL Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain T residue 92 ILE Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 15 VAL Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 37 SER Chi-restraints excluded: chain U residue 38 ASN Chi-restraints excluded: chain U residue 55 ASP Chi-restraints excluded: chain U residue 56 SER Chi-restraints excluded: chain U residue 61 ASN Chi-restraints excluded: chain U residue 84 VAL Chi-restraints excluded: chain U residue 95 LEU Chi-restraints excluded: chain V residue 5 LYS Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 38 TYR Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain W residue 91 ASN Chi-restraints excluded: chain W residue 117 ASP Chi-restraints excluded: chain X residue 31 VAL Chi-restraints excluded: chain X residue 37 LEU Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 58 THR Chi-restraints excluded: chain X residue 67 VAL Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Z residue 5 THR Chi-restraints excluded: chain v residue 39 ASP Chi-restraints excluded: chain v residue 51 HIS Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain y residue 27 THR Chi-restraints excluded: chain y residue 34 VAL Chi-restraints excluded: chain y residue 44 PHE Chi-restraints excluded: chain y residue 61 PHE Chi-restraints excluded: chain z residue 9 SER Chi-restraints excluded: chain 1 residue 12 THR Chi-restraints excluded: chain 1 residue 13 LEU Chi-restraints excluded: chain 1 residue 15 CYS Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 3 residue 33 LEU Chi-restraints excluded: chain 3 residue 44 LEU Chi-restraints excluded: chain 3 residue 50 VAL Chi-restraints excluded: chain 3 residue 51 SER Chi-restraints excluded: chain 4 residue 20 HIS Chi-restraints excluded: chain 4 residue 25 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1102 random chunks: chunk 358 optimal weight: 1.9990 chunk 959 optimal weight: 20.0000 chunk 210 optimal weight: 40.0000 chunk 625 optimal weight: 4.9990 chunk 262 optimal weight: 4.9990 chunk 1066 optimal weight: 20.0000 chunk 885 optimal weight: 20.0000 chunk 493 optimal weight: 0.8980 chunk 88 optimal weight: 20.0000 chunk 352 optimal weight: 20.0000 chunk 559 optimal weight: 0.2980 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 111 GLN ** h 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 128 ASN ** l 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 ASN J 32 GLN ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 111 HIS ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 HIS ** O 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 107 ASN ** P 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 53 ASN Q 28 HIS ** Q 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 62 GLN ** V 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 26 GLN ** W 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5814 moved from start: 0.6414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 165472 Z= 0.172 Angle : 0.653 23.231 247459 Z= 0.326 Chirality : 0.035 0.417 31649 Planarity : 0.006 0.164 13589 Dihedral : 25.022 178.941 82716 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 21.74 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.74 % Favored : 93.00 % Rotamer: Outliers : 5.45 % Allowed : 29.89 % Favored : 64.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.11 % 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: -1.52 (0.10), residues: 6087 helix: 0.05 (0.11), residues: 2010 sheet: -1.01 (0.15), residues: 1097 loop : -1.75 (0.11), residues: 2980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP N 92 HIS 0.015 0.001 HIS j 64 PHE 0.038 0.002 PHE U 50 TYR 0.036 0.002 TYR d 71 ARG 0.019 0.001 ARG f 77 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12174 Ramachandran restraints generated. 6087 Oldfield, 0 Emsley, 6087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12174 Ramachandran restraints generated. 6087 Oldfield, 0 Emsley, 6087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1609 residues out of total 5058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 1335 time to evaluate : 6.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 1 MET cc_start: 0.1180 (ptt) cc_final: 0.0871 (ptt) REVERT: r 74 VAL cc_start: 0.6299 (OUTLIER) cc_final: 0.5976 (p) REVERT: s 32 LYS cc_start: 0.1677 (tptt) cc_final: 0.1154 (tptt) REVERT: n 24 CYS cc_start: 0.6005 (OUTLIER) cc_final: 0.5177 (p) REVERT: b 198 TYR cc_start: 0.8431 (m-80) cc_final: 0.8023 (m-80) REVERT: m 75 GLN cc_start: 0.7736 (tm-30) cc_final: 0.7482 (tm-30) REVERT: D 89 GLU cc_start: 0.6828 (mm-30) cc_final: 0.6586 (mp0) REVERT: J 109 GLU cc_start: 0.7766 (tp30) cc_final: 0.7384 (tp30) REVERT: J 137 MET cc_start: 0.7806 (mmt) cc_final: 0.6936 (mmm) REVERT: L 59 LYS cc_start: 0.5789 (OUTLIER) cc_final: 0.5345 (ptpp) REVERT: M 72 ARG cc_start: 0.6460 (OUTLIER) cc_final: 0.4178 (tpt90) REVERT: S 27 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7340 (tp) REVERT: W 36 VAL cc_start: 0.5570 (OUTLIER) cc_final: 0.5112 (t) REVERT: W 38 TYR cc_start: 0.2922 (OUTLIER) cc_final: 0.1544 (m-80) outliers start: 274 outliers final: 192 residues processed: 1483 average time/residue: 1.3712 time to fit residues: 3467.7616 Evaluate side-chains 1390 residues out of total 5058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 1191 time to evaluate : 5.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 101 ASN Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain e residue 63 ILE Chi-restraints excluded: chain e residue 79 LYS Chi-restraints excluded: chain e residue 101 LEU Chi-restraints excluded: chain e residue 111 GLN Chi-restraints excluded: chain e residue 140 LEU Chi-restraints excluded: chain g residue 62 LEU Chi-restraints excluded: chain g residue 85 TYR Chi-restraints excluded: chain h residue 126 GLU Chi-restraints excluded: chain i residue 56 GLU Chi-restraints excluded: chain i residue 61 ASN Chi-restraints excluded: chain i residue 79 ASP Chi-restraints excluded: chain i residue 84 TYR Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 15 HIS Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain k residue 74 LEU Chi-restraints excluded: chain k residue 92 ASP Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 10 LYS Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 21 THR Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 74 LEU Chi-restraints excluded: chain l residue 97 ILE Chi-restraints excluded: chain o residue 49 ASP Chi-restraints excluded: chain q residue 43 ARG Chi-restraints excluded: chain q residue 74 VAL Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain r residue 35 THR Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 74 VAL Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain s residue 47 HIS Chi-restraints excluded: chain s residue 55 ARG Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 73 GLU Chi-restraints excluded: chain n residue 6 LEU Chi-restraints excluded: chain n residue 11 ASN Chi-restraints excluded: chain n residue 