Starting phenix.real_space_refine on Tue Mar 26 22:46:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zeb_6920/03_2024/5zeb_6920.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zeb_6920/03_2024/5zeb_6920.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/5zeb_6920/03_2024/5zeb_6920.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zeb_6920/03_2024/5zeb_6920.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zeb_6920/03_2024/5zeb_6920.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zeb_6920/03_2024/5zeb_6920.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= 0.002 sd= 0.018 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 107 5.16 5 C 75386 2.51 5 N 28100 2.21 5 O 41933 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 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 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 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 "m ARG 72": "NH1" <-> "NH2" Residue "m GLU 73": "OE1" <-> "OE2" 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 ASP 90": "OD1" <-> "OD2" Residue "L ASP 92": "OD1" <-> "OD2" 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 "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 "1 ARG 16": "NH1" <-> "NH2" Residue "1 ARG 20": "NH1" <-> "NH2" Residue "1 ARG 37": "NH1" <-> "NH2" Residue "1 ARG 44": "NH1" <-> "NH2" Residue "2 TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 62": "OE1" <-> "OE2" Residue "4 ARG 8": "NH1" <-> "NH2" Residue "4 ARG 21": "NH1" <-> "NH2" Residue "4 ARG 29": "NH1" <-> "NH2" Residue "4 ARG 30": "NH1" <-> "NH2" Residue "4 ARG 35": "NH1" <-> "NH2" Residue "4 GLU 53": "OE1" <-> "OE2" Residue "5 ARG 15": "NH1" <-> "NH2" Residue "5 ARG 24": "NH1" <-> "NH2" Residue "5 ARG 37": "NH1" <-> "NH2" Residue "5 ARG 43": "NH1" <-> "NH2" Residue "6 ARG 13": "NH1" <-> "NH2" Residue "6 ARG 15": "NH1" <-> "NH2" Residue "6 ARG 16": "NH1" <-> "NH2" Residue "6 ARG 24": "NH1" <-> "NH2" Residue "6 ARG 40": "NH1" <-> "NH2" Residue "6 ARG 42": "NH1" <-> "NH2" Residue "6 ARG 43": "NH1" <-> "NH2" Residue "6 ARG 47": "NH1" <-> "NH2" Residue "6 ARG 57": "NH1" <-> "NH2" Residue "7 ARG 15": "NH1" <-> "NH2" Residue "7 ARG 18": "NH1" <-> "NH2" Residue "7 ARG 22": "NH1" <-> "NH2" Residue "7 ARG 31": "NH1" <-> "NH2" Residue "7 ARG 35": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 150328 Number of models: 1 Model: "" Number of chains: 56 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: "v" 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': 3, 'rna3p_pur': 34, 'rna3p_pyr': 35} Link IDs: {'rna2p': 7, 'rna3p': 69} 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: "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: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1407 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 9, 'TRANS': 178} 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: "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': 299, 'rna2p_pyr': 149, 'rna3p_pur': 1477, 'rna3p_pyr': 1177} Link IDs: {'rna2p': 448, 'rna3p': 2653} Chain breaks: 5 Chain: "1" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 483 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "2" 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: "3" 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: "4" 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: "5" 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: "6" 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: "7" 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: "8" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 189 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Time building chain proxies: 56.64, per 1000 atoms: 0.38 Number of scatterers: 150328 At special positions: 0 Unit cell: (275.1, 258.3, 255.15, 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 107 16.00 P 4802 15.00 O 41933 8.00 N 28100 7.00 C 75386 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 2 16 " - pdb=" SG CYS 2 38 " distance=2.29 Simple disulfide: pdb=" SG CYS 4 18 " - pdb=" SG CYS 4 45 " distance=2.65 Simple disulfide: pdb=" SG CYS 7 11 " - pdb=" SG CYS 7 14 " distance=2.02 Simple disulfide: pdb=" SG CYS 7 14 " - pdb=" SG CYS 7 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 78957 O4' G B 45 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 59.83 Conformation dependent library (CDL) restraints added in 7.3 seconds 11978 Ramachandran restraints generated. 5989 Oldfield, 0 Emsley, 5989 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11112 Finding SS restraints... Secondary structure from input PDB file: 186 helices and 75 sheets defined 34.9% alpha, 18.0% beta 1571 base pairs and 2591 stacking pairs defined. Time for finding SS restraints: 54.18 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: 3.868A pdb=" N ILE c 86 " --> pdb=" O GLU c 82 " (cutoff:3.500A) Processing helix chain 'c' and resid 107 through 110 removed outlier: 3.700A pdb=" N SER c 110 " --> pdb=" O ASN c 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 107 through 110' Processing helix chain 'c' and resid 111 through 124 Processing helix chain 'c' and resid 128 through 140 removed outlier: 4.099A pdb=" N SER c 139 " --> pdb=" O LYS c 135 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA c 140 " --> pdb=" O ALA c 136 " (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: 3.604A pdb=" N ALA e 214 " --> pdb=" O ARG e 210 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 removed outlier: 3.744A 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: 3.606A pdb=" N LYS g 136 " --> pdb=" O GLY g 132 " (cutoff:3.500A) Processing helix chain 'g' and resid 149 through 155 removed outlier: 3.740A 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: 3.575A pdb=" N LYS i 69 " --> pdb=" O GLN i 65 " (cutoff:3.500A) Proline residue: i 71 - end of helix removed outlier: 3.614A 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: 3.572A pdb=" N LEU j 87 " --> pdb=" O THR j 83 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N MET j 88 " --> pdb=" O VAL j 84 " (cutoff:3.500A) removed outlier: 3.812A 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: 3.698A 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: 3.588A 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: 3.828A pdb=" N VAL s 67 " --> pdb=" O GLU s 64 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 75 removed outlier: 3.622A 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: 4.213A 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: 3.730A 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 64 removed outlier: 3.776A 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: 3.514A 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: 3.671A pdb=" N VAL b 195 " --> pdb=" O ASP b 192 " (cutoff:3.500A) Processing helix chain 'b' and resid 206 through 228 removed outlier: 4.130A pdb=" N ALA b 227 " --> pdb=" O GLU b 223 " (cutoff:3.500A) removed outlier: 3.701A 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: 3.885A pdb=" N GLN d 48 " --> pdb=" O SER d 44 " (cutoff:3.500A) removed outlier: 3.936A 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: 3.818A 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: 4.558A 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: 3.689A 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: 4.502A 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: 4.665A 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: 4.261A 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: 3.784A 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 removed outlier: 3.621A pdb=" N GLU m 73 " --> pdb=" O ASP m 69 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ALA m 76 " --> pdb=" O ARG m 72 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP m 77 " --> pdb=" O GLU m 73 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG m 79 " --> pdb=" O GLN m 75 " (cutoff:3.500A) Processing helix chain 'm' and resid 86 through 95 Processing helix chain 'm' and resid 107 through 112 removed outlier: 3.777A 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: 4.686A 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 'C' and resid 210 through 215 removed outlier: 3.903A pdb=" N LYS C 215 " --> pdb=" O ARG C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 226 removed outlier: 3.634A 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: 3.711A 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: 3.955A 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: 3.889A 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: 4.162A 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: 4.226A 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: 3.767A 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: 3.806A 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: 3.921A 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: 3.942A 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: 3.944A 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: 4.228A 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: 3.613A 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: 3.911A 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 84 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: 4.837A pdb=" N ALA Q 10 " --> pdb=" O PHE Q 6 " (cutoff:3.500A) removed outlier: 4.007A 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: 3.720A 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: 4.107A 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: 4.339A pdb=" N LYS R 54 " --> pdb=" O ARG R 50 " (cutoff:3.500A) removed outlier: 4.597A 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: 4.093A pdb=" N VAL T 27 " --> pdb=" O LYS T 23 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU T 30 " --> pdb=" O ARG T 26 " (cutoff:3.500A) removed outlier: 4.049A 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: 3.857A 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: 3.630A 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 '1' and resid 16 through 27 Processing helix chain '1' and resid 41 through 50 Processing helix chain '2' and resid 42 through 54 removed outlier: 3.523A pdb=" N LYS 2 48 " --> pdb=" O PHE 2 44 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER 2 54 " --> pdb=" O LYS 2 50 " (cutoff:3.500A) Processing helix chain '2' and resid 56 through 65 Processing helix chain '3' and resid 9 through 18 Processing helix chain '3' and resid 43 through 49 Processing helix chain '5' and resid 12 through 20 Processing helix chain '5' and resid 20 through 25 Processing helix chain '5' and resid 27 through 40 Processing helix chain '6' and resid 7 through 14 Processing helix chain '6' and resid 37 through 44 Processing helix chain '6' and resid 51 through 63 removed outlier: 4.118A pdb=" N LYS 6 60 " --> pdb=" O SER 6 56 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU 6 61 " --> pdb=" O ARG 6 57 " (cutoff:3.500A) Processing helix chain '8' and resid 3 through 11 Processing helix chain '8' and resid 12 through 14 No H-bonds generated for 'chain '8' 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: 6.868A 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: 6.810A 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: 6.145A pdb=" N SER e 57 " --> pdb=" O ARG e 45 " (cutoff:3.500A) removed outlier: 4.497A 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: 4.531A 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: 3.762A 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 75 Processing sheet with id=AA6, first strand: chain 'h' and resid 24 through 28 removed outlier: 3.741A 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 Processing sheet with id=AA9, first strand: chain 'j' and resid 97 through 101 removed outlier: 4.121A 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: 5.896A 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: 3.590A 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: 7.140A pdb=" N HIS s 52 " --> pdb=" O ILE s 31 " (cutoff:3.500A) removed outlier: 7.777A 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: 6.775A 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: 8.022A 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: 5.741A pdb=" N LEU b 68 " --> pdb=" O TRP b 162 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL b 183 " --> pdb=" O TYR b 198 " (cutoff:3.500A) removed outlier: 7.181A 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: 5.834A pdb=" N TYR f 60 " --> pdb=" O GLY f 44 " (cutoff:3.500A) removed outlier: 4.687A 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: 6.682A 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: 7.082A 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 'C' and resid 4 through 5 Processing sheet with id=AC7, first strand: chain 'C' and resid 36 through 37 removed outlier: 4.170A pdb=" N LEU C 37 " --> pdb=" O ARG C 60 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ARG C 60 " --> pdb=" O LEU C 37 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, 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=AC9, first strand: chain 'C' and resid 130 through 132 removed outlier: 5.801A 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: 4.536A 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=AD1, first strand: chain 'D' and resid 174 through 180 removed outlier: 5.811A 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: 7.075A pdb=" N LEU D 205 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 3.946A 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: 4.624A pdb=" N MET D 13 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 6.906A 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: 6.924A 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: 4.809A pdb=" N VAL D 185 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU D 193 " --> pdb=" O HIS D 183 " (cutoff:3.500A) Processing sheet with id=AD2, 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: 6.863A 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=AD3, first strand: chain 'D' and resid 123 through 124 Processing sheet with id=AD4, first strand: chain 'E' and resid 16 through 18 removed outlier: 3.546A pdb=" N GLY E 16 " --> pdb=" O VAL E 7 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ALA E 126 " --> pdb=" O ASP E 6 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 97 through 98 removed outlier: 6.958A 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: 6.171A pdb=" N THR F 162 " --> pdb=" O VAL F 41 " (cutoff:3.500A) Processing sheet with id=AD6, 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) Processing sheet with id=AD7, first strand: chain 'G' and resid 9 through 10 Processing sheet with id=AD8, first strand: chain 'G' and resid 16 through 20 removed outlier: 3.848A pdb=" N GLY G 31 " --> pdb=" O GLY G 28 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 122 through 128 removed outlier: 6.812A pdb=" N LYS G 131 " --> pdb=" O GLU G 127 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 96 through 100 removed outlier: 3.540A pdb=" N GLU G 105 " --> pdb=" O GLN G 98 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN G 103 " --> pdb=" O LYS G 100 " (cutoff:3.500A) Processing sheet with id=AE2, 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=AE3, first strand: chain 'H' and resid 78 through 81 removed outlier: 6.319A pdb=" N VAL H 78 " --> pdb=" O ASN H 147 " (cutoff:3.500A) removed outlier: 7.540A 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=AE4, first strand: chain 'I' and resid 47 through 51 removed outlier: 6.956A 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: 6.842A pdb=" N VAL I 25 " --> pdb=" O LYS I 106 " (cutoff:3.500A) Processing sheet with id=AE5, 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=AE6, 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=AE6 Processing sheet with id=AE7, first strand: chain 'K' and resid 54 through 56 Processing sheet with id=AE8, 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: 4.099A pdb=" N ARG K 76 " --> pdb=" O ARG K 85 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG K 85 " --> pdb=" O ARG K 76 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 6 through 9 removed outlier: 3.981A 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: 6.550A pdb=" N ILE L 19 " --> pdb=" O VAL