Starting phenix.real_space_refine on Fri Feb 23 23:18:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofx_20048/02_2024/6ofx_20048_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofx_20048/02_2024/6ofx_20048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofx_20048/02_2024/6ofx_20048.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofx_20048/02_2024/6ofx_20048.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofx_20048/02_2024/6ofx_20048_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofx_20048/02_2024/6ofx_20048_updated.pdb" } resolution = 3.3 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= 0.005 sd= 0.401 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 4654 5.49 5 S 143 5.16 5 C 72773 2.51 5 N 27034 2.21 5 O 40382 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b GLU 22": "OE1" <-> "OE2" Residue "b PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 13": "NH1" <-> "NH2" Residue "c ARG 33": "NH1" <-> "NH2" Residue "c ARG 59": "NH1" <-> "NH2" Residue "c ARG 77": "NH1" <-> "NH2" Residue "c ARG 83": "NH1" <-> "NH2" Residue "c ASP 131": "OD1" <-> "OD2" Residue "c ARG 169": "NH1" <-> "NH2" Residue "c ARG 184": "NH1" <-> "NH2" Residue "d GLU 16": "OE1" <-> "OE2" Residue "d PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ARG 44": "NH1" <-> "NH2" Residue "d ARG 49": "NH1" <-> "NH2" Residue "d ARG 61": "NH1" <-> "NH2" Residue "d ARG 88": "NH1" <-> "NH2" Residue "d ARG 102": "NH1" <-> "NH2" Residue "d GLU 155": "OE1" <-> "OE2" Residue "d ARG 162": "NH1" <-> "NH2" Residue "d ASP 168": "OD1" <-> "OD2" Residue "d ARG 170": "NH1" <-> "NH2" Residue "e ASP 50": "OD1" <-> "OD2" Residue "e ARG 70": "NH1" <-> "NH2" Residue "e ARG 79": "NH1" <-> "NH2" Residue "e ARG 91": "NH1" <-> "NH2" Residue "e ARG 101": "NH1" <-> "NH2" Residue "e ARG 109": "NH1" <-> "NH2" Residue "e ARG 111": "NH1" <-> "NH2" Residue "e ARG 114": "NH1" <-> "NH2" Residue "e ARG 132": "NH1" <-> "NH2" Residue "f ARG 2": "NH1" <-> "NH2" Residue "f ASP 15": "OD1" <-> "OD2" Residue "f GLU 80": "OE1" <-> "OE2" Residue "f GLU 129": "OE1" <-> "OE2" Residue "f ARG 152": "NH1" <-> "NH2" Residue "f ARG 162": "NH1" <-> "NH2" Residue "f ARG 169": "NH1" <-> "NH2" Residue "g ASP 98": "OD1" <-> "OD2" Residue "g GLU 129": "OE1" <-> "OE2" Residue "g GLU 137": "OE1" <-> "OE2" Residue "j GLU 9": "OE1" <-> "OE2" Residue "j ARG 13": "NH1" <-> "NH2" Residue "j ARG 37": "NH1" <-> "NH2" Residue "j GLU 91": "OE1" <-> "OE2" Residue "j ARG 96": "NH1" <-> "NH2" Residue "j ARG 120": "NH1" <-> "NH2" Residue "k GLU 121": "OE1" <-> "OE2" Residue "l ARG 21": "NH1" <-> "NH2" Residue "l ARG 33": "NH1" <-> "NH2" Residue "l ARG 41": "NH1" <-> "NH2" Residue "l ARG 47": "NH1" <-> "NH2" Residue "l ARG 60": "NH1" <-> "NH2" Residue "l GLU 76": "OE1" <-> "OE2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l ARG 126": "NH1" <-> "NH2" Residue "l GLU 136": "OE1" <-> "OE2" Residue "m ARG 10": "NH1" <-> "NH2" Residue "m ARG 18": "NH1" <-> "NH2" Residue "m PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 40": "NH1" <-> "NH2" Residue "m ARG 44": "NH1" <-> "NH2" Residue "m ARG 50": "NH1" <-> "NH2" Residue "m ARG 55": "NH1" <-> "NH2" Residue "m ARG 59": "NH1" <-> "NH2" Residue "m ARG 114": "NH1" <-> "NH2" Residue "n ARG 8": "NH1" <-> "NH2" Residue "n ARG 12": "NH1" <-> "NH2" Residue "n ARG 17": "NH1" <-> "NH2" Residue "n ARG 22": "NH1" <-> "NH2" Residue "n ARG 46": "NH1" <-> "NH2" Residue "n ARG 63": "NH1" <-> "NH2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n ARG 69": "NH1" <-> "NH2" Residue "n ARG 71": "NH1" <-> "NH2" Residue "n ARG 96": "NH1" <-> "NH2" Residue "n ARG 118": "NH1" <-> "NH2" Residue "o ARG 10": "NH1" <-> "NH2" Residue "o ARG 16": "NH1" <-> "NH2" Residue "o ARG 25": "NH1" <-> "NH2" Residue "o ARG 81": "NH1" <-> "NH2" Residue "o ARG 94": "NH1" <-> "NH2" Residue "o ARG 102": "NH1" <-> "NH2" Residue "o ASP 108": "OD1" <-> "OD2" Residue "o ARG 111": "NH1" <-> "NH2" Residue "p ARG 20": "NH1" <-> "NH2" Residue "p ARG 38": "NH1" <-> "NH2" Residue "p ARG 61": "NH1" <-> "NH2" Residue "p ARG 88": "NH1" <-> "NH2" Residue "p ARG 100": "NH1" <-> "NH2" Residue "p GLU 101": "OE1" <-> "OE2" Residue "p ARG 108": "NH1" <-> "NH2" Residue "q ARG 2": "NH1" <-> "NH2" Residue "q ARG 5": "NH1" <-> "NH2" Residue "q ARG 12": "NH1" <-> "NH2" Residue "q ARG 32": "NH1" <-> "NH2" Residue "q ARG 47": "NH1" <-> "NH2" Residue "q ARG 69": "NH1" <-> "NH2" Residue "q GLU 110": "OE1" <-> "OE2" Residue "r ARG 21": "NH1" <-> "NH2" Residue "r GLU 23": "OE1" <-> "OE2" Residue "r ASP 26": "OD1" <-> "OD2" Residue "r ARG 68": "NH1" <-> "NH2" Residue "r ARG 78": "NH1" <-> "NH2" Residue "r ARG 79": "NH1" <-> "NH2" Residue "r ARG 84": "NH1" <-> "NH2" Residue "s ASP 68": "OD1" <-> "OD2" Residue "s ARG 84": "NH1" <-> "NH2" Residue "s ARG 88": "NH1" <-> "NH2" Residue "s ARG 95": "NH1" <-> "NH2" Residue "s ARG 110": "NH1" <-> "NH2" Residue "t GLU 54": "OE1" <-> "OE2" Residue "t ARG 73": "NH1" <-> "NH2" Residue "u ARG 5": "NH1" <-> "NH2" Residue "u ARG 6": "NH1" <-> "NH2" Residue "u ARG 81": "NH1" <-> "NH2" Residue "u ARG 85": "NH1" <-> "NH2" Residue "u ARG 93": "NH1" <-> "NH2" Residue "v ASP 76": "OD1" <-> "OD2" Residue "x GLU 42": "OE1" <-> "OE2" Residue "y ARG 29": "NH1" <-> "NH2" Residue "y ARG 47": "NH1" <-> "NH2" Residue "y ARG 52": "NH1" <-> "NH2" Residue "z ARG 10": "NH1" <-> "NH2" Residue "z ARG 29": "NH1" <-> "NH2" Residue "z ARG 44": "NH1" <-> "NH2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 3": "NH1" <-> "NH2" Residue "D ARG 12": "NH1" <-> "NH2" Residue "D ARG 14": "NH1" <-> "NH2" Residue "D ARG 19": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 41": "NH1" <-> "NH2" Residue "E ARG 12": "NH1" <-> "NH2" Residue "E ARG 29": "NH1" <-> "NH2" Residue "E ARG 39": "NH1" <-> "NH2" Residue "E ARG 41": "NH1" <-> "NH2" Residue "F ARG 12": "NH1" <-> "NH2" Residue "F ARG 24": "NH1" <-> "NH2" Residue "G ASP 7": "OD1" <-> "OD2" Residue "G GLU 51": "OE1" <-> "OE2" Residue "G PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 115": "OD1" <-> "OD2" Residue "G ASP 122": "OD1" <-> "OD2" Residue "G ASP 166": "OD1" <-> "OD2" Residue "G GLU 222": "OE1" <-> "OE2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "H ARG 106": "NH1" <-> "NH2" Residue "H ASP 111": "OD1" <-> "OD2" Residue "H ARG 130": "NH1" <-> "NH2" Residue "I ASP 17": "OD1" <-> "OD2" Residue "I ASP 28": "OD1" <-> "OD2" Residue "I TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 141": "OD1" <-> "OD2" Residue "J ARG 156": "NH1" <-> "NH2" Residue "K TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 20": "OE1" <-> "OE2" Residue "L TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 41": "OE1" <-> "OE2" Residue "M ASP 47": "OD1" <-> "OD2" Residue "M GLU 59": "OE1" <-> "OE2" Residue "N GLU 52": "OE1" <-> "OE2" Residue "N ASP 106": "OD1" <-> "OD2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "O ASP 19": "OD1" <-> "OD2" Residue "O GLU 27": "OE1" <-> "OE2" Residue "O ASP 85": "OD1" <-> "OD2" Residue "O ASP 97": "OD1" <-> "OD2" Residue "Q GLU 24": "OE1" <-> "OE2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "R ASP 10": "OD1" <-> "OD2" Residue "R ASP 41": "OD1" <-> "OD2" Residue "S GLU 9": "OE1" <-> "OE2" Residue "T PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "U GLU 34": "OE1" <-> "OE2" Residue "V GLU 79": "OE1" <-> "OE2" Residue "W ARG 11": "NH1" <-> "NH2" Residue "X ASP 63": "OD1" <-> "OD2" Residue "Z GLU 30": "OE1" <-> "OE2" Residue "Z ARG 66": "NH1" <-> "NH2" Residue "a ARG 7": "NH1" <-> "NH2" Residue "a ARG 12": "NH1" <-> "NH2" Residue "a ARG 162": "NH1" <-> "NH2" Residue "a ASP 183": "OD1" <-> "OD2" Residue "a GLU 187": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 144986 Number of models: 1 Model: "" Number of chains: 55 Chain: "b" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2083 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "c" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "d" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "e" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1411 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "f" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "g" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "j" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "k" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 939 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "l" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "m" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "n" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 961 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "o" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "p" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "r" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "s" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "t" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 739 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "u" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 780 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "v" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "w" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "x" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "B" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "C" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 