24 CYS Chi-restraints excluded: chain b residue 42 ASP Chi-restraints excluded: chain b residue 51 ASP Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 93 ASN Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain b residue 196 VAL Chi-restraints excluded: chain b residue 200 ILE Chi-restraints excluded: chain d residue 50 LEU Chi-restraints excluded: chain d residue 156 THR Chi-restraints excluded: chain d residue 186 ILE Chi-restraints excluded: chain d residue 188 VAL Chi-restraints excluded: chain d residue 199 TYR Chi-restraints excluded: chain f residue 8 VAL Chi-restraints excluded: chain f residue 15 ASP Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 62 VAL Chi-restraints excluded: chain f residue 68 GLU Chi-restraints excluded: chain f residue 72 VAL Chi-restraints excluded: chain f residue 93 THR Chi-restraints excluded: chain m residue 8 ASP Chi-restraints excluded: chain m residue 40 ASP Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 10 LEU Chi-restraints excluded: chain u residue 3 SER Chi-restraints excluded: chain u residue 12 MET Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 262 LYS Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 172 ASN Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain L residue 13 ASN Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 59 LYS Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 72 ARG Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain N residue 67 ASN Chi-restraints excluded: chain N residue 131 ILE Chi-restraints excluded: chain O residue 23 ASN Chi-restraints excluded: chain O residue 35 LYS Chi-restraints excluded: chain O residue 47 TYR Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 80 PHE Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain O residue 116 VAL Chi-restraints excluded: chain P residue 10 ILE Chi-restraints excluded: chain P residue 55 LEU Chi-restraints excluded: chain P residue 99 THR Chi-restraints excluded: chain Q residue 11 SER Chi-restraints excluded: chain Q residue 14 ASP Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain Q residue 82 HIS Chi-restraints excluded: chain Q residue 88 ARG Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 63 SER Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain R residue 94 ASN Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain S residue 14 TYR Chi-restraints excluded: chain S residue 27 LEU Chi-restraints excluded: chain S residue 47 ASN Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 96 VAL Chi-restraints excluded: chain S residue 103 LYS Chi-restraints excluded: chain T residue 7 PHE Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 31 VAL Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 15 VAL Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 37 SER Chi-restraints excluded: chain U residue 38 ASN Chi-restraints excluded: chain U residue 56 SER Chi-restraints excluded: chain U residue 61 ASN Chi-restraints excluded: chain U residue 93 ILE Chi-restraints excluded: chain U residue 95 LEU Chi-restraints excluded: chain V residue 5 LYS Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 38 TYR Chi-restraints excluded: chain W residue 80 THR Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain W residue 91 ASN Chi-restraints excluded: chain W residue 117 ASP Chi-restraints excluded: chain X residue 31 VAL Chi-restraints excluded: chain X residue 37 LEU Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 58 THR Chi-restraints excluded: chain X residue 67 VAL Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Y residue 61 VAL Chi-restraints excluded: chain Z residue 5 THR Chi-restraints excluded: chain Z residue 22 LEU Chi-restraints excluded: chain v residue 6 ILE Chi-restraints excluded: chain v residue 39 ASP Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain y residue 24 THR Chi-restraints excluded: chain y residue 34 VAL Chi-restraints excluded: chain y residue 45 TYR Chi-restraints excluded: chain y residue 61 PHE Chi-restraints excluded: chain z residue 9 SER Chi-restraints excluded: chain 1 residue 12 THR Chi-restraints excluded: chain 1 residue 15 CYS Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 3 residue 50 VAL Chi-restraints excluded: chain 4 residue 3 VAL Chi-restraints excluded: chain 4 residue 19 ARG Chi-restraints excluded: chain 4 residue 20 HIS Chi-restraints excluded: chain 4 residue 24 MET Chi-restraints excluded: chain 4 residue 28 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1102 random chunks: chunk 1027 optimal weight: 40.0000 chunk 120 optimal weight: 40.0000 chunk 607 optimal weight: 9.9990 chunk 778 optimal weight: 20.0000 chunk 603 optimal weight: 0.1980 chunk 897 optimal weight: 20.0000 chunk 595 optimal weight: 6.9990 chunk 1062 optimal weight: 20.0000 chunk 664 optimal weight: 7.9990 chunk 647 optimal weight: 10.0000 chunk 490 optimal weight: 9.9990 overall best weight: 7.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 8 HIS ** c 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 111 GLN ** h 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 179 GLN ** f 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 146 HIS ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 107 ASN ** Q 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 67 ASN ** U 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 26 GLN ** W 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5913 moved from start: 0.6853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 165472 Z= 0.259 Angle : 0.685 20.122 247459 Z= 0.344 Chirality : 0.036 0.334 31649 Planarity : 0.006 0.131 13589 Dihedral : 25.036 179.280 82716 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 27.75 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.41 % Favored : 92.36 % Rotamer: Outliers : 6.16 % Allowed : 30.03 % Favored : 63.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.48 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.10), residues: 6087 helix: 0.07 (0.11), residues: 1994 sheet: -1.12 (0.15), residues: 1086 loop : -1.64 (0.11), residues: 3007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP C 250 HIS 0.015 0.001 HIS e 108 PHE 0.040 0.002 PHE U 50 TYR 0.058 0.002 TYR d 71 ARG 0.029 0.001 ARG Z 33 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12174 Ramachandran restraints generated. 6087 Oldfield, 0 Emsley, 6087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12174 Ramachandran restraints generated. 6087 Oldfield, 0 Emsley, 6087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1582 residues out of total 5058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 310 poor density : 1272 time to evaluate : 6.