L 43 " (cutoff:3.500A) removed outlier: 6.678A 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: 4.675A pdb=" N ILE L 39 " --> pdb=" O ARG L 23 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASP L 37 " --> pdb=" O VAL L 62 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LYS L 59 " --> pdb=" O ILE L 87 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 76 through 79 removed outlier: 6.660A pdb=" N THR Q 59 " --> pdb=" O ILE Q 47 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N GLU Q 63 " --> pdb=" O LYS Q 43 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N LYS Q 43 " --> pdb=" O GLU Q 63 " (cutoff:3.500A) removed outlier: 6.430A 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: 7.565A 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: 8.778A 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=AF2, 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: 7.305A 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=AF3, first strand: chain 'M' and resid 91 through 93 Processing sheet with id=AF4, first strand: chain 'N' and resid 64 through 66 removed outlier: 6.571A pdb=" N ILE N 34 " --> pdb=" O LEU N 103 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLU N 105 " --> pdb=" O TYR N 32 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N TYR N 32 " --> pdb=" O GLU N 105 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'N' and resid 72 through 75 removed outlier: 3.638A pdb=" N LEU N 74 " --> pdb=" O TRP N 92 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TRP N 92 " --> pdb=" O LEU N 74 " (cutoff:3.500A) Processing sheet with id=AF6, 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=AF7, first strand: chain 'P' and resid 58 through 64 removed outlier: 6.377A pdb=" N LEU P 51 " --> pdb=" O LEU P 60 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ALA P 62 " --> pdb=" O VAL P 49 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL P 49 " --> pdb=" O ALA P 62 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N SER P 64 " --> pdb=" O ILE P 47 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE P 47 " --> pdb=" O SER P 64 " (cutoff:3.500A) Processing sheet with id=AF8, 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=AF9, first strand: chain 'S' and resid 21 through 25 removed outlier: 3.663A 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=AG1, 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=AG2, first strand: chain 'T' and resid 9 through 17 removed outlier: 5.747A pdb=" N SER T 108 " --> pdb=" O TYR T 16 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS T 34 " --> pdb=" O VAL T 78 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'T' and resid 9 through 17 removed outlier: 5.747A 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: 5.479A pdb=" N GLU T 85 " --> pdb=" O HIS T 109 " (cutoff:3.500A) Processing sheet with id=AG4, 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: 4.537A 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=AG5, first strand: chain 'V' and resid 66 through 67 removed outlier: 3.633A pdb=" N VAL V 25 " --> pdb=" O LEU V 34 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N THR V 8 " --> pdb=" O VAL V 74 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'V' and resid 40 through 43 Processing sheet with id=AG7, 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=AG8, first strand: chain 'W' and resid 10 through 15 removed outlier: 8.256A pdb=" N THR W 12 " --> pdb=" O ASN W 50 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ASN W 50 " --> pdb=" O THR W 12 " (cutoff:3.500A) removed outlier: 4.120A 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: 8.805A pdb=" N ALA W 95 " --> pdb=" O LYS W 32 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N LEU W 97 " --> pdb=" O PRO W 34 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N VAL W 36 " --> pdb=" O LEU W 97 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP W 96 " --> pdb=" O LYS W 81 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN W 76 " --> pdb=" O LEU W 69 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'W' and resid 143 through 149 Processing sheet with id=AH1, first strand: chain 'W' and resid 122 through 126 Processing sheet with id=AH2, 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=AH3, first strand: chain 'X' and resid 30 through 31 Processing sheet with id=AH4, first strand: chain 'X' and resid 46 through 47 removed outlier: 6.522A pdb=" N HIS X 46 " --> pdb=" O VAL X 78 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'Y' and resid 13 through 18 removed outlier: 3.548A 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=AH6, first strand: chain 'Y' and resid 33 through 39 Processing sheet with id=AH7, first strand: chain '1' and resid 34 through 36 Processing sheet with id=AH8, first strand: chain '2' and resid 21 through 26 Processing sheet with id=AH9, first strand: chain '3' and resid 28 through 32 Processing sheet with id=AI1, first strand: chain '4' and resid 22 through 26 Processing sheet with id=AI2, first strand: chain '6' and resid 15 through 17 removed outlier: 3.529A pdb=" N LYS 6 21 " --> pdb=" O THR 6 17 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain '7' and resid 15 through 18 1876 hydrogen bonds defined for protein. 5322 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4002 hydrogen bonds 6310 hydrogen bond angles 0 basepair planarities 1571 basepair parallelities 2591 stacking parallelities Total time for adding SS restraints: 262.66 Time building geometry restraints manager: 65.12 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: 153215 1.54 - 1.90: 10126 1.90 - 2.25: 0 2.25 - 2.61: 0 2.61 - 2.96: 1 Bond restraints: 163342 Sorted by residual: bond pdb=" C VAL V 47 " pdb=" N SER V 56 " ideal model delta sigma weight residual 1.329 2.960 -1.631 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 1.390 -0.055 8.70e-03 1.32e+04 3.94e+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 3.40e+01 bond pdb=" C ARG O 45 " pdb=" N PRO O 46 " ideal model delta sigma weight residual 1.336 1.404 -0.068 1.23e-02 6.61e+03 3.06e+01 bond pdb=" C VAL i 42 " pdb=" N PRO i 43 " ideal model delta sigma weight residual 1.334 1.390 -0.057 1.11e-02 8.12e+03 2.60e+01 ... (remaining 163337 not shown) Histogram of bond angle deviations from ideal: 71.55 - 86.45: 2 86.45 - 101.35: 2330 101.35 - 116.24: 141420 116.24 - 131.14: 99318 131.14 - 146.03: 1467 Bond angle restraints: 244537 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 94.23 27.64 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 71.55 50.15 1.80e+00 3.09e-01 7.76e+02 angle pdb=" N GLY W 62 " pdb=" CA GLY W 62 " pdb=" C GLY W 62 " ideal model delta sigma weight residual 111.93 133.83 -21.90 1.15e+00 7.56e-01 3.63e+02 angle pdb=" CA VAL V 47 " pdb=" C VAL V 47 " pdb=" N SER V 56 " ideal model delta sigma weight residual 117.15 138.41 -21.26 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 85.09 23.95 1.52e+00 4.33e-01 2.48e+02 ... (remaining 244532 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 91847 35.91 - 71.82: 11928 71.82 - 107.73: 1365 107.73 - 143.65: 36 143.65 - 179.56: 57 Dihedral angle restraints: 105233 sinusoidal: 87945 harmonic: 17288 Sorted by residual: dihedral pdb=" CA ARG X 85 " pdb=" C ARG X 85 " pdb=" N PRO X 86 " pdb=" CA PRO X 86 " ideal model delta harmonic sigma weight residual 180.00 95.47 84.53 0 5.00e+00 4.00e-02 2.86e+02 dihedral pdb=" CA ASN L 91 " pdb=" C ASN L 91 " pdb=" N ASP L 92 " pdb=" CA ASP L 92 " ideal model delta harmonic sigma weight residual -180.00 -100.10 -79.90 0 5.00e+00 4.00e-02 2.55e+02 dihedral pdb=" CA ARG O 117 " pdb=" C ARG O 117 " pdb=" N GLU O 118 " pdb=" CA GLU O 118 " ideal model delta harmonic sigma weight residual 180.00 103.15 76.85 0 5.00e+00 4.00e-02 2.36e+02 ... (remaining 105230 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.156: 30639 0.156 - 0.313: 590 0.313 - 0.469: 35 0.469 - 0.625: 5 0.625 - 0.782: 1 Chirality restraints: 31270 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 -2.12 -0.62 2.00e-01 2.50e+01 9.72e+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 -2.06 -0.57 2.00e-01 2.50e+01 8.11e+00 ... (remaining 31267 not shown) Planarity restraints: 13186 Sorted by residual: 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=" C ASP L 92 " 0.096 5.00e-02 4.00e+02 1.48e-01 3.51e+01 pdb=" N PRO L 93 " -0.256 5.00e-02 4.00e+02 pdb=" CA PRO L 93 " 0.081 5.00e-02 4.00e+02 pdb=" CD PRO L 93 " 0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 144 " -0.026 2.00e-02 2.50e+03 5.03e-02 2.53e+01 pdb=" C ALA C 144 " 0.087 2.00e-02 2.50e+03 pdb=" O ALA C 144 " -0.031 2.00e-02 2.50e+03 pdb=" N VAL C 145 " -0.030 2.00e-02 2.50e+03 ... (remaining 13183 not shown) Histogram of nonbonded interaction distances: 1.09 - 1.85: 166 1.85 - 2.61: 4620 2.61 - 3.38: 173797 3.38 - 4.14: 491777 4.14 - 4.90: 697809 Nonbonded interactions: 1368169 Sorted by model distance: nonbonded pdb=" O2' G a1097 " pdb=" NH1 ARG i 126 " model vdw 1.088 2.520 nonbonded pdb=" OP1 G a 998 " pdb=" NE2 HIS s 14 " model vdw 1.091 2.520 nonbonded pdb=" O ASP m 69 " pdb=" CG GLU m 73 " model vdw 1.113 3.440 nonbonded pdb=" C2 A a 940 " pdb=" NE ARG s 55 " model vdw 1.123 3.420 nonbonded pdb=" NE ARG e 17 " pdb=" CD1 ILE e 85 " model vdw 1.155 3.540 ... (remaining 1368164 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.130 Extract box with map and model: 18.230 Check model and map are aligned: 1.690 Set scattering table: 1.060 Process input model: 537.640 Find NCS groups from input model: 2.930 Set up NCS constraints: 0.340 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:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 569.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 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 1.631 163342 Z= 0.609 Angle : 1.181 50.147 244537 Z= 0.623 Chirality : 0.058 0.782 31270 Planarity : 0.008 0.148 13186 Dihedral : 24.034 179.558 94106 Min Nonbonded Distance : 1.088 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 1.35 % Allowed : 8.37 % Favored : 90.28 % Rotamer: Outliers : 3.23 % Allowed : 5.98 % Favored : 90.78 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.87 % Twisted General : 0.87 % 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: -3.95 (0.09), residues: 5989 helix: -2.97 (0.09), residues: 1931 sheet: -1.89 (0.15), residues: 1075 loop : -2.63 (0.10), residues: 2983 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 0.060 0.005 PHE X 69 TYR 0.060 0.004 TYR L 32 ARG 0.030 0.002 ARG X 75 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11978 Ramachandran restraints generated. 5989 Oldfield, 0 Emsley, 5989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11978 Ramachandran restraints generated. 5989 Oldfield, 0 Emsley, 5989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1697 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 1537 time to evaluate : 6.112 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: c 142 ARG cc_start: 0.5631 (ttp-170) cc_final: 0.5253 (ttp-170) REVERT: e 182 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.6382 (mtm180) REVERT: i 75 VAL cc_start: 0.8275 (m) cc_final: 0.8028 (m) REVERT: i 86 HIS cc_start: 0.4802 (OUTLIER) cc_final: 0.4251 (m-70) REVERT: j 57 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.7835 (pttt) REVERT: l 3 THR cc_start: 0.7578 (p) cc_final: 0.7256 (p) REVERT: o 36 ILE cc_start: 0.8715 (mt) cc_final: 0.8493 (mt) REVERT: q 79 THR cc_start: 0.7658 (p) cc_final: 0.7303 (p) REVERT: n 33 VAL cc_start: 0.8472 (t) cc_final: 0.8210 (p) REVERT: n 47 MET cc_start: 0.7209 (mtp) cc_final: 0.7001 (mtp) REVERT: b 6 MET cc_start: 0.6152 (mtp) cc_final: 0.5872 (mtp) REVERT: b 7 LYS cc_start: 0.6429 (mttt) cc_final: 0.6137 (mttt) REVERT: b 168 LYS cc_start: 0.6237 (tptt) cc_final: 0.5943 (tptt) REVERT: m 86 CYS cc_start: 0.7112 (t) cc_final: 0.6802 (t) REVERT: C 85 ASP cc_start: 0.8989 (t0) cc_final: 0.8786 (t0) REVERT: C 91 ASN cc_start: 0.8846 (m-40) cc_final: 0.8640 (m-40) REVERT: C 201 GLN cc_start: 0.8823 (pp30) cc_final: 0.8505 (pp30) REVERT: C 247 VAL cc_start: 0.8550 (OUTLIER) cc_final: 0.8319 (m) REVERT: D 61 LYS cc_start: 0.8048 (mttt) cc_final: 0.6575 (mmtt) REVERT: E 178 ILE cc_start: 0.7610 (OUTLIER) cc_final: 0.7325 (mm) REVERT: F 33 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.6322 (tpp) REVERT: G 62 SER cc_start: 0.8751 (m) cc_final: 0.8144 (m) REVERT: G 165 TYR cc_start: 0.7660 (m-80) cc_final: 0.7317 (m-80) REVERT: H 1 MET cc_start: 0.6867 (ttm) cc_final: 0.6555 (ttp) REVERT: H 134 VAL cc_start: 0.8809 (t) cc_final: 0.8546 (m) REVERT: L 97 ARG cc_start: 0.7182 (ttp-170) cc_final: 0.6645 (ttp-170) REVERT: M 21 ARG cc_start: 0.8392 (mtp-110) cc_final: 0.7903 (mtm-85) REVERT: N 5 ARG cc_start: 0.7314 (tmm-80) cc_final: 0.7038 (mtm110) REVERT: N 67 ASN cc_start: 0.7463 (m-40) cc_final: 0.6222 (m-40) REVERT: N 92 TRP cc_start: 0.6888 (OUTLIER) cc_final: 0.5758 (p90) REVERT: N 128 LYS cc_start: 0.7249 (mttp) cc_final: 0.7043 (mttm) REVERT: O 8 PRO cc_start: 0.8803 (Cg_endo) cc_final: 0.8522 (Cg_exo) REVERT: O 104 LYS cc_start: 0.8415 (mtpp) cc_final: 0.8163 (mtpp) REVERT: P 83 ARG cc_start: 0.8001 (tpt170) cc_final: 0.7613 (tpm170) REVERT: U 65 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8586 (ptpp) REVERT: V 63 GLU cc_start: 0.6797 (mp0) cc_final: 0.6457 (mp0) REVERT: V 99 LYS cc_start: 0.6454 (OUTLIER) cc_final: 0.6047 (mttm) REVERT: W 125 THR cc_start: 0.6360 (m) cc_final: 0.5632 (p) REVERT: W 172 SER cc_start: 0.6224 (OUTLIER) cc_final: 0.5883 (t) REVERT: Y 37 ARG cc_start: 0.7831 (mtt-85) cc_final: 0.7588 (mmt180) REVERT: Y 57 LYS cc_start: 0.8659 (tttt) cc_final: 0.7718 (tptt) REVERT: Z 11 ARG cc_start: 0.5342 (mtt-85) cc_final: 0.4781 (ptp-170) REVERT: Z 25 SER cc_start: 0.7433 (m) cc_final: 0.7218 (m) REVERT: Z 64 ARG cc_start: 0.6944 (OUTLIER) cc_final: 0.6252 (mmp-170) REVERT: 4 23 TYR cc_start: 0.6031 (OUTLIER) cc_final: 0.4965 (t80) REVERT: 7 35 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8113 (ttp-110) REVERT: 8 15 LYS cc_start: 0.8330 (tmtp) cc_final: 0.8043 (tppt) outliers start: 160 outliers final: 66 residues processed: 1639 average time/residue: 1.5112 time to fit residues: 4054.6700 Evaluate side-chains 1193 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 1114 time to evaluate : 6.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 134 ARG Chi-restraints excluded: chain c residue 141 MET 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 42 VAL Chi-restraints excluded: chain i residue 83 ILE Chi-restraints excluded: chain i residue 86 HIS Chi-restraints excluded: chain j residue 57 LYS Chi-restraints excluded: chain k residue 47 GLN Chi-restraints excluded: chain q residue 76 LEU Chi-restraints excluded: chain s residue 6 LYS Chi-restraints excluded: chain t residue 8 ILE Chi-restraints excluded: chain m residue 70 LEU Chi-restraints excluded: chain m residue 71 ARG Chi-restraints excluded: chain m residue 72 ARG Chi-restraints excluded: chain m residue 73 GLU Chi-restraints excluded: chain u residue 6 LYS Chi-restraints excluded: chain u residue 10 LYS Chi-restraints excluded: chain u residue 30 LYS Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 36 PRO Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 258 ARG Chi-restraints excluded: chain D residue 154 CYS Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain F residue 92 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 L residue 90 ASP Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 92 TRP Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 14 SER Chi-restraints excluded: chain O residue 16 HIS Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain S residue 103 LYS Chi-restraints excluded: chain T residue 6 GLU Chi-restraints excluded: chain U residue 9 ASP Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 59 THR Chi-restraints excluded: chain U residue 65 LYS Chi-restraints excluded: chain U residue 67 LYS Chi-restraints excluded: chain U residue 79 THR Chi-restraints excluded: chain U residue 96 PHE Chi-restraints excluded: chain V residue 10 LEU Chi-restraints excluded: chain V residue 99 LYS Chi-restraints excluded: chain W residue 6 ASN Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain W residue 100 VAL Chi-restraints excluded: chain W residue 114 VAL Chi-restraints excluded: chain W residue 172 SER Chi-restraints excluded: chain X residue 14 ARG Chi-restraints excluded: chain X residue 15 ASP Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 85 ARG Chi-restraints excluded: chain Z residue 5 THR Chi-restraints excluded: chain Z residue 64 ARG Chi-restraints excluded: chain Z residue 65 GLU Chi-restraints excluded: chain 1 residue 51 HIS Chi-restraints excluded: chain 2 residue 44 PHE Chi-restraints excluded: chain 2 residue 60 ARG Chi-restraints excluded: chain 4 residue 22 ASN Chi-restraints excluded: chain 4 residue 23 TYR Chi-restraints excluded: chain 4 residue 32 ASP Chi-restraints excluded: chain 4 residue 42 CYS Chi-restraints excluded: chain 4 residue 52 LYS Chi-restraints excluded: chain 7 residue 20 HIS Chi-restraints excluded: chain 7 residue 34 GLN Chi-restraints excluded: chain 7 residue 35 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1066 random chunks: chunk 900 optimal weight: 3.9990 chunk 807 optimal weight: 0.7980 chunk 448 optimal weight: 8.9990 chunk 276 optimal weight: 10.0000 chunk 545 optimal weight: 6.9990 chunk 431 optimal weight: 0.5980 chunk 835 optimal weight: 20.0000 chunk 323 optimal weight: 9.9990 chunk 508 optimal weight: 10.0000 chunk 621 optimal weight: 1.9990 chunk 968 optimal weight: 5.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 27 GLN ** c 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 97 GLN g 106 ASN g 142 HIS ** g 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 57 ASN i 64 HIS i 86 HIS j 56 HIS j 99 ASN k 47 GLN k 78 ASN k 110 GLN l 29 GLN l 46 ASN l 77 HIS o 7 GLN q 33 GLN r 70 ASN s 23 ASN ** s 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 21 ASN t 68 HIS b 24 ASN b 167 ASN b 203 ASN d 51 GLN d 95 ASN f 80 ASN p 15 ASN C 58 HIS ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 ASN C 135 ASN C 205 ASN C 227 ASN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 GLN D 69 GLN D 183 HIS E 35 HIS E 50 HIS ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 ASN ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 ASN ** F 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 118 GLN J 33 HIS J 119 ASN K 40 HIS K 117 GLN K 132 HIS ** M 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 ASN M 127 ASN ** N 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 96 ASN ** O 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 79 ASN R 41 HIS R 94 ASN S 90 HIS T 66 GLN ** T 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 27 ASN U 58 ASN W 46 HIS W 94 HIS W 101 GLN X 29 GLN Y 22 HIS ** Z 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 52 GLN 1 8 GLN 1 33 GLN 1 42 GLN 1 51 HIS 2 40 GLN 4 48 HIS 5 11 ASN 5 19 HIS ** 6 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 31 HIS 8 13 HIS 8 17 ASN Total number of N/Q/H flips: 73 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.132 163342 Z= 0.273 Angle : 0.757 17.607 244537 Z= 0.382 Chirality : 0.041 0.344 31270 Planarity : 0.007 0.176 13186 Dihedral : 24.624 179.958 82526 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.88 % Favored : 92.67 % Rotamer: Outliers : 5.22 % Allowed : 12.92 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.37 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.10), residues: 5991 helix: -1.37 (0.10), residues: 2011 sheet: -1.37 (0.15), residues: 1052 loop : -2.22 (0.10), residues: 2928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP s 34 HIS 0.018 0.002 HIS O 77 PHE 0.024 0.003 PHE F 27 TYR 0.027 0.002 TYR h 130 ARG 0.017 0.001 ARG F 99 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11982 Ramachandran restraints generated. 5991 Oldfield, 0 Emsley, 5991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11982 Ramachandran restraints generated. 5991 Oldfield, 0 Emsley, 5991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1549 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 1291 time to evaluate : 6.209 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: e 63 ILE cc_start: 0.8332 (mm) cc_final: 0.8124 (mm) REVERT: h 61 VAL cc_start: 0.8525 (t) cc_final: 0.8222 (t) REVERT: i 54 THR cc_start: 0.7651 (p) cc_final: 0.7359 (m) REVERT: i 75 VAL cc_start: 0.7932 (m) cc_final: 0.7717 (m) REVERT: i 77 ARG cc_start: 0.6343 (mpp80) cc_final: 0.5590 (mtt180) REVERT: j 63 GLU cc_start: 0.5576 (pt0) cc_final: 0.5326 (pt0) REVERT: s 42 PRO cc_start: 0.5445 (Cg_exo) cc_final: 0.5132 (Cg_endo) REVERT: b 6 MET cc_start: 0.6264 (mtp) cc_final: 0.5933 (mtp) REVERT: b 7 LYS cc_start: 0.6415 (mttt) cc_final: 0.6180 (mttt) REVERT: m 58 ASP cc_start: 0.8366 (m-30) cc_final: 0.8155 (m-30) REVERT: C 25 THR cc_start: 0.7026 (OUTLIER) cc_final: 0.6611 (p) REVERT: C 72 LYS cc_start: 0.5478 (OUTLIER) cc_final: 0.4629 (mptp) REVERT: C 73 ASP cc_start: 0.6819 (OUTLIER) cc_final: 0.6522 (m-30) REVERT: C 162 SER cc_start: 0.8522 (p) cc_final: 0.8139 (m) REVERT: C 168 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7618 (pttp) REVERT: C 201 GLN cc_start: 0.8655 (pp30) cc_final: 0.8436 (pp30) REVERT: D 61 LYS cc_start: 0.8226 (mttt) cc_final: 0.6717 (mmtt) REVERT: D 84 LEU cc_start: 0.9003 (mt) cc_final: 0.8782 (mt) REVERT: D 142 GLN cc_start: 0.8224 (tp40) cc_final: 0.7525 (tt0) REVERT: F 29 TYR cc_start: 0.6392 (m-80) cc_final: 0.6034 (m-80) REVERT: F 150 VAL cc_start: 0.7303 (OUTLIER) cc_final: 0.6981 (m) REVERT: G 98 GLN cc_start: 0.7376 (pt0) cc_final: 0.6903 (mm110) REVERT: G 151 ARG cc_start: 0.6909 (mmt-90) cc_final: 0.6569 (mmt180) REVERT: G 166 GLU cc_start: 0.7628 (tp30) cc_final: 0.7343 (mt-10) REVERT: I 58 LYS cc_start: 0.3902 (mttt) cc_final: 0.3681 (tttm) REVERT: I 98 LYS cc_start: 0.6461 (mtmp) cc_final: 0.5957 (mtmp) REVERT: J 38 MET cc_start: 0.5074 (mmm) cc_final: 0.4681 (mmm) REVERT: L 1 MET cc_start: 0.7493 (mtm) cc_final: 0.7198 (mtp) REVERT: L 88 LYS cc_start: 0.7630 (ptpp) cc_final: 0.7167 (pttp) REVERT: N 5 ARG cc_start: 0.7280 (tmm-80) cc_final: 0.6941 (mtm110) REVERT: N 92 TRP cc_start: 0.6588 (OUTLIER) cc_final: 0.6134 (p90) REVERT: N 110 ASP cc_start: 0.6702 (OUTLIER) cc_final: 0.6318 (p0) REVERT: N 128 LYS cc_start: 0.7522 (mttp) cc_final: 0.7266 (mttm) REVERT: O 8 PRO cc_start: 0.8441 (Cg_endo) cc_final: 0.8025 (Cg_exo) REVERT: Q 38 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7593 (ptt90) REVERT: R 37 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8191 (mt-10) REVERT: U 66 ARG cc_start: 0.7148 (ttt90) cc_final: 0.6348 (mmm-85) REVERT: V 63 GLU cc_start: 0.6192 (mp0) cc_final: 0.5914 (mp0) REVERT: W 125 THR cc_start: 0.6950 (m) cc_final: 0.6569 (p) REVERT: X 81 VAL cc_start: 0.8661 (t) cc_final: 0.7892 (m) REVERT: Y 37 ARG cc_start: 0.7968 (mtt-85) cc_final: 0.7617 (mmt180) REVERT: Y 57 LYS cc_start: 0.8642 (tttt) cc_final: 0.7781 (tptt) REVERT: 1 8 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7324 (tp40) REVERT: 4 23 TYR cc_start: 0.6026 (OUTLIER) cc_final: 0.5248 (t80) REVERT: 8 15 LYS cc_start: 0.8435 (tmtp) cc_final: 0.8030 (tppt) REVERT: 8 17 ASN cc_start: 0.8240 (m110) cc_final: 0.7967 (m-40) outliers start: 258 outliers final: 134 residues processed: 1423 average time/residue: 1.4815 time to fit residues: 3538.7696 Evaluate side-chains 1248 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 1104 time to evaluate : 6.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 163 SER Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain c residue 200 VAL Chi-restraints excluded: chain e residue 64 VAL Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain g residue 48 GLU Chi-restraints excluded: chain h residue 4 THR Chi-restraints excluded: chain h residue 41 LYS Chi-restraints excluded: chain h residue 80 VAL Chi-restraints excluded: chain h residue 81 SER Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 39 VAL Chi-restraints excluded: chain i residue 42 VAL Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain k residue 27 HIS Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 93 VAL Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain o residue 45 VAL Chi-restraints excluded: chain q residue 24 ILE Chi-restraints excluded: chain q residue 28 VAL Chi-restraints excluded: chain q residue 76 LEU Chi-restraints excluded: chain s residue 6 LYS Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain n residue 24 CYS Chi-restraints excluded: chain n residue 56 VAL Chi-restraints excluded: chain b residue 50 ILE Chi-restraints excluded: chain d residue 45 GLU Chi-restraints excluded: chain d residue 114 SER Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 147 THR Chi-restraints excluded: chain d residue 154 ARG Chi-restraints excluded: chain d residue 182 GLU Chi-restraints excluded: chain m residue 66 VAL Chi-restraints excluded: chain m residue 70 LEU Chi-restraints excluded: chain m residue 72 ARG Chi-restraints excluded: chain p residue 75 LYS Chi-restraints excluded: chain u residue 6 LYS Chi-restraints excluded: chain u residue 10 LYS Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 31 LYS Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 72 LYS Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 127 GLU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 76 ARG Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 41 TYR Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 92 TRP Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 15 SER Chi-restraints excluded: chain O residue 18 SER Chi-restraints excluded: chain O residue 65 GLU Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 116 VAL Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 38 ARG Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 103 LYS Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain U residue 9 ASP Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 15 VAL Chi-restraints excluded: chain U residue 37 SER Chi-restraints excluded: chain U residue 38 ASN Chi-restraints excluded: chain U residue 59 THR Chi-restraints excluded: chain U residue 93 ILE Chi-restraints excluded: chain U residue 95 LEU Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 86 ARG Chi-restraints excluded: chain W residue 12 THR Chi-restraints excluded: chain W residue 14 ASN Chi-restraints excluded: chain W residue 17 THR Chi-restraints excluded: chain W residue 19 THR Chi-restraints excluded: chain W residue 107 THR Chi-restraints excluded: chain W residue 114 VAL Chi-restraints excluded: chain W residue 140 ILE Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain Y residue 26 SER Chi-restraints excluded: chain Z residue 5 THR Chi-restraints excluded: chain Z residue 41 LEU Chi-restraints excluded: chain Z residue 64 ARG Chi-restraints excluded: chain 1 residue 8 GLN Chi-restraints excluded: chain 1 residue 31 ILE Chi-restraints excluded: chain 1 residue 35 VAL Chi-restraints excluded: chain 1 residue 49 THR Chi-restraints excluded: chain 2 residue 13 THR Chi-restraints excluded: chain 3 residue 3 VAL Chi-restraints excluded: chain 3 residue 29 THR Chi-restraints excluded: chain 4 residue 7 VAL Chi-restraints excluded: chain 4 residue 23 TYR Chi-restraints excluded: chain 4 residue 39 LYS Chi-restraints excluded: chain 4 residue 52 LYS Chi-restraints excluded: chain 5 residue 45 LEU Chi-restraints excluded: chain 6 residue 6 THR Chi-restraints excluded: chain 7 residue 34 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1066 random chunks: chunk 537 optimal weight: 0.8980 chunk 300 optimal weight: 10.0000 chunk 805 optimal weight: 5.9990 chunk 659 optimal weight: 0.0570 chunk 267 optimal weight: 1.9990 chunk 969 optimal weight: 10.0000 chunk 1047 optimal weight: 0.4980 chunk 863 optimal weight: 8.9990 chunk 961 optimal weight: 8.9990 chunk 330 optimal weight: 0.7980 chunk 778 optimal weight: 7.9990 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 27 GLN ** c 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 107 ASN ** h 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 61 ASN ** i 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 86 HIS q 33 GLN ** t 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 70 ASN d 51 GLN ** f 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 106 ASN p 15 ASN C 76 ASN ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN E 83 GLN ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 ASN H 118 GLN H 137 HIS K 96 HIS ** M 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 66 GLN T 67 ASN T 68 ASN W 101 GLN X 29 GLN ** Z 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 8 GLN 1 48 ASN 8 13 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 163342 Z= 0.157 Angle : 0.617 18.844 244537 Z= 0.314 Chirality : 0.035 0.292 31270 Planarity : 0.005 0.176 13186 Dihedral : 24.412 179.966 82398 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.68 % Favored : 92.99 % Rotamer: Outliers : 4.39 % Allowed : 16.40 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.37 % Twisted General : 0.16 % 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: -1.86 (0.10), residues: 5991 helix: -0.34 (0.11), residues: 2007 sheet: -1.07 (0.16), residues: 1048 loop : -1.94 (0.11), residues: 2936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP b 96 HIS 0.061 0.001 HIS E 50 PHE 0.021 0.002 PHE d 58 TYR 0.024 0.002 TYR l 38 ARG 0.014 0.001 ARG L 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11982 Ramachandran restraints generated. 5991 Oldfield, 0 Emsley, 5991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11982 Ramachandran restraints generated. 5991 Oldfield, 0 Emsley, 5991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1423 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 1206 time to evaluate : 6.156 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: g 1 MET cc_start: 0.0971 (ptp) cc_final: -0.0292 (tpt) REVERT: g 151 PHE cc_start: 0.6574 (m-10) cc_final: 0.6043 (m-10) REVERT: h 45 TYR cc_start: 0.7614 (m-80) cc_final: 0.6959 (m-80) REVERT: h 46 ILE cc_start: 0.8387 (pt) cc_final: 0.8008 (pt) REVERT: i 77 ARG cc_start: 0.6114 (mpp80) cc_final: 0.5751 (mtt180) REVERT: j 64 HIS cc_start: 0.5993 (OUTLIER) cc_final: 0.5757 (p90) REVERT: r 41 TYR cc_start: 0.6992 (m-80) cc_final: 0.6727 (m-80) REVERT: n 29 ARG cc_start: 0.7887 (ttt90) cc_final: 0.7472 (ttt90) REVERT: b 6 MET cc_start: 0.6184 (mtp) cc_final: 0.5809 (mtp) REVERT: b 97 LEU cc_start: 0.6848 (mt) cc_final: 0.6454 (mt) REVERT: d 190 LEU cc_start: 0.3522 (OUTLIER) cc_final: 0.3217 (mt) REVERT: m 43 MET cc_start: 0.7622 (mtm) cc_final: 0.7305 (ptm) REVERT: m 58 ASP cc_start: 0.8389 (m-30) cc_final: 0.8145 (m-30) REVERT: p 36 VAL cc_start: 0.8050 (m) cc_final: 0.7837 (t) REVERT: u 6 LYS cc_start: 0.4779 (OUTLIER) cc_final: 0.4045 (pptt) REVERT: C 118 GLU cc_start: 0.6020 (pm20) cc_final: 0.5801 (pm20) REVERT: D 61 LYS cc_start: 0.8111 (mttt) cc_final: 0.6645 (mmtt) REVERT: D 142 GLN cc_start: 0.8014 (tp40) cc_final: 0.7410 (tt0) REVERT: D 210 SER cc_start: 0.8004 (t) cc_final: 0.7493 (p) REVERT: G 60 ARG cc_start: 0.6872 (ttp-110) cc_final: 0.6657 (ptm160) REVERT: G 98 GLN cc_start: 0.7302 (pt0) cc_final: 0.6791 (mt0) REVERT: K 54 VAL cc_start: 0.9169 (p) cc_final: 0.8967 (t) REVERT: K 108 MET cc_start: 0.8390 (mmt) cc_final: 0.7729 (mmt) REVERT: L 88 LYS cc_start: 0.7657 (ptpp) cc_final: 0.7175 (pttp) REVERT: M 21 ARG cc_start: 0.8373 (mtp85) cc_final: 0.8082 (mtp85) REVERT: M 124 VAL cc_start: 0.8970 (t) cc_final: 0.8705 (m) REVERT: N 5 ARG cc_start: 0.7282 (tmm-80) cc_final: 0.6920 (mtm110) REVERT: N 92 TRP cc_start: 0.6511 (OUTLIER) cc_final: 0.6096 (p90) REVERT: N 110 ASP cc_start: 0.6451 (OUTLIER) cc_final: 0.6195 (p0) REVERT: N 128 LYS cc_start: 0.7430 (mttp) cc_final: 0.7152 (mttm) REVERT: O 8 PRO cc_start: 0.7866 (Cg_endo) cc_final: 0.7383 (Cg_exo) REVERT: R 37 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8156 (mt-10) REVERT: S 95 THR cc_start: 0.8861 (m) cc_final: 0.8606 (m) REVERT: U 61 ASN cc_start: 0.8899 (OUTLIER) cc_final: 0.8687 (p0) REVERT: U 75 LYS cc_start: 0.8108 (ttmm) cc_final: 0.7700 (tppt) REVERT: X 81 VAL cc_start: 0.8334 (t) cc_final: 0.7666 (m) REVERT: Y 37 ARG cc_start: 0.7812 (mtt-85) cc_final: 0.7430 (mmt180) REVERT: Y 57 LYS cc_start: 0.8557 (tttt) cc_final: 0.7640 (tptt) REVERT: 4 23 TYR cc_start: 0.5881 (OUTLIER) cc_final: 0.5494 (t80) REVERT: 6 47 ARG cc_start: 0.8078 (mtm-85) cc_final: 0.7675 (mtm110) REVERT: 8 15 LYS cc_start: 0.8431 (tmtp) cc_final: 0.7969 (tppt) REVERT: 8 17 ASN cc_start: 0.8125 (m110) cc_final: 0.7848 (m-40) outliers start: 217 outliers final: 114 residues processed: 1324 average time/residue: 1.3840 time to fit residues: 3073.5302 Evaluate side-chains 1203 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 1082 time to evaluate : 6.