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 1 MET cc_start: 0.1000 (ptt) cc_final: 0.0668 (ptt) REVERT: n 24 CYS cc_start: 0.5706 (OUTLIER) cc_final: 0.5141 (p) REVERT: b 152 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7680 (tpp-160) REVERT: m 75 GLN cc_start: 0.7668 (tm-30) cc_final: 0.7415 (tm-30) REVERT: G 82 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7644 (mp0) REVERT: J 109 GLU cc_start: 0.7915 (tp30) cc_final: 0.7503 (tp30) REVERT: J 137 MET cc_start: 0.7799 (mmt) cc_final: 0.6506 (mmt) REVERT: M 15 GLU cc_start: 0.6062 (mm-30) cc_final: 0.5742 (mm-30) REVERT: M 72 ARG cc_start: 0.6507 (OUTLIER) cc_final: 0.4335 (tpt90) REVERT: N 41 TYR cc_start: 0.4464 (OUTLIER) cc_final: 0.4110 (p90) REVERT: R 73 ASP cc_start: 0.6654 (t0) cc_final: 0.6452 (t0) REVERT: S 27 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7396 (tp) REVERT: W 36 VAL cc_start: 0.5663 (OUTLIER) cc_final: 0.5249 (t) REVERT: W 38 TYR cc_start: 0.3745 (OUTLIER) cc_final: 0.2237 (m-80) outliers start: 310 outliers final: 233 residues processed: 1430 average time/residue: 1.3673 time to fit residues: 3336.7264 Evaluate side-chains 1430 residues out of total 5058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 1190 time to evaluate : 6.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 101 ASN Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain c residue 207 ILE Chi-restraints excluded: chain e residue 51 LYS Chi-restraints excluded: chain e residue 63 ILE Chi-restraints excluded: chain e residue 79 LYS Chi-restraints excluded: chain e residue 101 LEU Chi-restraints excluded: chain e residue 111 GLN Chi-restraints excluded: chain e residue 140 LEU Chi-restraints excluded: chain g residue 62 LEU Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 85 TYR Chi-restraints excluded: chain h residue 19 SER Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain h residue 126 GLU Chi-restraints excluded: chain i residue 42 VAL Chi-restraints excluded: chain i residue 47 GLN Chi-restraints excluded: chain i residue 56 GLU Chi-restraints excluded: chain i residue 61 ASN Chi-restraints excluded: chain i residue 79 ASP Chi-restraints excluded: chain i residue 84 TYR Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 15 HIS Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain k residue 67 SER Chi-restraints excluded: chain k residue 92 ASP Chi-restraints excluded: chain k residue 95 VAL Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 127 HIS Chi-restraints excluded: chain l residue 21 THR Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 74 LEU Chi-restraints excluded: chain l residue 89 ASP Chi-restraints excluded: chain l residue 97 ILE Chi-restraints excluded: chain o residue 49 ASP Chi-restraints excluded: chain q residue 22 THR Chi-restraints excluded: chain q residue 24 ILE Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain q residue 43 ARG Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 72 ASP Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain r residue 35 THR Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 47 HIS Chi-restraints excluded: chain s residue 55 ARG Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 71 LEU Chi-restraints excluded: chain s residue 73 GLU Chi-restraints excluded: chain n residue 11 ASN Chi-restraints excluded: chain n residue 24 CYS Chi-restraints excluded: chain n residue 59 SER Chi-restraints excluded: chain b residue 42 ASP Chi-restraints excluded: chain b residue 51 ASP Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 93 ASN Chi-restraints excluded: chain b residue 100 MET Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain b residue 133 GLU Chi-restraints excluded: chain b residue 152 ARG Chi-restraints excluded: chain b residue 153 ASP Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain b residue 196 VAL Chi-restraints excluded: chain b residue 200 ILE Chi-restraints excluded: chain d residue 50 LEU Chi-restraints excluded: chain d residue 156 THR Chi-restraints excluded: chain d residue 186 ILE Chi-restraints excluded: chain d residue 188 VAL Chi-restraints excluded: chain d residue 198 LEU Chi-restraints excluded: chain d residue 199 TYR Chi-restraints excluded: chain f residue 8 VAL Chi-restraints excluded: chain f residue 15 ASP Chi-restraints excluded: chain f residue 18 THR Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 62 VAL Chi-restraints excluded: chain f residue 68 GLU Chi-restraints excluded: chain f residue 72 VAL Chi-restraints excluded: chain f residue 93 THR Chi-restraints excluded: chain m residue 40 ASP Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain p residue 10 LEU Chi-restraints excluded: chain u residue 3 SER Chi-restraints excluded: chain u residue 12 MET Chi-restraints excluded: chain x residue 129 LYS Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 161 PHE Chi-restraints excluded: chain D residue 172 ASN Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 76 ARG Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain L residue 13 ASN Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 59 LYS Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 72 ARG Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain N residue 41 TYR Chi-restraints excluded: chain N residue 67 ASN Chi-restraints excluded: chain N residue 92 TRP Chi-restraints excluded: chain N residue 131 ILE Chi-restraints excluded: chain O residue 35 LYS Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 47 TYR Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain O residue 110 MET Chi-restraints excluded: chain O residue 116 VAL Chi-restraints excluded: chain P residue 10 ILE Chi-restraints excluded: chain P residue 99 THR Chi-restraints excluded: chain Q residue 11 SER Chi-restraints excluded: chain Q residue 14 ASP Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain Q residue 82 HIS Chi-restraints excluded: chain Q residue 88 ARG Chi-restraints excluded: chain Q residue 109 ILE Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain R residue 91 ASP Chi-restraints excluded: chain R residue 94 ASN Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain S residue 14 TYR Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain S residue 27 LEU Chi-restraints excluded: chain S residue 47 ASN Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 103 LYS Chi-restraints excluded: chain T residue 7 PHE Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 15 VAL Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 37 SER Chi-restraints excluded: chain U residue 38 ASN Chi-restraints excluded: chain U residue 84 VAL Chi-restraints excluded: chain U residue 93 ILE Chi-restraints excluded: chain V residue 5 LYS Chi-restraints excluded: chain V residue 43 LYS Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain W residue 30 ASP Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 38 TYR Chi-restraints excluded: chain W residue 52 ARG Chi-restraints excluded: chain W residue 80 THR Chi-restraints excluded: chain W residue 91 ASN Chi-restraints excluded: chain W residue 117 ASP Chi-restraints excluded: chain X residue 31 VAL Chi-restraints excluded: chain X residue 37 LEU Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 58 THR Chi-restraints excluded: chain X residue 67 VAL Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 36 VAL Chi-restraints excluded: chain Y residue 49 ILE Chi-restraints excluded: chain Y residue 61 VAL Chi-restraints excluded: chain Z residue 5 THR Chi-restraints excluded: chain Z residue 14 THR Chi-restraints excluded: chain v residue 6 ILE Chi-restraints excluded: chain v residue 22 SER Chi-restraints excluded: chain v residue 31 ILE Chi-restraints excluded: chain v residue 39 ASP Chi-restraints excluded: chain v residue 51 HIS Chi-restraints excluded: chain y residue 24 THR Chi-restraints excluded: chain y residue 27 THR Chi-restraints excluded: chain y residue 34 VAL Chi-restraints excluded: chain y residue 45 TYR Chi-restraints excluded: chain z residue 9 SER Chi-restraints excluded: chain 1 residue 12 THR Chi-restraints excluded: chain 1 residue 15 CYS Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 2 residue 36 ASN Chi-restraints excluded: chain 3 residue 44 LEU Chi-restraints excluded: chain 3 residue 50 VAL Chi-restraints excluded: chain 4 residue 19 ARG Chi-restraints excluded: chain 4 residue 20 HIS Chi-restraints excluded: chain 4 residue 24 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1102 random chunks: chunk 657 optimal weight: 20.0000 chunk 424 optimal weight: 50.0000 chunk 634 optimal weight: 5.9990 chunk 319 optimal weight: 3.9990 chunk 208 optimal weight: 10.0000 chunk 205 optimal weight: 7.9990 chunk 675 optimal weight: 0.3980 chunk 723 optimal weight: 30.0000 chunk 525 optimal weight: 5.9990 chunk 98 optimal weight: 30.0000 chunk 834 optimal weight: 20.0000 overall best weight: 4.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 111 GLN ** h 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 167 ASN ** d 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 169 GLN ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 106 GLN ** K 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 HIS ** N 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 107 ASN ** Q 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 66 GLN T 67 ASN ** U 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 26 GLN ** W 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5873 moved from start: 0.7070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 165472 Z= 0.201 Angle : 0.665 20.182 247459 Z= 0.332 Chirality : 0.035 0.389 31649 Planarity : 0.005 0.127 13589 Dihedral : 25.000 179.539 82714 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 24.34 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.77 % Favored : 93.02 % Rotamer: Outliers : 5.29 % Allowed : 31.44 % Favored : 63.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.48 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.10), residues: 6087 helix: 0.09 (0.11), residues: 2009 sheet: -1.04 (0.15), residues: 1060 loop : -1.61 (0.11), residues: 3018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP C 250 HIS 0.015 0.001 HIS e 108 PHE 0.028 0.002 PHE t 35 TYR 0.061 0.002 TYR d 71 ARG 0.021 0.001 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12174 Ramachandran restraints generated. 6087 Oldfield, 0 Emsley, 6087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12174 Ramachandran restraints generated. 6087 Oldfield, 0 Emsley, 6087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1561 residues out of total 5058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 1295 time to evaluate : 8.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 1 MET cc_start: 0.1300 (ptt) cc_final: 0.0778 (ptt) REVERT: o 34 LYS cc_start: 0.4408 (pttm) cc_final: 0.4198 (ptpp) REVERT: q 77 MET cc_start: 0.6615 (ppp) cc_final: 0.6355 (ppp) REVERT: n 24 CYS cc_start: 0.5363 (OUTLIER) cc_final: 0.4702 (p) REVERT: m 75 GLN cc_start: 0.7813 (tm-30) cc_final: 0.7561 (tm-30) REVERT: u 19 LYS cc_start: 0.7120 (mttt) cc_final: 0.6891 (mmtt) REVERT: G 82 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7720 (mp0) REVERT: G 169 GLN cc_start: 0.7330 (mm110) cc_final: 0.7094 (mp10) REVERT: J 109 GLU cc_start: 0.7979 (tp30) cc_final: 0.7613 (tp30) REVERT: J 137 MET cc_start: 0.7710 (mmt) cc_final: 0.6448 (mmt) REVERT: M 72 ARG cc_start: 0.6368 (OUTLIER) cc_final: 0.4128 (tpt90) REVERT: N 41 TYR cc_start: 0.4397 (OUTLIER) cc_final: 0.4125 (p90) REVERT: R 73 ASP cc_start: 0.6674 (t0) cc_final: 0.6460 (t0) REVERT: S 27 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7399 (tp) REVERT: Y 60 LYS cc_start: 0.7950 (mmtm) cc_final: 0.7662 (mmtt) REVERT: z 8 MET cc_start: 0.5948 (tmm) cc_final: 0.5726 (tmm) REVERT: 4 1 MET cc_start: 0.4057 (tpp) cc_final: 0.3786 (tpt) outliers start: 266 outliers final: 223 residues processed: 1437 average time/residue: 1.3650 time to fit residues: 3351.0768 Evaluate side-chains 1432 residues out of total 5058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 1205 time to evaluate : 6.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 101 ASN Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain e residue 63 ILE Chi-restraints excluded: chain e residue 101 LEU Chi-restraints excluded: chain e residue 140 LEU Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 62 LEU Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 85 TYR Chi-restraints excluded: chain h residue 19 SER Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain h residue 126 GLU Chi-restraints excluded: chain i residue 42 VAL Chi-restraints excluded: chain i residue 47 GLN Chi-restraints excluded: chain i residue 56 GLU Chi-restraints excluded: chain i residue 61 ASN Chi-restraints excluded: chain i residue 79 ASP Chi-restraints excluded: chain i residue 84 TYR Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 9 ARG Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 15 HIS Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain k residue 59 VAL Chi-restraints excluded: chain k residue 92 ASP Chi-restraints excluded: chain k residue 95 VAL Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 10 LYS Chi-restraints excluded: chain l residue 21 THR Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 89 ASP Chi-restraints excluded: chain l residue 97 ILE Chi-restraints excluded: chain o residue 49 ASP Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain q residue 43 ARG Chi-restraints excluded: chain q residue 53 ILE Chi-restraints excluded: chain q residue 72 ASP Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain r residue 35 THR Chi-restraints excluded: chain s residue 16 LEU Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 47 HIS Chi-restraints excluded: chain s residue 55 ARG Chi-restraints excluded: chain s residue 73 GLU Chi-restraints excluded: chain t residue 15 GLU Chi-restraints excluded: chain t residue 81 LEU Chi-restraints excluded: chain n residue 11 ASN Chi-restraints excluded: chain n residue 24 CYS Chi-restraints excluded: chain n residue 59 SER Chi-restraints excluded: chain b residue 42 ASP Chi-restraints excluded: chain b residue 51 ASP Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 93 ASN Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain b residue 133 GLU Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain b residue 196 VAL Chi-restraints excluded: chain b residue 200 ILE Chi-restraints excluded: chain d residue 50 LEU Chi-restraints excluded: chain d residue 156 THR Chi-restraints excluded: chain d residue 186 ILE Chi-restraints excluded: chain d residue 188 VAL Chi-restraints excluded: chain d residue 198 LEU Chi-restraints excluded: chain f residue 8 VAL Chi-restraints excluded: chain f residue 15 ASP Chi-restraints excluded: chain f residue 18 THR Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 62 VAL Chi-restraints excluded: chain f residue 68 GLU Chi-restraints excluded: chain f residue 72 VAL Chi-restraints excluded: chain f residue 74 GLU Chi-restraints excluded: chain f residue 93 THR Chi-restraints excluded: chain m residue 4 LEU Chi-restraints excluded: chain m residue 40 ASP Chi-restraints excluded: chain m residue 50 ASP Chi-restraints excluded: chain p residue 10 LEU Chi-restraints excluded: chain p residue 95 VAL Chi-restraints excluded: chain u residue 3 SER Chi-restraints excluded: chain u residue 12 MET Chi-restraints excluded: chain x residue 129 LYS Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 172 ASN Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 76 ARG Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain L residue 13 ASN Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 72 ARG Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain N residue 25 THR Chi-restraints excluded: chain N residue 41 TYR Chi-restraints excluded: chain N residue 67 ASN Chi-restraints excluded: chain N residue 92 TRP Chi-restraints excluded: chain N residue 131 ILE Chi-restraints excluded: chain O residue 31 HIS Chi-restraints excluded: chain O residue 35 LYS Chi-restraints excluded: chain O residue 47 TYR Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain O residue 116 VAL Chi-restraints excluded: chain P residue 10 ILE Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 99 THR Chi-restraints excluded: chain Q residue 11 SER Chi-restraints excluded: chain Q residue 14 ASP Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain Q residue 82 HIS Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain R residue 94 ASN Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain S residue 14 TYR Chi-restraints excluded: chain S residue 27 LEU Chi-restraints excluded: chain S residue 47 ASN Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 103 LYS Chi-restraints excluded: chain T residue 7 PHE Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 31 VAL Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain T residue 78 VAL Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 15 VAL Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 37 SER Chi-restraints excluded: chain U residue 38 ASN Chi-restraints excluded: chain U residue 61 ASN Chi-restraints excluded: chain U residue 84 VAL Chi-restraints excluded: chain V residue 5 LYS Chi-restraints excluded: chain V residue 43 LYS Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain W residue 30 ASP Chi-restraints excluded: chain W residue 50 ASN Chi-restraints excluded: chain W residue 80 THR Chi-restraints excluded: chain W residue 91 ASN Chi-restraints excluded: chain W residue 117 ASP Chi-restraints excluded: chain X residue 37 LEU Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 67 VAL Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Y residue 36 VAL Chi-restraints excluded: chain Y residue 61 VAL Chi-restraints excluded: chain Z residue 5 THR Chi-restraints excluded: chain Z residue 14 THR Chi-restraints excluded: chain v residue 6 ILE Chi-restraints excluded: chain v residue 39 ASP Chi-restraints excluded: chain v residue 50 VAL Chi-restraints excluded: chain y residue 24 THR Chi-restraints excluded: chain y residue 34 VAL Chi-restraints excluded: chain y residue 45 TYR Chi-restraints excluded: chain y residue 61 PHE Chi-restraints excluded: chain 1 residue 12 THR Chi-restraints excluded: chain 1 residue 15 CYS Chi-restraints excluded: chain 2 residue 23 LEU Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 3 residue 44 LEU Chi-restraints excluded: chain 3 residue 50 VAL Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain 4 residue 4 ASN Chi-restraints excluded: chain 4 residue 19 ARG Chi-restraints excluded: chain 4 residue 20 HIS Chi-restraints excluded: chain 4 residue 23 VAL Chi-restraints excluded: chain 4 residue 24 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1102 random chunks: chunk 966 optimal weight: 20.0000 chunk 1017 optimal weight: 20.0000 chunk 928 optimal weight: 20.0000 chunk 989 optimal weight: 20.0000 chunk 595 optimal weight: 9.9990 chunk 431 optimal weight: 9.9990 chunk 777 optimal weight: 30.0000 chunk 303 optimal weight: 7.9990 chunk 894 optimal weight: 20.0000 chunk 936 optimal weight: 20.0000 chunk 986 optimal weight: 20.0000 overall best weight: 13.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 138 GLN ** e 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 49 ASN ** i 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 56 ASN ** s 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 84 ASN ** b 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 185 GLN ** f 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 17 GLN p 41 HIS ** x 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 84 GLN C 38 HIS C 53 HIS ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN E 151 ASN ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 147 GLN ** N 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 107 ASN ** Q 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 67 ASN ** U 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 26 GLN ** W 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6086 moved from start: 0.7929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 165472 Z= 0.424 Angle : 0.839 20.772 247459 Z= 0.417 Chirality : 0.042 0.371 31649 Planarity : 0.007 0.125 13589 Dihedral : 25.358 179.540 82714 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 41.20 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.54 % Favored : 91.23 % Rotamer: Outliers : 6.46 % Allowed : 31.00 % Favored : 62.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.48 % Twisted General : 0.05 % 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: -1.76 (0.10), residues: 6087 helix: -0.29 (0.11), residues: 1998 sheet: -1.24 (0.15), residues: 1095 loop : -1.73 (0.11), residues: 2994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP N 92 HIS 0.013 0.002 HIS e 108 PHE 0.039 0.003 PHE Q 73 TYR 0.047 0.003 TYR K 80 ARG 0.026 0.001 ARG L 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12174 Ramachandran restraints generated. 6087 Oldfield, 0 Emsley, 6087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12174 Ramachandran restraints generated. 6087 Oldfield, 0 Emsley, 6087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1532 residues out of total 5058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 325 poor density : 1207 time to evaluate : 6.