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 163 SER Chi-restraints excluded: chain e residue 64 VAL Chi-restraints excluded: chain e residue 145 VAL Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain e residue 159 ILE Chi-restraints excluded: chain h residue 41 LYS Chi-restraints excluded: chain h residue 80 VAL Chi-restraints excluded: chain h residue 91 SER Chi-restraints excluded: chain i residue 39 VAL Chi-restraints excluded: chain i residue 62 LYS Chi-restraints excluded: chain i residue 88 ASP Chi-restraints excluded: chain j residue 57 LYS Chi-restraints excluded: chain j residue 64 HIS Chi-restraints excluded: chain k residue 27 HIS Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 93 VAL Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain o residue 45 VAL Chi-restraints excluded: chain q residue 37 VAL Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain q residue 76 LEU Chi-restraints excluded: chain s residue 6 LYS Chi-restraints excluded: chain s residue 21 VAL Chi-restraints excluded: chain s residue 23 ASN Chi-restraints excluded: chain t residue 8 ILE Chi-restraints excluded: chain n residue 4 LYS Chi-restraints excluded: chain b residue 50 ILE Chi-restraints excluded: chain d residue 45 GLU Chi-restraints excluded: chain d residue 50 LEU Chi-restraints excluded: chain d residue 114 SER Chi-restraints excluded: chain d residue 147 THR Chi-restraints excluded: chain d residue 154 ARG Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain f residue 30 ILE Chi-restraints excluded: chain f residue 93 THR Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain p residue 12 LYS Chi-restraints excluded: chain u residue 6 LYS Chi-restraints excluded: chain u residue 10 LYS Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 72 LYS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 113 LEU Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 41 TYR Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 80 GLU Chi-restraints excluded: chain N residue 92 TRP Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 15 SER Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain P residue 43 SER Chi-restraints excluded: chain P residue 56 ASN Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain S residue 103 LYS Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain U residue 9 ASP Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 15 VAL Chi-restraints excluded: chain U residue 37 SER Chi-restraints excluded: chain U residue 61 ASN Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 86 ARG Chi-restraints excluded: chain W residue 14 ASN Chi-restraints excluded: chain W residue 17 THR Chi-restraints excluded: chain W residue 19 THR Chi-restraints excluded: chain W residue 68 THR Chi-restraints excluded: chain W residue 107 THR Chi-restraints excluded: chain W residue 123 LEU Chi-restraints excluded: chain W residue 131 ILE Chi-restraints excluded: chain W residue 140 ILE Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 181 VAL Chi-restraints excluded: chain X residue 11 ARG Chi-restraints excluded: chain X residue 15 ASP Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain Z residue 5 THR Chi-restraints excluded: chain 1 residue 7 THR Chi-restraints excluded: chain 2 residue 13 THR Chi-restraints excluded: chain 3 residue 3 VAL Chi-restraints excluded: chain 4 residue 11 ILE Chi-restraints excluded: chain 4 residue 23 TYR Chi-restraints excluded: chain 4 residue 39 LYS Chi-restraints excluded: chain 6 residue 12 LYS Chi-restraints excluded: chain 6 residue 34 GLU Chi-restraints excluded: chain 6 residue 59 ASN Chi-restraints excluded: chain 7 residue 27 CYS Chi-restraints excluded: chain 7 residue 34 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1066 random chunks: chunk 958 optimal weight: 20.0000 chunk 729 optimal weight: 10.0000 chunk 503 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 462 optimal weight: 0.0270 chunk 651 optimal weight: 6.9990 chunk 973 optimal weight: 10.0000 chunk 1030 optimal weight: 5.9990 chunk 508 optimal weight: 3.9990 chunk 922 optimal weight: 8.9990 chunk 277 optimal weight: 3.9990 overall best weight: 3.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 93 ASN i 66 GLN ** i 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 86 HIS j 47 ASN o 46 HIS q 33 GLN ** t 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 7 GLN t 21 ASN t 68 HIS t 70 ASN ** n 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 49 HIS d 66 GLN ** d 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 41 HIS ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 47 GLN ** F 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 GLN ** F 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 ASN G 86 GLN ** G 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 118 GLN H 147 ASN ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 7 HIS ** M 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 9 HIS O 107 ASN ** P 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 40 GLN S 76 HIS T 66 GLN U 58 ASN W 101 GLN ** W 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 29 GLN Z 44 ASN ** 1 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 20 HIS 4 20 HIS ** 4 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 28 ASN 8 13 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 163342 Z= 0.291 Angle : 0.693 20.155 244537 Z= 0.352 Chirality : 0.039 0.309 31270 Planarity : 0.006 0.175 13186 Dihedral : 24.308 179.877 82370 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.41 % Favored : 92.27 % Rotamer: Outliers : 5.66 % Allowed : 17.91 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.75 % Twisted General : 0.14 % 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: -1.66 (0.10), residues: 5991 helix: -0.04 (0.11), residues: 2000 sheet: -1.16 (0.16), residues: 1016 loop : -1.83 (0.11), residues: 2975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP s 34 HIS 0.012 0.002 HIS 4 20 PHE 0.039 0.002 PHE c 10 TYR 0.027 0.002 TYR h 130 ARG 0.021 0.001 ARG r 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11982 Ramachandran restraints generated. 5991 Oldfield, 0 Emsley, 5991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11982 Ramachandran restraints generated. 5991 Oldfield, 0 Emsley, 5991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1430 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 280 poor density : 1150 time to evaluate : 6.246 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: c 61 ASP cc_start: 0.4851 (p0) cc_final: 0.4458 (p0) REVERT: c 193 PHE cc_start: 0.6312 (m-80) cc_final: 0.6053 (m-80) REVERT: g 103 TRP cc_start: 0.7253 (m-10) cc_final: 0.6989 (m-10) REVERT: i 77 ARG cc_start: 0.6308 (mpp80) cc_final: 0.6070 (mtt180) REVERT: j 57 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7242 (pptt) REVERT: j 64 HIS cc_start: 0.6098 (OUTLIER) cc_final: 0.5647 (p90) REVERT: q 33 GLN cc_start: 0.7179 (mt0) cc_final: 0.6737 (mt0) REVERT: t 7 GLN cc_start: 0.6976 (OUTLIER) cc_final: 0.6423 (pt0) REVERT: n 4 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7981 (mttt) REVERT: b 6 MET cc_start: 0.6241 (mtp) cc_final: 0.5894 (mtp) REVERT: b 7 LYS cc_start: 0.6772 (mttt) cc_final: 0.6502 (mttt) REVERT: d 65 LYS cc_start: 0.7325 (mmtm) cc_final: 0.7046 (ttpt) REVERT: d 171 GLU cc_start: 0.4505 (pm20) cc_final: 0.4223 (pm20) REVERT: d 190 LEU cc_start: 0.4302 (OUTLIER) cc_final: 0.4009 (mt) REVERT: f 11 ASP cc_start: 0.8202 (OUTLIER) cc_final: 0.7709 (m-30) REVERT: f 26 PHE cc_start: 0.7907 (m-80) cc_final: 0.7502 (m-10) REVERT: f 66 LYS cc_start: 0.8461 (ttmm) cc_final: 0.8006 (tmtt) REVERT: m 43 MET cc_start: 0.7466 (mtm) cc_final: 0.7156 (ptm) REVERT: m 58 ASP cc_start: 0.8467 (m-30) cc_final: 0.8177 (m-30) REVERT: m 99 ARG cc_start: 0.6853 (mmt90) cc_final: 0.6331 (ttm170) REVERT: p 73 LEU cc_start: 0.7781 (mp) cc_final: 0.7562 (mt) REVERT: u 10 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7352 (tptt) REVERT: C 118 GLU cc_start: 0.5869 (pm20) cc_final: 0.5594 (pm20) REVERT: C 168 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7542 (pttt) REVERT: D 142 GLN cc_start: 0.8211 (tp40) cc_final: 0.7562 (tt0) REVERT: D 210 SER cc_start: 0.8312 (t) cc_final: 0.7787 (p) REVERT: E 201 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8559 (tt) REVERT: F 33 MET cc_start: 0.5772 (mtm) cc_final: 0.5522 (ttm) REVERT: G 60 ARG cc_start: 0.6886 (ttp-110) cc_final: 0.6609 (ptm160) REVERT: G 82 GLU cc_start: 0.7017 (mm-30) cc_final: 0.6806 (mp0) REVERT: G 98 GLN cc_start: 0.7283 (pt0) cc_final: 0.6745 (mt0) REVERT: G 99 LEU cc_start: 0.8106 (pt) cc_final: 0.7551 (tp) REVERT: G 146 SER cc_start: 0.7337 (OUTLIER) cc_final: 0.7134 (t) REVERT: G 169 GLN cc_start: 0.7562 (mm-40) cc_final: 0.7343 (mm-40) REVERT: H 1 MET cc_start: 0.6809 (ttm) cc_final: 0.6370 (ttp) REVERT: J 38 MET cc_start: 0.4679 (mmm) cc_final: 0.4373 (tmm) REVERT: N 5 ARG cc_start: 0.7541 (tmm-80) cc_final: 0.7017 (mtm110) REVERT: N 92 TRP cc_start: 0.6701 (OUTLIER) cc_final: 0.6332 (p90) REVERT: N 105 GLU cc_start: 0.7764 (mp0) cc_final: 0.7518 (mp0) REVERT: N 110 ASP cc_start: 0.6299 (OUTLIER) cc_final: 0.5919 (p0) REVERT: N 128 LYS cc_start: 0.7496 (mttp) cc_final: 0.7283 (mttm) REVERT: Q 24 THR cc_start: 0.9033 (m) cc_final: 0.8770 (t) REVERT: Q 38 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7787 (ptm-80) REVERT: T 85 GLU cc_start: 0.7729 (tp30) cc_final: 0.7526 (tp30) REVERT: U 61 ASN cc_start: 0.9057 (OUTLIER) cc_final: 0.8849 (p0) REVERT: Y 37 ARG cc_start: 0.8188 (mtt-85) cc_final: 0.7645 (mmt180) REVERT: Y 57 LYS cc_start: 0.8586 (tttt) cc_final: 0.7714 (tptt) REVERT: 2 22 PHE cc_start: 0.6225 (m-80) cc_final: 0.5866 (m-10) REVERT: 4 23 TYR cc_start: 0.6344 (OUTLIER) cc_final: 0.5602 (t80) REVERT: 5 9 GLN cc_start: 0.8867 (mm110) cc_final: 0.8572 (mm110) REVERT: 5 28 ARG cc_start: 0.8511 (tpp80) cc_final: 0.8251 (ttm-80) REVERT: 8 6 ARG cc_start: 0.8465 (ttp-110) cc_final: 0.7687 (ttp-110) REVERT: 8 15 LYS cc_start: 0.8649 (tmtp) cc_final: 0.8128 (tppt) REVERT: 8 17 ASN cc_start: 0.8326 (m110) cc_final: 0.8026 (m-40) outliers start: 280 outliers final: 177 residues processed: 1310 average time/residue: 1.3852 time to fit residues: 3057.9271 Evaluate side-chains 1260 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1068 time to evaluate : 6.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 117 GLN Chi-restraints excluded: chain c residue 163 SER Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 200 VAL Chi-restraints excluded: chain e residue 37 ILE Chi-restraints excluded: chain e residue 40 VAL Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 64 VAL Chi-restraints excluded: chain e residue 148 ILE Chi-restraints excluded: chain e residue 159 ILE Chi-restraints excluded: chain g residue 31 LEU Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain h residue 4 THR Chi-restraints excluded: chain h residue 41 LYS Chi-restraints excluded: chain h residue 80 VAL Chi-restraints excluded: chain h residue 91 SER Chi-restraints excluded: chain h residue 123 VAL Chi-restraints excluded: chain h residue 130 TYR Chi-restraints excluded: chain i residue 88 ASP Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain j residue 57 LYS Chi-restraints excluded: chain j residue 64 HIS Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain k residue 27 HIS Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 93 VAL Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 80 VAL Chi-restraints excluded: chain o residue 45 VAL Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain q residue 24 ILE Chi-restraints excluded: chain q residue 28 VAL Chi-restraints excluded: chain q residue 37 VAL Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain q residue 76 LEU Chi-restraints excluded: chain r residue 64 ILE Chi-restraints excluded: chain s residue 6 LYS Chi-restraints excluded: chain s residue 21 VAL Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain s residue 67 VAL Chi-restraints excluded: chain t residue 7 GLN Chi-restraints excluded: chain n residue 4 LYS Chi-restraints excluded: chain n residue 24 CYS Chi-restraints excluded: chain n residue 32 SER Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain d residue 9 THR Chi-restraints excluded: chain d residue 27 GLU Chi-restraints excluded: chain d residue 50 LEU Chi-restraints excluded: chain d residue 91 SER Chi-restraints excluded: chain d residue 114 SER Chi-restraints excluded: chain d residue 125 VAL Chi-restraints excluded: chain d residue 147 THR Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 196 VAL Chi-restraints excluded: chain f residue 11 ASP Chi-restraints excluded: chain f residue 30 ILE Chi-restraints excluded: chain f residue 93 THR Chi-restraints excluded: chain m residue 4 LEU Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 66 VAL Chi-restraints excluded: chain p residue 12 LYS Chi-restraints excluded: chain u residue 6 LYS Chi-restraints excluded: chain u residue 10 LYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 168 LYS Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 75 ARG Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 127 GLU Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 13 HIS Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 41 TYR Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 92 TRP Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 15 SER Chi-restraints excluded: chain O residue 18 SER Chi-restraints excluded: chain O residue 30 GLU Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain P residue 28 LYS Chi-restraints excluded: chain P residue 43 SER Chi-restraints excluded: chain P residue 49 VAL Chi-restraints excluded: chain P residue 56 ASN Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain Q residue 30 LYS Chi-restraints excluded: chain Q residue 38 ARG Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 103 LYS Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 42 ILE Chi-restraints excluded: chain T residue 78 VAL Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain U residue 9 ASP Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 15 VAL Chi-restraints excluded: chain U residue 37 SER Chi-restraints excluded: chain U residue 38 ASN Chi-restraints excluded: chain U residue 46 ILE Chi-restraints excluded: chain U residue 61 ASN Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain U residue 93 ILE Chi-restraints excluded: chain V residue 8 THR Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 86 ARG Chi-restraints excluded: chain V residue 95 VAL Chi-restraints excluded: chain W residue 12 THR Chi-restraints excluded: chain W residue 14 ASN Chi-restraints excluded: chain W residue 17 THR Chi-restraints excluded: chain W residue 53 ASP Chi-restraints excluded: chain W residue 68 THR Chi-restraints excluded: chain W residue 107 THR Chi-restraints excluded: chain W residue 131 ILE Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain X residue 11 ARG Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain Z residue 5 THR Chi-restraints excluded: chain Z residue 49 THR Chi-restraints excluded: chain 1 residue 4 LEU Chi-restraints excluded: chain 1 residue 7 THR Chi-restraints excluded: chain 1 residue 31 ILE Chi-restraints excluded: chain 1 residue 36 VAL Chi-restraints excluded: chain 2 residue 13 THR Chi-restraints excluded: chain 2 residue 62 GLU Chi-restraints excluded: chain 3 residue 3 VAL Chi-restraints excluded: chain 3 residue 29 THR Chi-restraints excluded: chain 3 residue 31 SER Chi-restraints excluded: chain 4 residue 23 TYR Chi-restraints excluded: chain 4 residue 39 LYS Chi-restraints excluded: chain 6 residue 12 LYS Chi-restraints excluded: chain 6 residue 34 GLU Chi-restraints excluded: chain 7 residue 26 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1066 random chunks: chunk 858 optimal weight: 8.9990 chunk 584 optimal weight: 3.9990 chunk 14 optimal weight: 20.0000 chunk 767 optimal weight: 10.0000 chunk 425 optimal weight: 5.9990 chunk 879 optimal weight: 30.0000 chunk 712 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 526 optimal weight: 7.9990 chunk 924 optimal weight: 10.0000 chunk 260 optimal weight: 0.1980 overall best weight: 5.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 117 GLN ** i 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 111 GLN k 110 GLN ** k 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 69 HIS t 3 ASN t 21 ASN ** n 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 48 GLN d 51 GLN d 179 GLN p 41 HIS ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS F 134 ASN ** F 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 ASN ** G 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 ASN ** M 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 85 HIS T 66 GLN T 67 ASN ** W 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 29 GLN ** 2 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 12 ASN ** 4 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 35 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.128 163342 Z= 0.432 Angle : 0.791 16.888 244537 Z= 0.396 Chirality : 0.044 0.345 31270 Planarity : 0.007 0.163 13186 Dihedral : 24.362 179.972 82367 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.41 % Favored : 91.24 % Rotamer: Outliers : 6.89 % Allowed : 18.40 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.12 % Twisted General : 0.14 % 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: -1.82 (0.10), residues: 5991 helix: -0.05 (0.11), residues: 1993 sheet: -1.34 (0.15), residues: 1048 loop : -1.99 (0.11), residues: 2950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP s 34 HIS 0.020 0.002 HIS E 50 PHE 0.044 0.003 PHE s 74 TYR 0.080 0.003 TYR G 95 ARG 0.018 0.001 ARG L 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11982 Ramachandran restraints generated. 5991 Oldfield, 0 Emsley, 5991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11982 Ramachandran restraints generated. 5991 Oldfield, 0 Emsley, 5991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1485 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 341 poor density : 1144 time to evaluate : 6.280 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: c 23 TYR cc_start: 0.7292 (t80) cc_final: 0.7032 (t80) REVERT: h 3 MET cc_start: 0.4855 (mmm) cc_final: 0.2491 (tpp) REVERT: h 31 LYS cc_start: 0.7806 (mmmt) cc_final: 0.7593 (mmmm) REVERT: i 77 ARG cc_start: 0.6331 (mpp80) cc_final: 0.5856 (mtt180) REVERT: i 80 GLN cc_start: 0.6701 (pp30) cc_final: 0.6450 (pp30) REVERT: j 57 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.7480 (pptt) REVERT: l 46 ASN cc_start: 0.5995 (t0) cc_final: 0.5548 (p0) REVERT: s 66 MET cc_start: 0.6888 (OUTLIER) cc_final: 0.6392 (mmp) REVERT: t 11 ILE cc_start: 0.7552 (mt) cc_final: 0.6940 (mt) REVERT: t 67 ILE cc_start: 0.7810 (mm) cc_final: 0.7586 (mt) REVERT: n 11 ASN cc_start: 0.5959 (m-40) cc_final: 0.5276 (t0) REVERT: b 6 MET cc_start: 0.6316 (mtp) cc_final: 0.5934 (mtp) REVERT: d 142 GLU cc_start: 0.7042 (mp0) cc_final: 0.6792 (mp0) REVERT: f 66 LYS cc_start: 0.8567 (ttmm) cc_final: 0.7973 (tmtt) REVERT: m 99 ARG cc_start: 0.7267 (mmt90) cc_final: 0.6634 (ttm170) REVERT: p 48 LEU cc_start: 0.7687 (tp) cc_final: 0.7469 (mm) REVERT: u 8 ARG cc_start: 0.6541 (mtp-110) cc_final: 0.6145 (mtp85) REVERT: u 10 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7567 (tptt) REVERT: C 118 GLU cc_start: 0.6073 (pm20) cc_final: 0.5706 (pm20) REVERT: C 148 ARG cc_start: 0.8284 (mtp-110) cc_final: 0.7832 (mtp180) REVERT: D 20 ASN cc_start: 0.6420 (OUTLIER) cc_final: 0.6156 (p0) REVERT: D 142 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7572 (tt0) REVERT: E 201 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8583 (tt) REVERT: F 111 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7685 (mt) REVERT: G 41 ILE cc_start: 0.5768 (OUTLIER) cc_final: 0.5536 (mt) REVERT: G 60 ARG cc_start: 0.7085 (ttp-110) cc_final: 0.6615 (ptm160) REVERT: G 76 LEU cc_start: 0.6734 (tp) cc_final: 0.6528 (mm) REVERT: G 98 GLN cc_start: 0.7057 (pt0) cc_final: 0.6569 (mt0) REVERT: G 108 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7397 (mt) REVERT: G 130 THR cc_start: 0.7435 (p) cc_final: 0.7144 (t) REVERT: G 146 SER cc_start: 0.7380 (OUTLIER) cc_final: 0.7049 (t) REVERT: H 1 MET cc_start: 0.6904 (ttm) cc_final: 0.6684 (ttp) REVERT: N 5 ARG cc_start: 0.7748 (tmm-80) cc_final: 0.7038 (mtm110) REVERT: N 92 TRP cc_start: 0.6898 (OUTLIER) cc_final: 0.6675 (p90) REVERT: N 110 ASP cc_start: 0.6428 (OUTLIER) cc_final: 0.5971 (p0) REVERT: P 58 THR cc_start: 0.7866 (p) cc_final: 0.7595 (t) REVERT: R 37 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8314 (mt-10) REVERT: T 85 GLU cc_start: 0.7790 (tp30) cc_final: 0.7555 (tp30) REVERT: W 113 LEU cc_start: 0.7941 (tp) cc_final: 0.7447 (mt) REVERT: W 145 THR cc_start: 0.7728 (m) cc_final: 0.7527 (t) REVERT: Y 37 ARG cc_start: 0.8361 (mtt-85) cc_final: 0.7723 (mmt180) REVERT: Y 57 LYS cc_start: 0.8477 (tttt) cc_final: 0.7361 (tptt) REVERT: 4 23 TYR cc_start: 0.6507 (OUTLIER) cc_final: 0.5547 (t80) REVERT: 7 19 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8119 (mtt-85) REVERT: 8 6 ARG cc_start: 0.8489 (ttp-110) cc_final: 0.8273 (ttp-110) REVERT: 8 15 LYS cc_start: 0.8813 (tmtp) cc_final: 0.8105 (tppt) REVERT: 8 17 ASN cc_start: 0.8460 (m110) cc_final: 0.8069 (m-40) outliers start: 341 outliers final: 218 residues processed: 1337 average time/residue: 1.4044 time to fit residues: 3181.4061 Evaluate side-chains 1304 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 1072 time to evaluate : 6.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 90 LEU Chi-restraints excluded: chain c residue 117 GLN Chi-restraints excluded: chain c residue 200 VAL Chi-restraints excluded: chain e residue 37 ILE Chi-restraints excluded: chain e residue 40 VAL Chi-restraints excluded: chain e residue 64 VAL Chi-restraints excluded: chain e residue 145 VAL Chi-restraints excluded: chain e residue 148 ILE Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain e residue 159 ILE Chi-restraints excluded: chain e residue 171 LEU Chi-restraints excluded: chain g residue 79 ARG Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain h residue 41 LYS Chi-restraints excluded: chain h residue 80 VAL Chi-restraints excluded: chain h residue 91 SER Chi-restraints excluded: chain h residue 123 VAL Chi-restraints excluded: chain h residue 130 TYR Chi-restraints excluded: chain i residue 39 VAL Chi-restraints excluded: chain i residue 54 THR Chi-restraints excluded: chain i residue 68 ILE Chi-restraints excluded: chain i residue 88 ASP Chi-restraints excluded: chain i residue 108 ILE Chi-restraints excluded: chain i residue 147 TYR Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain j residue 57 LYS Chi-restraints excluded: chain j residue 64 HIS Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain k residue 27 HIS Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 67 SER Chi-restraints excluded: chain k residue 93 VAL Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 63 VAL Chi-restraints excluded: chain l residue 80 VAL Chi-restraints excluded: chain o residue 45 VAL Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain q residue 24 ILE Chi-restraints excluded: chain q residue 28 VAL Chi-restraints excluded: chain q residue 37 VAL Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain r residue 64 ILE Chi-restraints excluded: chain s residue 6 LYS Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain s residue 66 MET Chi-restraints excluded: chain s residue 67 VAL Chi-restraints excluded: chain t residue 8 ILE Chi-restraints excluded: chain n residue 4 LYS Chi-restraints excluded: chain n residue 24 CYS Chi-restraints excluded: chain n residue 32 SER Chi-restraints excluded: chain b residue 70 VAL Chi-restraints excluded: chain b residue 117 LEU Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain d residue 9 THR Chi-restraints excluded: chain d residue 50 LEU Chi-restraints excluded: chain d residue 87 ARG Chi-restraints excluded: chain d residue 114 SER Chi-restraints excluded: chain d residue 125 VAL Chi-restraints excluded: chain d residue 147 THR Chi-restraints excluded: chain d residue 196 VAL Chi-restraints excluded: chain f residue 30 ILE Chi-restraints excluded: chain f residue 38 ASP Chi-restraints excluded: chain f residue 93 THR Chi-restraints excluded: chain m residue 4 LEU Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 56 LEU Chi-restraints excluded: chain m residue 66 VAL Chi-restraints excluded: chain m residue 81 LYS Chi-restraints excluded: chain p residue 12 LYS Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 86 LEU Chi-restraints excluded: chain p residue 92 THR Chi-restraints excluded: chain u residue 6 LYS Chi-restraints excluded: chain u residue 10 LYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 266 LYS Chi-restraints excluded: chain D residue 20 ASN Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 142 GLN Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 75 ARG Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 127 GLU Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 83 ILE Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 13 HIS Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 39 HIS Chi-restraints excluded: chain N residue 41 TYR Chi-restraints excluded: chain N residue 42 ILE Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 92 TRP Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain N residue 112 LYS Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 15 SER Chi-restraints excluded: chain O residue 18 SER Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain P residue 28 LYS Chi-restraints excluded: chain P residue 43 SER Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 56 ASN Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 30 LYS Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 103 LYS Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 42 ILE Chi-restraints excluded: chain T residue 78 VAL Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain U residue 9 ASP Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 15 VAL Chi-restraints excluded: chain U residue 37 SER Chi-restraints excluded: chain U residue 38 ASN Chi-restraints excluded: chain U residue 46 ILE Chi-restraints excluded: chain U residue 79 THR Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain U residue 93 ILE Chi-restraints excluded: chain V residue 8 THR Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain V residue 86 ARG Chi-restraints excluded: chain V residue 95 VAL Chi-restraints excluded: chain W residue 12 THR Chi-restraints excluded: chain W residue 14 ASN Chi-restraints excluded: chain W residue 17 THR Chi-restraints excluded: chain W residue 19 THR Chi-restraints excluded: chain W residue 53 ASP Chi-restraints excluded: chain W residue 68 THR Chi-restraints excluded: chain W residue 122 THR Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain X residue 80 ILE Chi-restraints excluded: chain Z residue 5 THR Chi-restraints excluded: chain Z residue 25 SER Chi-restraints excluded: chain Z residue 49 THR Chi-restraints excluded: chain 1 residue 4 LEU Chi-restraints excluded: chain 1 residue 7 THR Chi-restraints excluded: chain 1 residue 11 SER Chi-restraints excluded: chain 1 residue 31 ILE Chi-restraints excluded: chain 1 residue 36 VAL Chi-restraints excluded: chain 1 residue 49 THR Chi-restraints excluded: chain 2 residue 13 THR Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 3 residue 3 VAL Chi-restraints excluded: chain 3 residue 15 SER Chi-restraints excluded: chain 3 residue 29 THR Chi-restraints excluded: chain 3 residue 31 SER Chi-restraints excluded: chain 3 residue 52 VAL Chi-restraints excluded: chain 4 residue 23 TYR Chi-restraints excluded: chain 4 residue 39 LYS Chi-restraints excluded: chain 5 residue 45 LEU Chi-restraints excluded: chain 6 residue 12 LYS Chi-restraints excluded: chain 6 residue 59 ASN Chi-restraints excluded: chain 7 residue 19 ARG Chi-restraints excluded: chain 7 residue 26 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1066 random chunks: chunk 346 optimal weight: 0.7980 chunk 927 optimal weight: 10.0000 chunk 203 optimal weight: 9.9990 chunk 604 optimal weight: 0.9990 chunk 254 optimal weight: 8.9990 chunk 1031 optimal weight: 0.6980 chunk 856 optimal weight: 5.9990 chunk 477 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 341 optimal weight: 0.8980 chunk 541 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 95 GLN k 37 ASN ** k 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 68 HIS ** f 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS E 182 GLN ** E 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 ASN G 86 GLN G 103 ASN K 136 GLN ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 41 ASN T 66 GLN ** W 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 29 GLN 2 15 GLN 4 51 HIS 8 13 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 163342 Z= 0.149 Angle : 0.604 17.975 244537 Z= 0.306 Chirality : 0.034 0.315 31270 Planarity : 0.005 0.167 13186 Dihedral : 24.291 179.991 82365 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.44 % Favored : 93.26 % Rotamer: Outliers : 4.04 % Allowed : 21.75 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.12 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.11), residues: 5991 helix: 0.44 (0.12), residues: 2007 sheet: -1.14 (0.16), residues: 1027 loop : -1.76 (0.11), residues: 2957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 206 HIS 0.007 0.001 HIS D 183 PHE 0.026 0.002 PHE c 10 TYR 0.025 0.001 TYR c 184 ARG 0.013 0.001 ARG l 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11982 Ramachandran restraints generated. 5991 Oldfield, 0 Emsley, 5991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11982 Ramachandran restraints generated. 5991 Oldfield, 0 Emsley, 5991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1311 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 1111 time to evaluate : 6.269 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: c 55 GLU cc_start: 0.6262 (tm-30) cc_final: 0.5839 (tm-30) REVERT: g 1 MET cc_start: 0.0218 (OUTLIER) cc_final: -0.0768 (tpt) REVERT: i 77 ARG cc_start: 0.6014 (mpp80) cc_final: 0.5769 (mtt180) REVERT: i 81 PHE cc_start: 0.7276 (OUTLIER) cc_final: 0.6573 (t80) REVERT: i 87 LEU cc_start: 0.5931 (OUTLIER) cc_final: 0.5696 (pp) REVERT: j 57 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7329 (pptt) REVERT: q 35 THR cc_start: 0.6966 (OUTLIER) cc_final: 0.6723 (t) REVERT: s 6 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.6974 (mmmt) REVERT: n 4 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7955 (mtmt) REVERT: n 47 MET cc_start: 0.7591 (mtp) cc_final: 0.7346 (mtp) REVERT: b 6 MET cc_start: 0.6097 (mtp) cc_final: 0.5722 (mtp) REVERT: b 89 MET cc_start: 0.5683 (mmm) cc_final: 0.5211 (mmm) REVERT: b 100 MET cc_start: 0.5304 (mtt) cc_final: 0.4841 (ptp) REVERT: d 43 GLU cc_start: 0.5411 (mp0) cc_final: 0.5138 (tp30) REVERT: d 119 LEU cc_start: 0.6414 (OUTLIER) cc_final: 0.6209 (mp) REVERT: d 182 GLU cc_start: 0.6981 (mt-10) cc_final: 0.6562 (mt-10) REVERT: f 66 LYS cc_start: 0.8457 (ttmm) cc_final: 0.7844 (tmtt) REVERT: m 43 MET cc_start: 0.7710 (mtm) cc_final: 0.7194 (ptm) REVERT: m 58 ASP cc_start: 0.8456 (m-30) cc_final: 0.8126 (m-30) REVERT: m 99 ARG cc_start: 0.7233 (mmt90) cc_final: 0.6534 (ttm170) REVERT: u 8 ARG cc_start: 0.6294 (mtp-110) cc_final: 0.5889 (mtp85) REVERT: u 10 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.7432 (tptt) REVERT: C 88 ARG cc_start: 0.8460 (mmt-90) cc_final: 0.7411 (mmt-90) REVERT: D 142 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7507 (tt0) REVERT: E 75 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8052 (pmt170) REVERT: G 41 ILE cc_start: 0.5674 (OUTLIER) cc_final: 0.5471 (mt) REVERT: G 60 ARG cc_start: 0.7036 (ttp-110) cc_final: 0.6630 (ptm160) REVERT: G 98 GLN cc_start: 0.7018 (pt0) cc_final: 0.6544 (mt0) REVERT: G 130 THR cc_start: 0.7199 (p) cc_final: 0.6921 (t) REVERT: H 1 MET cc_start: 0.6644 (ttm) cc_final: 0.6442 (ttp) REVERT: I 101 LYS cc_start: 0.4652 (mmtt) cc_final: 0.4443 (mmpt) REVERT: K 54 VAL cc_start: 0.9215 (p) cc_final: 0.8964 (t) REVERT: K 108 MET cc_start: 0.8446 (mmt) cc_final: 0.7720 (mmt) REVERT: L 65 THR cc_start: 0.8872 (p) cc_final: 0.8568 (t) REVERT: L 97 ARG cc_start: 0.8173 (ptm160) cc_final: 0.7642 (ttp-170) REVERT: M 21 ARG cc_start: 0.8322 (mtp85) cc_final: 0.8027 (mtp85) REVERT: M 24 ARG cc_start: 0.8703 (mmt-90) cc_final: 0.7545 (mmt-90) REVERT: N 5 ARG cc_start: 0.7577 (tmm-80) cc_final: 0.6989 (mtm110) REVERT: N 110 ASP cc_start: 0.6278 (OUTLIER) cc_final: 0.5870 (p0) REVERT: P 58 THR cc_start: 0.7791 (p) cc_final: 0.7493 (t) REVERT: P 109 TYR cc_start: 0.8342 (t80) cc_final: 0.8080 (t80) REVERT: Q 24 THR cc_start: 0.9067 (m) cc_final: 0.8867 (t) REVERT: R 37 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8189 (mt-10) REVERT: S 95 THR cc_start: 0.8841 (m) cc_final: 0.8600 (m) REVERT: U 12 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.7012 (pt) REVERT: W 100 VAL cc_start: 0.6738 (m) cc_final: 0.6494 (p) REVERT: W 113 LEU cc_start: 0.7879 (tp) cc_final: 0.7657 (mp) REVERT: Y 37 ARG cc_start: 0.8114 (mtt-85) cc_final: 0.7608 (mmt180) REVERT: Y 57 LYS cc_start: 0.8513 (tttt) cc_final: 0.7356 (tptt) REVERT: Z 36 MET cc_start: 0.5685 (tpp) cc_final: 0.5436 (mmt) REVERT: 2 61 PHE cc_start: 0.5504 (OUTLIER) cc_final: 0.4689 (m-80) REVERT: 4 23 TYR cc_start: 0.5984 (OUTLIER) cc_final: 0.5633 (t80) REVERT: 5 28 ARG cc_start: 0.8397 (tpp80) cc_final: 0.8089 (ttm-80) REVERT: 8 15 LYS cc_start: 0.8476 (tmtp) cc_final: 0.8011 (tppt) REVERT: 8 17 ASN cc_start: 0.8285 (m110) cc_final: 0.8008 (m-40) outliers start: 200 outliers final: 124 residues processed: 1223 average time/residue: 1.4187 time to fit residues: 2925.7052 Evaluate side-chains 1177 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 1037 time to evaluate : 6.