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 154 TYR cc_start: 0.7306 (m-80) cc_final: 0.7078 (m-10) REVERT: q 37 VAL cc_start: 0.7216 (t) cc_final: 0.6990 (t) REVERT: q 43 ARG cc_start: 0.5331 (OUTLIER) cc_final: 0.4463 (mtm180) REVERT: s 32 LYS cc_start: 0.2260 (tptt) cc_final: 0.1533 (tptt) REVERT: n 24 CYS cc_start: 0.5405 (OUTLIER) cc_final: 0.4671 (p) REVERT: n 26 LYS cc_start: 0.7095 (OUTLIER) cc_final: 0.6861 (tppt) REVERT: b 152 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7843 (tpp80) REVERT: m 75 GLN cc_start: 0.7939 (tm-30) cc_final: 0.7586 (tm-30) REVERT: F 144 MET cc_start: 0.4184 (mmm) cc_final: 0.3945 (mmp) REVERT: J 137 MET cc_start: 0.7756 (mmt) cc_final: 0.6399 (mmt) REVERT: K 147 GLN cc_start: 0.2913 (OUTLIER) cc_final: 0.2121 (tm-30) REVERT: M 72 ARG cc_start: 0.6645 (OUTLIER) cc_final: 0.4406 (tpt90) REVERT: U 61 ASN cc_start: 0.6800 (OUTLIER) cc_final: 0.6506 (p0) REVERT: W 52 ARG cc_start: 0.3171 (OUTLIER) cc_final: 0.1136 (ptp90) REVERT: z 8 MET cc_start: 0.6347 (tmm) cc_final: 0.6034 (tmm) outliers start: 325 outliers final: 259 residues processed: 1376 average time/residue: 1.5016 time to fit residues: 3569.2285 Evaluate side-chains 1412 residues out of total 5058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 1145 time to evaluate : 6.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 101 ASN Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain c residue 207 ILE Chi-restraints excluded: chain e residue 63 ILE Chi-restraints excluded: chain e residue 101 LEU Chi-restraints excluded: chain e residue 140 LEU Chi-restraints excluded: chain g residue 62 LEU Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 85 TYR Chi-restraints excluded: chain h residue 19 SER Chi-restraints excluded: chain h residue 38 GLU Chi-restraints excluded: chain h residue 65 LYS Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain h residue 126 GLU Chi-restraints excluded: chain i residue 42 VAL Chi-restraints excluded: chain i residue 56 GLU Chi-restraints excluded: chain i residue 61 ASN Chi-restraints excluded: chain i residue 79 ASP Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 9 ARG Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 11 LYS Chi-restraints excluded: chain j residue 15 HIS Chi-restraints excluded: chain j residue 29 VAL Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain k residue 59 VAL Chi-restraints excluded: chain k residue 74 LEU Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 10 LYS Chi-restraints excluded: chain l residue 21 THR Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 89 ASP Chi-restraints excluded: chain l residue 97 ILE Chi-restraints excluded: chain o residue 49 ASP Chi-restraints excluded: chain q residue 24 ILE Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain q residue 43 ARG Chi-restraints excluded: chain q residue 53 ILE Chi-restraints excluded: chain q residue 63 ASP Chi-restraints excluded: chain q residue 72 ASP Chi-restraints excluded: chain q residue 74 VAL Chi-restraints excluded: chain q residue 79 THR Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain r residue 35 THR Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain s residue 47 HIS Chi-restraints excluded: chain s residue 55 ARG Chi-restraints excluded: chain s residue 73 GLU Chi-restraints excluded: chain t residue 15 GLU Chi-restraints excluded: chain t residue 81 LEU Chi-restraints excluded: chain n residue 11 ASN Chi-restraints excluded: chain n residue 24 CYS Chi-restraints excluded: chain n residue 25 ASN Chi-restraints excluded: chain n residue 26 LYS Chi-restraints excluded: chain n residue 42 ILE Chi-restraints excluded: chain n residue 59 SER Chi-restraints excluded: chain b residue 42 ASP Chi-restraints excluded: chain b residue 51 ASP Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 74 LYS Chi-restraints excluded: chain b residue 93 ASN Chi-restraints excluded: chain b residue 100 MET Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain b residue 133 GLU Chi-restraints excluded: chain b residue 152 ARG Chi-restraints excluded: chain b residue 153 ASP Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain b residue 196 VAL Chi-restraints excluded: chain b residue 200 ILE Chi-restraints excluded: chain d residue 50 LEU Chi-restraints excluded: chain d residue 94 ASP Chi-restraints excluded: chain d residue 136 ASP Chi-restraints excluded: chain d residue 186 ILE Chi-restraints excluded: chain d residue 188 VAL Chi-restraints excluded: chain d residue 198 LEU Chi-restraints excluded: chain f residue 15 ASP Chi-restraints excluded: chain f residue 18 THR Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 62 VAL Chi-restraints excluded: chain f residue 68 GLU Chi-restraints excluded: chain f residue 72 VAL Chi-restraints excluded: chain f residue 78 GLN Chi-restraints excluded: chain f residue 93 THR Chi-restraints excluded: chain m residue 4 LEU Chi-restraints excluded: chain m residue 40 ASP Chi-restraints excluded: chain p residue 10 LEU Chi-restraints excluded: chain p residue 13 ILE Chi-restraints excluded: chain p residue 20 ILE Chi-restraints excluded: chain p residue 39 ARG Chi-restraints excluded: chain p residue 95 VAL Chi-restraints excluded: chain u residue 3 SER Chi-restraints excluded: chain u residue 12 MET Chi-restraints excluded: chain x residue 129 LYS Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 172 ASN Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 201 ARG Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 55 LYS Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 147 GLN Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 13 ASN Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 72 ARG Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 67 ASN Chi-restraints excluded: chain N residue 92 TRP Chi-restraints excluded: chain N residue 116 ASP Chi-restraints excluded: chain N residue 131 ILE Chi-restraints excluded: chain O residue 27 SER Chi-restraints excluded: chain O residue 31 HIS Chi-restraints excluded: chain O residue 35 LYS Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 47 TYR Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain O residue 116 VAL Chi-restraints excluded: chain P residue 10 ILE Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 99 THR Chi-restraints excluded: chain Q residue 14 ASP Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain Q residue 82 HIS Chi-restraints excluded: chain Q residue 86 LEU Chi-restraints excluded: chain Q residue 109 ILE Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain R residue 91 ASP Chi-restraints excluded: chain R residue 94 ASN Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain S residue 14 TYR Chi-restraints excluded: chain S residue 27 LEU Chi-restraints excluded: chain S residue 47 ASN Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 103 LYS Chi-restraints excluded: chain T residue 7 PHE Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 31 VAL Chi-restraints excluded: chain T residue 38 GLU Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 15 VAL Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 37 SER Chi-restraints excluded: chain U residue 38 ASN Chi-restraints excluded: chain U residue 61 ASN Chi-restraints excluded: chain U residue 84 VAL Chi-restraints excluded: chain U residue 95 LEU Chi-restraints excluded: chain V residue 5 LYS Chi-restraints excluded: chain V residue 36 GLU Chi-restraints excluded: chain V residue 43 LYS Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain W residue 30 ASP Chi-restraints excluded: chain W residue 50 ASN Chi-restraints excluded: chain W residue 52 ARG Chi-restraints excluded: chain W residue 80 THR Chi-restraints excluded: chain W residue 89 ARG Chi-restraints excluded: chain W residue 91 ASN Chi-restraints excluded: chain W residue 96 ASP Chi-restraints excluded: chain W residue 117 ASP Chi-restraints excluded: chain W residue 124 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 37 LEU Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 50 ASN Chi-restraints excluded: chain X residue 67 VAL Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 30 ASN Chi-restraints excluded: chain Y residue 36 VAL Chi-restraints excluded: chain Y residue 49 ILE Chi-restraints excluded: chain Y residue 61 VAL Chi-restraints excluded: chain Z residue 5 THR Chi-restraints excluded: chain Z residue 14 THR Chi-restraints excluded: chain Z residue 29 LEU Chi-restraints excluded: chain v residue 6 ILE Chi-restraints excluded: chain v residue 31 ILE Chi-restraints excluded: chain v residue 39 ASP Chi-restraints excluded: chain v residue 50 VAL Chi-restraints excluded: chain v residue 51 HIS Chi-restraints excluded: chain v residue 53 LEU Chi-restraints excluded: chain y residue 24 THR Chi-restraints excluded: chain y residue 34 VAL Chi-restraints excluded: chain y residue 45 TYR Chi-restraints excluded: chain z residue 38 LYS Chi-restraints excluded: chain 1 residue 12 THR Chi-restraints excluded: chain 1 residue 15 CYS Chi-restraints excluded: chain 1 residue 24 ILE Chi-restraints excluded: chain 1 residue 44 ASN Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 2 residue 36 ASN Chi-restraints excluded: chain 2 residue 46 THR Chi-restraints excluded: chain 3 residue 44 LEU Chi-restraints excluded: chain 3 residue 50 VAL Chi-restraints excluded: chain 4 residue 4 ASN Chi-restraints excluded: chain 4 residue 15 ARG Chi-restraints excluded: chain 4 residue 19 ARG Chi-restraints excluded: chain 4 residue 20 HIS Chi-restraints excluded: chain 4 residue 23 VAL Chi-restraints excluded: chain 4 residue 24 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1102 random chunks: chunk 649 optimal weight: 3.9990 chunk 1046 optimal weight: 10.0000 chunk 638 optimal weight: 20.0000 chunk 496 optimal weight: 4.9990 chunk 727 optimal weight: 7.9990 chunk 1097 optimal weight: 20.0000 chunk 1010 optimal weight: 10.0000 chunk 874 optimal weight: 20.0000 chunk 90 optimal weight: 30.0000 chunk 675 optimal weight: 0.2980 chunk 536 optimal weight: 6.9990 overall best weight: 4.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 111 GLN ** h 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 56 ASN ** t 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 107 ASN ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN ** E 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 169 GLN ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 GLN ** O 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 HIS O 107 ASN ** P 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 67 ASN ** U 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 26 GLN ** W 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 156 GLN ** X 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5940 moved from start: 0.7887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 165472 Z= 0.208 Angle : 0.704 20.371 247459 Z= 0.351 Chirality : 0.036 0.400 31649 Planarity : 0.005 0.123 13589 Dihedral : 25.217 179.699 82710 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 26.70 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.06 % Favored : 92.74 % Rotamer: Outliers : 4.41 % Allowed : 34.02 % Favored : 61.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.48 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.10), residues: 6087 helix: -0.14 (0.11), residues: 2010 sheet: -0.98 (0.16), residues: 1053 loop : -1.67 (0.11), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP N 92 HIS 0.012 0.001 HIS j 64 PHE 0.038 0.003 PHE U 50 TYR 0.042 0.003 TYR d 199 ARG 0.017 0.001 ARG l 36 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12174 Ramachandran restraints generated. 6087 Oldfield, 0 Emsley, 6087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12174 Ramachandran restraints generated. 6087 Oldfield, 0 Emsley, 6087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1463 residues out of total 5058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 1241 time to evaluate : 6.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: s 32 LYS cc_start: 0.2227 (tptt) cc_final: 0.1681 (tptt) REVERT: n 24 CYS cc_start: 0.5405 (OUTLIER) cc_final: 0.4501 (p) REVERT: b 27 MET cc_start: 0.5931 (OUTLIER) cc_final: 0.5605 (mtp) REVERT: b 198 TYR cc_start: 0.8617 (m-80) cc_final: 0.8066 (m-80) REVERT: f 95 LYS cc_start: 0.6042 (tttt) cc_final: 0.5182 (mttt) REVERT: u 23 ARG cc_start: 0.7654 (ttp80) cc_final: 0.7062 (ptt-90) REVERT: G 168 GLU cc_start: 0.5915 (pt0) cc_final: 0.5261 (pt0) REVERT: J 137 MET cc_start: 0.7600 (mmt) cc_final: 0.6874 (mmm) REVERT: M 15 GLU cc_start: 0.6245 (mm-30) cc_final: 0.6012 (mm-30) REVERT: M 72 ARG cc_start: 0.6370 (OUTLIER) cc_final: 0.4080 (tpt90) REVERT: R 73 ASP cc_start: 0.6662 (t0) cc_final: 0.6427 (t0) REVERT: S 27 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7508 (tt) outliers start: 222 outliers final: 190 residues processed: 1363 average time/residue: 1.3789 time to fit residues: 3220.9811 Evaluate side-chains 1379 residues out of total 5058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 1185 time to evaluate : 6.