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 117 GLN Chi-restraints excluded: chain e residue 40 VAL Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 96 PHE Chi-restraints excluded: chain e residue 145 VAL Chi-restraints excluded: chain e residue 159 ILE Chi-restraints excluded: chain e residue 171 LEU Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain g residue 31 LEU Chi-restraints excluded: chain h residue 41 LYS Chi-restraints excluded: chain i residue 39 VAL Chi-restraints excluded: chain i residue 54 THR Chi-restraints excluded: chain i residue 81 PHE Chi-restraints excluded: chain i residue 87 LEU Chi-restraints excluded: chain i residue 88 ASP Chi-restraints excluded: chain i residue 108 ILE Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain j residue 57 LYS Chi-restraints excluded: chain j residue 64 HIS Chi-restraints excluded: chain k residue 27 HIS Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 37 VAL Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain s residue 6 LYS Chi-restraints excluded: chain s residue 23 ASN Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain t residue 15 GLU Chi-restraints excluded: chain n residue 4 LYS Chi-restraints excluded: chain n residue 8 HIS Chi-restraints excluded: chain b residue 70 VAL Chi-restraints excluded: chain d residue 50 LEU Chi-restraints excluded: chain d residue 86 LEU Chi-restraints excluded: chain d residue 91 SER Chi-restraints excluded: chain d residue 94 ASP Chi-restraints excluded: chain d residue 119 LEU Chi-restraints excluded: chain d residue 147 THR Chi-restraints excluded: chain d residue 152 ILE Chi-restraints excluded: chain d residue 154 ARG Chi-restraints excluded: chain f residue 18 THR Chi-restraints excluded: chain f residue 30 ILE Chi-restraints excluded: chain f residue 93 THR Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 66 VAL Chi-restraints excluded: chain p residue 12 LYS Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 92 THR Chi-restraints excluded: chain u residue 6 LYS Chi-restraints excluded: chain u residue 10 LYS Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 266 LYS Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 142 GLN Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 75 ARG Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 127 GLU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 39 HIS Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 18 SER Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain P residue 43 SER Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 56 ASN Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain S residue 103 LYS Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain U residue 9 ASP Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 15 VAL Chi-restraints excluded: chain U residue 37 SER Chi-restraints excluded: chain U residue 38 ASN Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain U residue 93 ILE Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain V residue 86 ARG Chi-restraints excluded: chain W residue 14 ASN Chi-restraints excluded: chain W residue 19 THR Chi-restraints excluded: chain W residue 53 ASP Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 122 THR Chi-restraints excluded: chain W residue 140 ILE Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain Z residue 5 THR Chi-restraints excluded: chain 1 residue 11 SER Chi-restraints excluded: chain 2 residue 13 THR Chi-restraints excluded: chain 2 residue 61 PHE Chi-restraints excluded: chain 2 residue 62 GLU Chi-restraints excluded: chain 3 residue 3 VAL Chi-restraints excluded: chain 3 residue 15 SER Chi-restraints excluded: chain 3 residue 29 THR Chi-restraints excluded: chain 3 residue 31 SER Chi-restraints excluded: chain 4 residue 7 VAL Chi-restraints excluded: chain 4 residue 23 TYR Chi-restraints excluded: chain 4 residue 39 LYS Chi-restraints excluded: chain 6 residue 11 SER Chi-restraints excluded: chain 6 residue 62 LEU Chi-restraints excluded: chain 7 residue 26 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1066 random chunks: chunk 994 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 587 optimal weight: 1.9990 chunk 753 optimal weight: 20.0000 chunk 583 optimal weight: 0.9990 chunk 868 optimal weight: 10.0000 chunk 575 optimal weight: 6.9990 chunk 1027 optimal weight: 10.0000 chunk 642 optimal weight: 0.3980 chunk 626 optimal weight: 0.9980 chunk 474 optimal weight: 5.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 35 ASN ** i 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 51 GLN ** d 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 178 HIS ** f 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 ASN ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 HIS ** N 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 66 GLN ** V 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 29 GLN 2 15 GLN 8 13 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 163342 Z= 0.209 Angle : 0.609 12.175 244537 Z= 0.308 Chirality : 0.035 0.282 31270 Planarity : 0.005 0.095 13186 Dihedral : 24.187 179.775 82361 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.56 % Favored : 92.17 % Rotamer: Outliers : 4.27 % Allowed : 22.46 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.75 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.11), residues: 5991 helix: 0.54 (0.12), residues: 2013 sheet: -1.11 (0.16), residues: 1049 loop : -1.70 (0.11), residues: 2929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP s 34 HIS 0.007 0.001 HIS e 108 PHE 0.026 0.002 PHE c 10 TYR 0.026 0.002 TYR c 184 ARG 0.013 0.001 ARG U 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11982 Ramachandran restraints generated. 5991 Oldfield, 0 Emsley, 5991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11982 Ramachandran restraints generated. 5991 Oldfield, 0 Emsley, 5991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1285 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 1074 time to evaluate : 5.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 150 ARG cc_start: 0.7141 (ttm-80) cc_final: 0.6720 (ttp-170) REVERT: e 194 MET cc_start: 0.6872 (ppp) cc_final: 0.6467 (mtm) REVERT: g 1 MET cc_start: 0.0491 (OUTLIER) cc_final: -0.0631 (tpt) REVERT: i 62 LYS cc_start: 0.5272 (OUTLIER) cc_final: 0.4962 (mptt) REVERT: i 77 ARG cc_start: 0.6063 (mpp80) cc_final: 0.5725 (mtt180) REVERT: i 81 PHE cc_start: 0.7022 (OUTLIER) cc_final: 0.6393 (t80) REVERT: i 87 LEU cc_start: 0.6166 (OUTLIER) cc_final: 0.5923 (pp) REVERT: j 57 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7378 (pptt) REVERT: j 88 MET cc_start: 0.4554 (tpp) cc_final: 0.4203 (tpp) REVERT: q 35 THR cc_start: 0.7156 (t) cc_final: 0.6919 (t) REVERT: n 4 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7983 (mttt) REVERT: b 6 MET cc_start: 0.6132 (mtp) cc_final: 0.5749 (mtp) REVERT: b 89 MET cc_start: 0.5676 (mmm) cc_final: 0.5233 (mmm) REVERT: d 43 GLU cc_start: 0.5358 (mp0) cc_final: 0.5109 (tp30) REVERT: d 150 PHE cc_start: 0.6382 (t80) cc_final: 0.6000 (t80) REVERT: d 182 GLU cc_start: 0.6986 (mt-10) cc_final: 0.6555 (mp0) REVERT: d 192 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6506 (pt0) REVERT: m 58 ASP cc_start: 0.8491 (m-30) cc_final: 0.8175 (m-30) REVERT: m 99 ARG cc_start: 0.7250 (mmt90) cc_final: 0.6511 (ttm170) REVERT: p 21 ILE cc_start: 0.7709 (tp) cc_final: 0.7452 (tp) REVERT: u 10 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7485 (tptt) REVERT: C 88 ARG cc_start: 0.8633 (mmt-90) cc_final: 0.7583 (mmt-90) REVERT: D 135 GLN cc_start: 0.8683 (mt0) cc_final: 0.8445 (mt0) REVERT: D 142 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7455 (tt0) REVERT: F 182 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.7632 (t80) REVERT: G 41 ILE cc_start: 0.5742 (OUTLIER) cc_final: 0.5537 (mt) REVERT: G 60 ARG cc_start: 0.7055 (ttp-110) cc_final: 0.6636 (ptm160) REVERT: G 98 GLN cc_start: 0.7035 (pt0) cc_final: 0.6521 (mt0) REVERT: G 130 THR cc_start: 0.7114 (p) cc_final: 0.6828 (t) REVERT: M 21 ARG cc_start: 0.8271 (mtp85) cc_final: 0.7720 (mtp85) REVERT: M 24 ARG cc_start: 0.8724 (mmt-90) cc_final: 0.7593 (mmt-90) REVERT: N 5 ARG cc_start: 0.7637 (tmm-80) cc_final: 0.7158 (mtm110) REVERT: N 110 ASP cc_start: 0.6315 (OUTLIER) cc_final: 0.5732 (p0) REVERT: P 58 THR cc_start: 0.7870 (p) cc_final: 0.7567 (t) REVERT: P 109 TYR cc_start: 0.8464 (t80) cc_final: 0.8224 (t80) REVERT: Q 24 THR cc_start: 0.9058 (m) cc_final: 0.8823 (t) REVERT: Q 71 ARG cc_start: 0.8947 (ttt90) cc_final: 0.8738 (ttt90) REVERT: R 31 LEU cc_start: 0.8756 (mt) cc_final: 0.8540 (mt) REVERT: R 37 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8150 (mt-10) REVERT: U 12 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.7150 (pt) REVERT: W 58 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7208 (mp) REVERT: W 68 THR cc_start: 0.8668 (OUTLIER) cc_final: 0.8427 (m) REVERT: W 113 LEU cc_start: 0.7915 (tp) cc_final: 0.7633 (mp) REVERT: W 145 THR cc_start: 0.7723 (m) cc_final: 0.7482 (t) REVERT: Y 37 ARG cc_start: 0.8185 (mtt-85) cc_final: 0.7584 (mmt180) REVERT: Z 13 LEU cc_start: 0.6804 (tp) cc_final: 0.6132 (tp) REVERT: 2 61 PHE cc_start: 0.5585 (OUTLIER) cc_final: 0.4739 (m-80) REVERT: 4 23 TYR cc_start: 0.6210 (OUTLIER) cc_final: 0.5677 (t80) REVERT: 8 6 ARG cc_start: 0.8454 (ttp-110) cc_final: 0.8077 (ttp-110) REVERT: 8 15 LYS cc_start: 0.8564 (tmtp) cc_final: 0.8049 (tppt) REVERT: 8 17 ASN cc_start: 0.8329 (m110) cc_final: 0.8033 (m-40) outliers start: 211 outliers final: 153 residues processed: 1188 average time/residue: 1.4178 time to fit residues: 2842.1085 Evaluate side-chains 1203 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1033 time to evaluate : 6.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 117 GLN Chi-restraints excluded: chain c residue 200 VAL Chi-restraints excluded: chain e residue 38 GLU Chi-restraints excluded: chain e residue 40 VAL Chi-restraints excluded: chain e residue 120 MET Chi-restraints excluded: chain e residue 145 VAL Chi-restraints excluded: chain e residue 148 ILE Chi-restraints excluded: chain e residue 159 ILE Chi-restraints excluded: chain e residue 171 LEU Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain h residue 80 VAL Chi-restraints excluded: chain h residue 130 TYR Chi-restraints excluded: chain i residue 39 VAL Chi-restraints excluded: chain i residue 54 THR Chi-restraints excluded: chain i residue 62 LYS Chi-restraints excluded: chain i residue 81 PHE Chi-restraints excluded: chain i residue 87 LEU Chi-restraints excluded: chain i residue 88 ASP Chi-restraints excluded: chain i residue 108 ILE Chi-restraints excluded: chain i residue 124 LEU Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain j residue 57 LYS Chi-restraints excluded: chain j residue 64 HIS Chi-restraints excluded: chain k residue 27 HIS Chi-restraints excluded: chain k residue 67 SER Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain q residue 24 ILE Chi-restraints excluded: chain q residue 37 VAL Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain q residue 76 LEU Chi-restraints excluded: chain s residue 6 LYS Chi-restraints excluded: chain s residue 23 ASN Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain t residue 15 GLU Chi-restraints excluded: chain n residue 4 LYS Chi-restraints excluded: chain n residue 8 HIS Chi-restraints excluded: chain b residue 70 VAL Chi-restraints excluded: chain b residue 117 LEU Chi-restraints excluded: chain d residue 9 THR Chi-restraints excluded: chain d residue 50 LEU Chi-restraints excluded: chain d residue 86 LEU Chi-restraints excluded: chain d residue 91 SER Chi-restraints excluded: chain d residue 94 ASP Chi-restraints excluded: chain d residue 125 VAL Chi-restraints excluded: chain d residue 147 THR Chi-restraints excluded: chain d residue 152 ILE Chi-restraints excluded: chain d residue 154 ARG Chi-restraints excluded: chain d residue 192 GLU Chi-restraints excluded: chain f residue 18 THR Chi-restraints excluded: chain f residue 30 ILE Chi-restraints excluded: chain f residue 91 LEU Chi-restraints excluded: chain f residue 93 THR Chi-restraints excluded: chain m residue 4 LEU Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 66 VAL Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain m residue 98 VAL Chi-restraints excluded: chain p residue 12 LYS Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 86 LEU Chi-restraints excluded: chain p residue 92 THR Chi-restraints excluded: chain u residue 6 LYS Chi-restraints excluded: chain u residue 10 LYS Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 266 LYS Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 142 GLN Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 75 ARG Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 182 PHE Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 127 GLU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 13 HIS Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 18 SER Chi-restraints excluded: chain O residue 35 LYS Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain P residue 43 SER Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 56 ASN Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain S residue 103 LYS Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 42 ILE Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain U residue 9 ASP Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 15 VAL Chi-restraints excluded: chain U residue 37 SER Chi-restraints excluded: chain U residue 38 ASN Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain U residue 90 SER Chi-restraints excluded: chain U residue 93 ILE Chi-restraints excluded: chain V residue 23 VAL Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 86 ARG Chi-restraints excluded: chain V residue 101 ASN Chi-restraints excluded: chain W residue 12 THR Chi-restraints excluded: chain W residue 14 ASN Chi-restraints excluded: chain W residue 17 THR Chi-restraints excluded: chain W residue 53 ASP Chi-restraints excluded: chain W residue 58 LEU Chi-restraints excluded: chain W residue 68 THR Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 122 THR Chi-restraints excluded: chain W residue 140 ILE Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain Z residue 5 THR Chi-restraints excluded: chain 1 residue 11 SER Chi-restraints excluded: chain 1 residue 31 ILE Chi-restraints excluded: chain 2 residue 13 THR Chi-restraints excluded: chain 2 residue 61 PHE Chi-restraints excluded: chain 3 residue 3 VAL Chi-restraints excluded: chain 3 residue 15 SER Chi-restraints excluded: chain 3 residue 31 SER Chi-restraints excluded: chain 4 residue 23 TYR Chi-restraints excluded: chain 4 residue 39 LYS Chi-restraints excluded: chain 6 residue 12 LYS Chi-restraints excluded: chain 6 residue 59 ASN Chi-restraints excluded: chain 6 residue 62 LEU Chi-restraints excluded: chain 7 residue 26 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1066 random chunks: chunk 635 optimal weight: 6.9990 chunk 410 optimal weight: 2.9990 chunk 613 optimal weight: 0.4980 chunk 309 optimal weight: 5.9990 chunk 201 optimal weight: 2.9990 chunk 199 optimal weight: 0.8980 chunk 653 optimal weight: 0.4980 chunk 699 optimal weight: 1.9990 chunk 507 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 807 optimal weight: 6.