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 101 ASN Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain c residue 207 ILE Chi-restraints excluded: chain e residue 63 ILE Chi-restraints excluded: chain e residue 111 GLN Chi-restraints excluded: chain e residue 140 LEU Chi-restraints excluded: chain g residue 62 LEU Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 85 TYR Chi-restraints excluded: chain h residue 4 THR Chi-restraints excluded: chain h residue 19 SER Chi-restraints excluded: chain h residue 126 GLU Chi-restraints excluded: chain i residue 42 VAL Chi-restraints excluded: chain i residue 56 GLU Chi-restraints excluded: chain i residue 61 ASN Chi-restraints excluded: chain i residue 79 ASP Chi-restraints excluded: chain i residue 84 TYR Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 9 ARG Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 11 LYS Chi-restraints excluded: chain j residue 15 HIS Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain k residue 59 VAL Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 89 ASP Chi-restraints excluded: chain l residue 97 ILE Chi-restraints excluded: chain o residue 36 ILE Chi-restraints excluded: chain o residue 49 ASP Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain q residue 43 ARG Chi-restraints excluded: chain q residue 53 ILE Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 74 VAL Chi-restraints excluded: chain q residue 94 LEU Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain s residue 47 HIS Chi-restraints excluded: chain s residue 55 ARG Chi-restraints excluded: chain s residue 73 GLU Chi-restraints excluded: chain t residue 15 GLU Chi-restraints excluded: chain t residue 66 VAL Chi-restraints excluded: chain t residue 81 LEU Chi-restraints excluded: chain n residue 11 ASN Chi-restraints excluded: chain n residue 24 CYS Chi-restraints excluded: chain n residue 25 ASN Chi-restraints excluded: chain b residue 27 MET Chi-restraints excluded: chain b residue 42 ASP Chi-restraints excluded: chain b residue 51 ASP Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 93 ASN Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain b residue 153 ASP Chi-restraints excluded: chain b residue 183 VAL Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain b residue 196 VAL Chi-restraints excluded: chain b residue 200 ILE Chi-restraints excluded: chain d residue 50 LEU Chi-restraints excluded: chain d residue 186 ILE Chi-restraints excluded: chain d residue 188 VAL Chi-restraints excluded: chain f residue 15 ASP Chi-restraints excluded: chain f residue 18 THR Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 62 VAL Chi-restraints excluded: chain f residue 68 GLU Chi-restraints excluded: chain f residue 72 VAL Chi-restraints excluded: chain f residue 93 THR Chi-restraints excluded: chain m residue 40 ASP Chi-restraints excluded: chain p residue 10 LEU Chi-restraints excluded: chain p residue 95 VAL Chi-restraints excluded: chain u residue 3 SER Chi-restraints excluded: chain u residue 12 MET Chi-restraints excluded: chain x residue 129 LYS Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 172 ASN Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain L residue 13 ASN Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 72 ARG Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain N residue 67 ASN Chi-restraints excluded: chain N residue 131 ILE Chi-restraints excluded: chain O residue 35 LYS Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 47 TYR Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain O residue 113 ILE Chi-restraints excluded: chain O residue 116 VAL Chi-restraints excluded: chain P residue 10 ILE Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 99 THR Chi-restraints excluded: chain Q residue 14 ASP Chi-restraints excluded: chain Q residue 77 SER Chi-restraints excluded: chain Q residue 86 LEU Chi-restraints excluded: chain Q residue 109 ILE Chi-restraints excluded: chain R residue 36 LYS Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 90 VAL Chi-restraints excluded: chain R residue 91 ASP Chi-restraints excluded: chain R residue 94 ASN Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain S residue 14 TYR Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain S residue 27 LEU Chi-restraints excluded: chain S residue 47 ASN Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 103 LYS Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 31 VAL Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 15 VAL Chi-restraints excluded: chain U residue 26 ASP Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 37 SER Chi-restraints excluded: chain U residue 38 ASN Chi-restraints excluded: chain U residue 49 ILE Chi-restraints excluded: chain U residue 61 ASN Chi-restraints excluded: chain U residue 84 VAL Chi-restraints excluded: chain V residue 5 LYS Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain W residue 30 ASP Chi-restraints excluded: chain W residue 50 ASN Chi-restraints excluded: chain W residue 80 THR Chi-restraints excluded: chain W residue 91 ASN Chi-restraints excluded: chain W residue 117 ASP Chi-restraints excluded: chain W residue 124 VAL Chi-restraints excluded: chain X residue 37 LEU Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 67 VAL Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Y residue 36 VAL Chi-restraints excluded: chain Z residue 5 THR Chi-restraints excluded: chain Z residue 14 THR Chi-restraints excluded: chain Z residue 29 LEU Chi-restraints excluded: chain v residue 6 ILE Chi-restraints excluded: chain v residue 39 ASP Chi-restraints excluded: chain v residue 50 VAL Chi-restraints excluded: chain y residue 24 THR Chi-restraints excluded: chain y residue 34 VAL Chi-restraints excluded: chain y residue 45 TYR Chi-restraints excluded: chain 1 residue 12 THR Chi-restraints excluded: chain 1 residue 15 CYS Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 2 residue 46 THR Chi-restraints excluded: chain 3 residue 44 LEU Chi-restraints excluded: chain 3 residue 50 VAL Chi-restraints excluded: chain 4 residue 19 ARG Chi-restraints excluded: chain 4 residue 23 VAL Chi-restraints excluded: chain 4 residue 24 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1102 random chunks: chunk 694 optimal weight: 8.9990 chunk 931 optimal weight: 20.0000 chunk 267 optimal weight: 20.0000 chunk 806 optimal weight: 20.0000 chunk 129 optimal weight: 30.0000 chunk 242 optimal weight: 8.9990 chunk 875 optimal weight: 20.0000 chunk 366 optimal weight: 0.8980 chunk 899 optimal weight: 20.0000 chunk 110 optimal weight: 30.0000 chunk 161 optimal weight: 9.9990 overall best weight: 9.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 64 HIS ** k 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 26 GLN ** W 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.053286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.042168 restraints weight = 1093420.128| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 3.93 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.7902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.338 165472 Z= 0.361 Angle : 0.756 59.183 247459 Z= 0.378 Chirality : 0.038 0.763 31649 Planarity : 0.006 0.226 13589 Dihedral : 25.207 179.661 82708 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 28.60 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.33 % Favored : 92.49 % Rotamer: Outliers : 4.65 % Allowed : 33.82 % Favored : 61.53 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.48 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.10), residues: 6087 helix: -0.15 (0.11), residues: 2012 sheet: -0.94 (0.15), residues: 1077 loop : -1.67 (0.11), residues: 2998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP N 92 HIS 0.074 0.002 HIS g 153 PHE 0.038 0.003 PHE U 50 TYR 0.090 0.004 TYR E 66 ARG 0.091 0.001 ARG E 73 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 49624.36 seconds wall clock time: 864 minutes 29.52 seconds (51869.52 seconds total)