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 51 GLN ** d 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 146 ASN ** f 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 GLN ** F 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 ASN ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 66 GLN ** W 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 34 GLN 2 15 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 163342 Z= 0.165 Angle : 0.584 11.312 244537 Z= 0.296 Chirality : 0.033 0.281 31270 Planarity : 0.005 0.093 13186 Dihedral : 24.178 179.924 82361 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.68 % Favored : 93.06 % Rotamer: Outliers : 3.94 % Allowed : 22.66 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.75 % 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: -1.11 (0.11), residues: 5991 helix: 0.64 (0.12), residues: 2022 sheet: -1.02 (0.16), residues: 1022 loop : -1.63 (0.11), residues: 2947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP b 96 HIS 0.041 0.001 HIS N 13 PHE 0.023 0.002 PHE c 10 TYR 0.028 0.001 TYR c 184 ARG 0.015 0.001 ARG E 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11982 Ramachandran restraints generated. 5991 Oldfield, 0 Emsley, 5991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11982 Ramachandran restraints generated. 5991 Oldfield, 0 Emsley, 5991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1250 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 1055 time to evaluate : 6.212 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: c 55 GLU cc_start: 0.6338 (tm-30) cc_final: 0.5824 (tm-30) REVERT: c 150 ARG cc_start: 0.7115 (ttm-80) cc_final: 0.6746 (ttp-170) REVERT: e 194 MET cc_start: 0.7111 (ppp) cc_final: 0.6617 (mtm) REVERT: g 1 MET cc_start: 0.0271 (OUTLIER) cc_final: -0.0746 (tpt) REVERT: i 62 LYS cc_start: 0.5222 (OUTLIER) cc_final: 0.4905 (mptt) REVERT: i 77 ARG cc_start: 0.6043 (mpp80) cc_final: 0.5520 (mtt180) REVERT: i 81 PHE cc_start: 0.6948 (OUTLIER) cc_final: 0.6388 (t80) REVERT: i 87 LEU cc_start: 0.6127 (OUTLIER) cc_final: 0.5927 (pp) REVERT: j 57 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7249 (pptt) REVERT: q 35 THR cc_start: 0.7109 (t) cc_final: 0.6890 (t) REVERT: s 66 MET cc_start: 0.6143 (mmp) cc_final: 0.5877 (mmt) REVERT: n 4 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7976 (mttt) REVERT: b 6 MET cc_start: 0.6103 (mtp) cc_final: 0.5710 (mtp) REVERT: b 89 MET cc_start: 0.5632 (mmm) cc_final: 0.5192 (mmm) REVERT: d 43 GLU cc_start: 0.5381 (mp0) cc_final: 0.5113 (tp30) REVERT: d 94 ASP cc_start: 0.5791 (OUTLIER) cc_final: 0.5453 (m-30) REVERT: d 150 PHE cc_start: 0.6351 (t80) cc_final: 0.5997 (t80) REVERT: d 182 GLU cc_start: 0.7032 (mt-10) cc_final: 0.6633 (mp0) REVERT: m 58 ASP cc_start: 0.8489 (m-30) cc_final: 0.8234 (m-30) REVERT: m 99 ARG cc_start: 0.7237 (mmt90) cc_final: 0.6501 (ttm170) REVERT: p 21 ILE cc_start: 0.7695 (tp) cc_final: 0.7448 (tp) REVERT: p 40 TYR cc_start: 0.7537 (t80) cc_final: 0.7312 (t80) REVERT: u 10 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7470 (tptt) REVERT: D 135 GLN cc_start: 0.8617 (mt0) cc_final: 0.8391 (mt0) REVERT: D 142 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7529 (tt0) REVERT: F 182 PHE cc_start: 0.8018 (OUTLIER) cc_final: 0.7441 (t80) REVERT: G 41 ILE cc_start: 0.5743 (OUTLIER) cc_final: 0.5525 (mt) REVERT: G 60 ARG cc_start: 0.7021 (ttp-110) cc_final: 0.6596 (ptm160) REVERT: G 98 GLN cc_start: 0.7011 (pt0) cc_final: 0.6524 (mt0) REVERT: G 130 THR cc_start: 0.7193 (p) cc_final: 0.6894 (t) REVERT: G 170 ILE cc_start: 0.5628 (OUTLIER) cc_final: 0.5026 (tp) REVERT: I 101 LYS cc_start: 0.4759 (mmtt) cc_final: 0.4251 (mmpt) REVERT: K 54 VAL cc_start: 0.9231 (p) cc_final: 0.8948 (t) REVERT: L 97 ARG cc_start: 0.8124 (ptm160) cc_final: 0.7677 (ttp-170) REVERT: M 21 ARG cc_start: 0.8181 (mtp85) cc_final: 0.7777 (mtp85) REVERT: M 24 ARG cc_start: 0.8692 (mmt-90) cc_final: 0.7649 (mmt-90) REVERT: N 5 ARG cc_start: 0.7608 (tmm-80) cc_final: 0.6998 (mtm110) REVERT: P 58 THR cc_start: 0.7871 (p) cc_final: 0.7542 (t) REVERT: P 109 TYR cc_start: 0.8416 (t80) cc_final: 0.8116 (t80) REVERT: Q 30 LYS cc_start: 0.8200 (mtpt) cc_final: 0.7938 (ptmm) REVERT: R 37 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8129 (mt-10) REVERT: S 95 THR cc_start: 0.8844 (m) cc_final: 0.8574 (m) REVERT: U 12 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.7064 (pt) REVERT: W 58 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7153 (mp) REVERT: W 113 LEU cc_start: 0.7886 (tp) cc_final: 0.7650 (mp) REVERT: W 145 THR cc_start: 0.7685 (m) cc_final: 0.7435 (t) REVERT: Y 37 ARG cc_start: 0.8148 (mtt-85) cc_final: 0.7565 (mmt180) REVERT: 2 61 PHE cc_start: 0.5438 (OUTLIER) cc_final: 0.4585 (m-80) REVERT: 4 23 TYR cc_start: 0.6090 (OUTLIER) cc_final: 0.5716 (t80) REVERT: 8 6 ARG cc_start: 0.8430 (ttp-110) cc_final: 0.7933 (ttp-110) REVERT: 8 15 LYS cc_start: 0.8554 (tmtp) cc_final: 0.8008 (tppt) REVERT: 8 17 ASN cc_start: 0.8304 (m110) cc_final: 0.7973 (m-40) outliers start: 195 outliers final: 152 residues processed: 1165 average time/residue: 1.3765 time to fit residues: 2714.4868 Evaluate side-chains 1194 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 1026 time to evaluate : 5.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 117 GLN Chi-restraints excluded: chain c residue 200 VAL Chi-restraints excluded: chain e residue 38 GLU Chi-restraints excluded: chain e residue 40 VAL Chi-restraints excluded: chain e residue 96 PHE Chi-restraints excluded: chain e residue 120 MET Chi-restraints excluded: chain e residue 140 LEU Chi-restraints excluded: chain e residue 145 VAL Chi-restraints excluded: chain e residue 159 ILE Chi-restraints excluded: chain e residue 171 LEU Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain h residue 41 LYS Chi-restraints excluded: chain h residue 80 VAL Chi-restraints excluded: chain h residue 130 TYR Chi-restraints excluded: chain i residue 39 VAL Chi-restraints excluded: chain i residue 54 THR Chi-restraints excluded: chain i residue 62 LYS Chi-restraints excluded: chain i residue 81 PHE Chi-restraints excluded: chain i residue 87 LEU Chi-restraints excluded: chain i residue 88 ASP Chi-restraints excluded: chain i residue 103 ILE Chi-restraints excluded: chain i residue 108 ILE Chi-restraints excluded: chain i residue 124 LEU Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain j residue 57 LYS Chi-restraints excluded: chain j residue 64 HIS Chi-restraints excluded: chain k residue 27 HIS Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain q residue 24 ILE Chi-restraints excluded: chain q residue 37 VAL Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain q residue 76 LEU Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 21 VAL Chi-restraints excluded: chain s residue 23 ASN Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain t residue 15 GLU Chi-restraints excluded: chain n residue 4 LYS Chi-restraints excluded: chain n residue 8 HIS Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain b residue 117 LEU Chi-restraints excluded: chain d residue 9 THR Chi-restraints excluded: chain d residue 50 LEU Chi-restraints excluded: chain d residue 86 LEU Chi-restraints excluded: chain d residue 91 SER Chi-restraints excluded: chain d residue 94 ASP Chi-restraints excluded: chain d residue 125 VAL Chi-restraints excluded: chain d residue 147 THR Chi-restraints excluded: chain d residue 152 ILE Chi-restraints excluded: chain d residue 154 ARG Chi-restraints excluded: chain f residue 18 THR Chi-restraints excluded: chain f residue 30 ILE Chi-restraints excluded: chain f residue 91 LEU Chi-restraints excluded: chain f residue 93 THR Chi-restraints excluded: chain m residue 4 LEU Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 66 VAL Chi-restraints excluded: chain m residue 98 VAL Chi-restraints excluded: chain p residue 12 LYS Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 92 THR Chi-restraints excluded: chain u residue 6 LYS Chi-restraints excluded: chain u residue 10 LYS Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 266 LYS Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 142 GLN Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 75 ARG Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 182 PHE Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 127 GLU Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 114 LYS Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 13 HIS Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 18 SER Chi-restraints excluded: chain O residue 35 LYS Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 56 ASN Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain S residue 103 LYS Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 42 ILE Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain U residue 9 ASP Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 15 VAL Chi-restraints excluded: chain U residue 37 SER Chi-restraints excluded: chain U residue 38 ASN Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain U residue 90 SER Chi-restraints excluded: chain U residue 93 ILE Chi-restraints excluded: chain V residue 23 VAL Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 86 ARG Chi-restraints excluded: chain V residue 101 ASN Chi-restraints excluded: chain W residue 12 THR Chi-restraints excluded: chain W residue 14 ASN Chi-restraints excluded: chain W residue 17 THR Chi-restraints excluded: chain W residue 53 ASP Chi-restraints excluded: chain W residue 58 LEU Chi-restraints excluded: chain W residue 122 THR Chi-restraints excluded: chain W residue 140 ILE Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain Z residue 5 THR Chi-restraints excluded: chain 1 residue 11 SER Chi-restraints excluded: chain 1 residue 36 VAL Chi-restraints excluded: chain 2 residue 13 THR Chi-restraints excluded: chain 2 residue 61 PHE Chi-restraints excluded: chain 3 residue 3 VAL Chi-restraints excluded: chain 3 residue 15 SER Chi-restraints excluded: chain 3 residue 31 SER Chi-restraints excluded: chain 4 residue 23 TYR Chi-restraints excluded: chain 4 residue 39 LYS Chi-restraints excluded: chain 6 residue 11 SER Chi-restraints excluded: chain 6 residue 12 LYS Chi-restraints excluded: chain 6 residue 59 ASN Chi-restraints excluded: chain 6 residue 62 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1066 random chunks: chunk 934 optimal weight: 10.0000 chunk 984 optimal weight: 6.9990 chunk 898 optimal weight: 10.0000 chunk 957 optimal weight: 30.0000 chunk 576 optimal weight: 4.9990 chunk 417 optimal weight: 7.9990 chunk 751 optimal weight: 10.0000 chunk 293 optimal weight: 4.9990 chunk 865 optimal weight: 7.9990 chunk 905 optimal weight: 7.9990 chunk 954 optimal weight: 30.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 72 HIS q 33 GLN r 56 ASN ** d 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 146 ASN ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 ASN ** F 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 ASN ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 66 GLN ** W 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 23 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.4763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.142 163342 Z= 0.517 Angle : 0.873 13.840 244537 Z= 0.431 Chirality : 0.047 0.365 31270 Planarity : 0.007 0.093 13186 Dihedral : 24.307 179.886 82357 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.30 % Favored : 90.39 % Rotamer: Outliers : 5.52 % Allowed : 21.59 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.49 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.10), residues: 5991 helix: 0.09 (0.11), residues: 2009 sheet: -1.34 (0.16), residues: 1022 loop : -1.90 (0.11), residues: 2960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP s 34 HIS 0.019 0.002 HIS N 13 PHE 0.042 0.004 PHE c 10 TYR 0.040 0.003 TYR n 21 ARG 0.013 0.001 ARG 4 8 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11982 Ramachandran restraints generated. 5991 Oldfield, 0 Emsley, 5991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11982 Ramachandran restraints generated. 5991 Oldfield, 0 Emsley, 5991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1363 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 1090 time to evaluate : 6.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 61 ASP cc_start: 0.5070 (p0) cc_final: 0.4619 (p0) REVERT: e 100 PRO cc_start: 0.7768 (Cg_endo) cc_final: 0.7418 (Cg_exo) REVERT: g 1 MET cc_start: 0.0496 (OUTLIER) cc_final: -0.0350 (tpt) REVERT: i 77 ARG cc_start: 0.6051 (mpp80) cc_final: 0.5730 (mtt180) REVERT: i 81 PHE cc_start: 0.7008 (OUTLIER) cc_final: 0.6387 (t80) REVERT: j 57 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.7541 (pptt) REVERT: j 88 MET cc_start: 0.4579 (tpp) cc_final: 0.4222 (tpp) REVERT: k 127 HIS cc_start: 0.4093 (OUTLIER) cc_final: 0.2108 (p90) REVERT: o 17 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7640 (tt) REVERT: s 66 MET cc_start: 0.6443 (mmp) cc_final: 0.6166 (mmt) REVERT: b 6 MET cc_start: 0.6277 (mtp) cc_final: 0.5869 (mtp) REVERT: b 89 MET cc_start: 0.5794 (mmm) cc_final: 0.5384 (mmm) REVERT: d 150 PHE cc_start: 0.6509 (t80) cc_final: 0.6223 (t80) REVERT: d 182 GLU cc_start: 0.7069 (mt-10) cc_final: 0.6825 (mt-10) REVERT: u 10 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7702 (tptt) REVERT: C 88 ARG cc_start: 0.8998 (mmt-90) cc_final: 0.8116 (mmt-90) REVERT: C 148 ARG cc_start: 0.8307 (mtp-110) cc_final: 0.7931 (mtp180) REVERT: C 176 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.7370 (ttp-110) REVERT: D 92 VAL cc_start: 0.8001 (t) cc_final: 0.7740 (t) REVERT: D 142 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7325 (tt0) REVERT: F 182 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.8002 (t80) REVERT: G 41 ILE cc_start: 0.5690 (OUTLIER) cc_final: 0.5460 (mt) REVERT: G 60 ARG cc_start: 0.7131 (ttp-110) cc_final: 0.6654 (ptm160) REVERT: G 98 GLN cc_start: 0.7051 (pt0) cc_final: 0.6609 (mt0) REVERT: G 130 THR cc_start: 0.7382 (p) cc_final: 0.7109 (t) REVERT: H 11 HIS cc_start: 0.7244 (m-70) cc_final: 0.7028 (m90) REVERT: I 3 LYS cc_start: 0.3183 (tptt) cc_final: 0.1403 (tppt) REVERT: I 58 LYS cc_start: 0.3967 (pttp) cc_final: 0.3675 (ttpp) REVERT: P 58 THR cc_start: 0.7809 (p) cc_final: 0.7603 (t) REVERT: R 37 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8227 (mt-10) REVERT: T 23 LYS cc_start: 0.8294 (mttp) cc_final: 0.7938 (mtpp) REVERT: V 86 ARG cc_start: 0.5613 (OUTLIER) cc_final: 0.5388 (ttp-110) REVERT: W 113 LEU cc_start: 0.7995 (tp) cc_final: 0.7550 (mt) REVERT: W 134 GLU cc_start: 0.6857 (tt0) cc_final: 0.6445 (tm-30) REVERT: Y 37 ARG cc_start: 0.8337 (mtt-85) cc_final: 0.7698 (mmt180) REVERT: Y 57 LYS cc_start: 0.8433 (tttt) cc_final: 0.7258 (tptt) REVERT: 2 61 PHE cc_start: 0.5465 (OUTLIER) cc_final: 0.4559 (m-80) REVERT: 8 15 LYS cc_start: 0.8833 (tmtp) cc_final: 0.8122 (tppt) REVERT: 8 17 ASN cc_start: 0.8457 (m110) cc_final: 0.8132 (m-40) outliers start: 273 outliers final: 202 residues processed: 1228 average time/residue: 1.3623 time to fit residues: 2843.2584 Evaluate side-chains 1263 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 1049 time to evaluate : 6.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 117 GLN Chi-restraints excluded: chain c residue 163 SER Chi-restraints excluded: chain c residue 200 VAL Chi-restraints excluded: chain e residue 38 GLU Chi-restraints excluded: chain e residue 40 VAL Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 140 LEU Chi-restraints excluded: chain e residue 148 ILE Chi-restraints excluded: chain e residue 159 ILE Chi-restraints excluded: chain e residue 171 LEU Chi-restraints excluded: chain e residue 188 ASP Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain h residue 80 VAL Chi-restraints excluded: chain h residue 91 SER Chi-restraints excluded: chain h residue 130 TYR Chi-restraints excluded: chain i residue 54 THR Chi-restraints excluded: chain i residue 81 PHE Chi-restraints excluded: chain i residue 88 ASP Chi-restraints excluded: chain i residue 103 ILE Chi-restraints excluded: chain i residue 108 ILE Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain j residue 57 LYS Chi-restraints excluded: chain j residue 64 HIS Chi-restraints excluded: chain k residue 27 HIS Chi-restraints excluded: chain k residue 67 SER Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 127 HIS Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain l residue 80 VAL Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain o residue 45 VAL Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain q residue 24 ILE Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 37 VAL Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain r residue 64 ILE Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 23 ASN Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain t residue 15 GLU Chi-restraints excluded: chain n residue 4 LYS Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain b residue 117 LEU Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain d residue 9 THR Chi-restraints excluded: chain d residue 50 LEU Chi-restraints excluded: chain d residue 86 LEU Chi-restraints excluded: chain d residue 91 SER Chi-restraints excluded: chain d residue 94 ASP Chi-restraints excluded: chain d residue 125 VAL Chi-restraints excluded: chain d residue 147 THR Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 18 THR Chi-restraints excluded: chain f residue 30 ILE Chi-restraints excluded: chain f residue 91 LEU Chi-restraints excluded: chain f residue 93 THR Chi-restraints excluded: chain m residue 4 LEU Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 56 LEU Chi-restraints excluded: chain m residue 66 VAL Chi-restraints excluded: chain m residue 98 VAL Chi-restraints excluded: chain p residue 12 LYS Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 86 LEU Chi-restraints excluded: chain p residue 92 THR Chi-restraints excluded: chain u residue 6 LYS Chi-restraints excluded: chain u residue 10 LYS Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 176 ARG Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 142 GLN Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 75 ARG Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 182 PHE Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 127 GLU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 105 LYS Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 124 ASP Chi-restraints excluded: chain J residue 137 MET Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 83 ILE Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain M residue 125 THR Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 13 HIS Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 41 TYR Chi-restraints excluded: chain N residue 42 ILE Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 15 SER Chi-restraints excluded: chain O residue 18 SER Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain P residue 28 LYS Chi-restraints excluded: chain P residue 43 SER Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 52 VAL Chi-restraints excluded: chain P residue 56 ASN Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 103 LYS Chi-restraints excluded: chain T residue 37 GLU Chi-restraints excluded: chain T residue 42 ILE Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain U residue 9 ASP Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 15 VAL Chi-restraints excluded: chain U residue 34 HIS Chi-restraints excluded: chain U residue 37 SER Chi-restraints excluded: chain U residue 38 ASN Chi-restraints excluded: chain U residue 46 ILE Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain U residue 90 SER Chi-restraints excluded: chain U residue 93 ILE Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain V residue 86 ARG Chi-restraints excluded: chain V residue 101 ASN Chi-restraints excluded: chain W residue 12 THR Chi-restraints excluded: chain W residue 14 ASN Chi-restraints excluded: chain W residue 17 THR Chi-restraints excluded: chain W residue 19 THR Chi-restraints excluded: chain W residue 53 ASP Chi-restraints excluded: chain W residue 122 THR Chi-restraints excluded: chain W residue 177 LEU Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain Z residue 5 THR Chi-restraints excluded: chain Z residue 54 ILE Chi-restraints excluded: chain 1 residue 4 LEU Chi-restraints excluded: chain 1 residue 7 THR Chi-restraints excluded: chain 1 residue 31 ILE Chi-restraints excluded: chain 1 residue 36 VAL Chi-restraints excluded: chain 2 residue 13 THR Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 2 residue 42 HIS Chi-restraints excluded: chain 2 residue 61 PHE Chi-restraints excluded: chain 3 residue 3 VAL Chi-restraints excluded: chain 3 residue 13 THR Chi-restraints excluded: chain 3 residue 15 SER Chi-restraints excluded: chain 3 residue 29 THR Chi-restraints excluded: chain 3 residue 31 SER Chi-restraints excluded: chain 4 residue 39 LYS Chi-restraints excluded: chain 6 residue 11 SER Chi-restraints excluded: chain 6 residue 12 LYS Chi-restraints excluded: chain 6 residue 59 ASN Chi-restraints excluded: chain 7 residue 26 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1066 random chunks: chunk 628 optimal weight: 0.1980 chunk 1012 optimal weight: 1.9990 chunk 617 optimal weight: 0.9990 chunk 480 optimal weight: 4.9990 chunk 703 optimal weight: 2.9990 chunk 1062 optimal weight: 7.9990 chunk 977 optimal weight: 5.9990 chunk 845 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 653 optimal weight: 0.8980 chunk 518 optimal weight: 0.0870 overall best weight: 0.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 72 HIS r 56 ASN ** t 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 146 ASN ** f 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 78 GLN ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 GLN ** F 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 ASN ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 76 HIS ** W 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 34 GLN 2 15 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.4885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 163342 Z= 0.153 Angle : 0.617 11.338 244537 Z= 0.313 Chirality : 0.034 0.287 31270 Planarity : 0.005 0.093 13186 Dihedral : 24.260 179.869 82355 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.63 % Favored : 93.11 % Rotamer: Outliers : 3.05 % Allowed : 24.69 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.49 % 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: -1.29 (0.11), residues: 5991 helix: 0.51 (0.12), residues: 2014 sheet: -1.15 (0.16), residues: 1040 loop : -1.73 (0.11), residues: 2937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP N 92 HIS 0.010 0.001 HIS l 72 PHE 0.021 0.002 PHE c 10 TYR 0.029 0.002 TYR c 184 ARG 0.018 0.001 ARG L 71 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11982 Ramachandran restraints generated. 5991 Oldfield, 0 Emsley, 5991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11982 Ramachandran restraints generated. 5991 Oldfield, 0 Emsley, 5991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1238 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 1087 time to evaluate : 6.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 100 PRO cc_start: 0.7496 (Cg_endo) cc_final: 0.7189 (Cg_exo) REVERT: g 1 MET cc_start: 0.0385 (OUTLIER) cc_final: -0.0354 (tpt) REVERT: h 3 MET cc_start: 0.5593 (tpt) cc_final: 0.4113 (tpt) REVERT: i 81 PHE cc_start: 0.6838 (OUTLIER) cc_final: 0.6221 (t80) REVERT: j 57 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.7006 (pptt) REVERT: j 88 MET cc_start: 0.4477 (tpp) cc_final: 0.4092 (tpp) REVERT: o 17 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7507 (tt) REVERT: q 35 THR cc_start: 0.7170 (t) cc_final: 0.6928 (t) REVERT: s 66 MET cc_start: 0.6118 (mmp) cc_final: 0.5911 (mmt) REVERT: b 1 MET cc_start: 0.0901 (ptt) cc_final: 0.0685 (ptt) REVERT: b 6 MET cc_start: 0.6117 (mtp) cc_final: 0.5734 (mtp) REVERT: b 89 MET cc_start: 0.5961 (mmm) cc_final: 0.5674 (mmm) REVERT: d 72 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7829 (tm-30) REVERT: d 182 GLU cc_start: 0.6959 (mt-10) cc_final: 0.6643 (mp0) REVERT: m 58 ASP cc_start: 0.8571 (m-30) cc_final: 0.8255 (m-30) REVERT: p 21 ILE cc_start: 0.7815 (tp) cc_final: 0.7602 (tp) REVERT: p 48 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7565 (mm) REVERT: u 10 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7500 (tptt) REVERT: C 88 ARG cc_start: 0.8586 (mmt-90) cc_final: 0.7532 (mmt-90) REVERT: C 148 ARG cc_start: 0.8060 (mtp-110) cc_final: 0.7664 (mtp180) REVERT: D 142 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7162 (tt0) REVERT: D 170 MET cc_start: 0.8416 (ptm) cc_final: 0.8172 (ptm) REVERT: F 45 MET cc_start: 0.6204 (OUTLIER) cc_final: 0.5529 (mpp) REVERT: F 182 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.7426 (t80) REVERT: G 60 ARG cc_start: 0.7009 (ttp-110) cc_final: 0.6594 (ptm160) REVERT: G 98 GLN cc_start: 0.6915 (pt0) cc_final: 0.6524 (mt0) REVERT: G 130 THR cc_start: 0.7305 (p) cc_final: 0.7047 (t) REVERT: I 58 LYS cc_start: 0.4054 (pttp) cc_final: 0.3757 (ttpp) REVERT: I 91 LYS cc_start: 0.5994 (mmtm) cc_final: 0.5505 (mmtt) REVERT: K 108 MET cc_start: 0.8462 (mmt) cc_final: 0.7683 (mmt) REVERT: M 24 ARG cc_start: 0.8682 (mmt-90) cc_final: 0.7765 (mmt-90) REVERT: N 5 ARG cc_start: 0.7396 (ttp80) cc_final: 0.6831 (mtm110) REVERT: P 58 THR cc_start: 0.7890 (p) cc_final: 0.7619 (t) REVERT: R 37 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8164 (mt-10) REVERT: W 38 TYR cc_start: 0.7842 (p90) cc_final: 0.7355 (p90) REVERT: W 113 LEU cc_start: 0.7993 (tp) cc_final: 0.7618 (mt) REVERT: W 115 GLU cc_start: 0.5173 (tp30) cc_final: 0.4847 (tp30) REVERT: W 134 GLU cc_start: 0.6592 (tt0) cc_final: 0.6259 (tm-30) REVERT: Y 37 ARG cc_start: 0.8243 (mtt-85) cc_final: 0.7623 (mmt180) REVERT: 8 11 ARG cc_start: 0.8471 (ptm-80) cc_final: 0.8203 (ptt-90) REVERT: 8 15 LYS cc_start: 0.8487 (tmtp) cc_final: 0.7912 (tppt) REVERT: 8 17 ASN cc_start: 0.8302 (m110) cc_final: 0.8035 (m-40) REVERT: 8 21 ARG cc_start: 0.8371 (ttt-90) cc_final: 0.7736 (ttt180) outliers start: 151 outliers final: 124 residues processed: 1170 average time/residue: 1.4055 time to fit residues: 2777.9697 Evaluate side-chains 1173 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 1040 time to evaluate : 6.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 117 GLN Chi-restraints excluded: chain c residue 166 GLU Chi-restraints excluded: chain c residue 200 VAL Chi-restraints excluded: chain e residue 40 VAL Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 140 LEU Chi-restraints excluded: chain e residue 159 ILE Chi-restraints excluded: chain e residue 171 LEU Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain g residue 70 LYS Chi-restraints excluded: chain i residue 54 THR Chi-restraints excluded: chain i residue 81 PHE Chi-restraints excluded: chain i residue 88 ASP Chi-restraints excluded: chain i residue 103 ILE Chi-restraints excluded: chain i residue 108 ILE Chi-restraints excluded: chain j residue 57 LYS Chi-restraints excluded: chain k residue 27 HIS Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain q residue 24 ILE Chi-restraints excluded: chain q residue 37 VAL Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 23 ASN Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain t residue 15 GLU Chi-restraints excluded: chain n residue 4 LYS Chi-restraints excluded: chain b residue 117 LEU Chi-restraints excluded: chain d residue 50 LEU Chi-restraints excluded: chain d residue 86 LEU Chi-restraints excluded: chain d residue 91 SER Chi-restraints excluded: chain d residue 94 ASP Chi-restraints excluded: chain d residue 125 VAL Chi-restraints excluded: chain d residue 147 THR Chi-restraints excluded: chain f residue 18 THR Chi-restraints excluded: chain f residue 30 ILE Chi-restraints excluded: chain f residue 38 ASP Chi-restraints excluded: chain f residue 91 LEU Chi-restraints excluded: chain f residue 93 THR Chi-restraints excluded: chain m residue 4 LEU Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 66 VAL Chi-restraints excluded: chain m residue 98 VAL Chi-restraints excluded: chain p residue 12 LYS Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 48 LEU Chi-restraints excluded: chain p residue 70 VAL Chi-restraints excluded: chain p residue 92 THR Chi-restraints excluded: chain u residue 6 LYS Chi-restraints excluded: chain u residue 10 LYS Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 266 LYS Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 142 GLN Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 75 ARG Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 45 MET Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 182 PHE Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 127 GLU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 13 HIS Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain P residue 56 ASN Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain S residue 103 LYS Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain U residue 9 ASP Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 15 VAL Chi-restraints excluded: chain U residue 38 ASN Chi-restraints excluded: chain U residue 79 THR Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain U residue 90 SER Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain W residue 12 THR Chi-restraints excluded: chain W residue 14 ASN Chi-restraints excluded: chain X residue 43 THR Chi-restraints excluded: chain Z residue 5 THR Chi-restraints excluded: chain 1 residue 36 VAL Chi-restraints excluded: chain 2 residue 13 THR Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 3 residue 3 VAL Chi-restraints excluded: chain 3 residue 31 SER Chi-restraints excluded: chain 4 residue 39 LYS Chi-restraints excluded: chain 6 residue 11 SER Chi-restraints excluded: chain 6 residue 12 LYS Chi-restraints excluded: chain 6 residue 59 ASN Chi-restraints excluded: chain 6 residue 62 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1066 random chunks: chunk 671 optimal weight: 10.0000 chunk 900 optimal weight: 7.9990 chunk 259 optimal weight: 5.9990 chunk 779 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 235 optimal weight: 0.7980 chunk 847 optimal weight: 10.0000 chunk 354 optimal weight: 1.9990 chunk 869 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 156 optimal weight: 10.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 64 HIS ** k 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 72 HIS ** t 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 146 ASN f 78 GLN ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 ASN ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 66 GLN ** W 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.157847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.125418 restraints weight = 243948.609| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.21 r_work: 0.3195 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.4965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.113 163342 Z= 0.416 Angle : 0.779 13.275 244537 Z= 0.389 Chirality : 0.043 0.342 31270 Planarity : 0.006 0.094 13186 Dihedral : 24.242 179.916 82355 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.45 % Favored : 90.27 % Rotamer: Outliers : 3.74 % Allowed : 24.02 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 1.49 % 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: -1.56 (0.11), residues: 5991 helix: 0.24 (0.12), residues: 2005 sheet: -1.35 (0.16), residues: 1013 loop : -1.83 (0.11), residues: 2973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 206 HIS 0.010 0.002 HIS Q 76 PHE 0.034 0.003 PHE c 10 TYR 0.037 0.003 TYR n 21 ARG 0.016 0.001 ARG L 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 42819.82 seconds wall clock time: 746 minutes 40.18 seconds (44800.18 seconds total)