410 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "D" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "E" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "F" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "G" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1757 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "H" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1625 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "I" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "J" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1157 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "K" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 824 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "L" Number of atoms: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1182 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "M" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "N" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "O" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 787 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "P" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 870 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "Q" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "R" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 884 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "S" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "T" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "U" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "V" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 649 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "W" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 536 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "X" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "Y" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "Z" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 545 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "a" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1027 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain breaks: 1 Chain: "3" Number of atoms: 33012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33012 Classifications: {'RNA': 1539} Modifications used: {'5*END': 1, 'rna2p_pur': 91, 'rna2p_pyr': 49, 'rna3p_pur': 783, 'rna3p_pyr': 616} Link IDs: {'rna2p': 140, 'rna3p': 1398} Chain: "1" Number of atoms: 62317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62317 Classifications: {'RNA': 2903} Modifications used: {'5*END': 1, 'rna2p_pur': 218, 'rna2p_pyr': 98, 'rna3p_pur': 1456, 'rna3p_pyr': 1131} Link IDs: {'rna2p': 316, 'rna3p': 2586} Chain: "2" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2568 Classifications: {'RNA': 120} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 61, 'rna3p_pyr': 53} Link IDs: {'rna2p': 6, 'rna3p': 113} Chain: "5" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1640 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 3, 'rna3p_pur': 33, 'rna3p_pyr': 35} Link IDs: {'rna2p': 8, 'rna3p': 68} Chain: "4" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 437 Classifications: {'RNA': 20} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 14, 'rna3p_pyr': 3} Link IDs: {'rna2p': 3, 'rna3p': 16} Chain: "5" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 54.72, per 1000 atoms: 0.38 Number of scatterers: 144986 At special positions: 0 Unit cell: (233.45, 260.13, 269.468, 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 143 16.00 P 4654 15.00 O 40382 8.00 N 27034 7.00 C 72773 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 61.81 Conformation dependent library (CDL) restraints added in 6.7 seconds 11304 Ramachandran restraints generated. 5652 Oldfield, 0 Emsley, 5652 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10572 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 174 helices and 70 sheets defined 37.9% alpha, 18.8% beta 1213 base pairs and 2375 stacking pairs defined. Time for finding SS restraints: 69.61 Creating SS restraints... Processing helix chain 'b' and resid 9 through 15 removed outlier: 8.021A pdb=" N HIS b 14 " --> pdb=" O PRO b 10 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N VAL b 15 " --> pdb=" O GLY b 11 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 135 Proline residue: b 135 - end of helix Processing helix chain 'b' and resid 206 through 214 removed outlier: 3.835A pdb=" N ALA b 210 " --> pdb=" O LYS b 206 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG b 213 " --> pdb=" O ALA b 209 " (cutoff:3.500A) Processing helix chain 'b' and resid 220 through 225 removed outlier: 3.639A pdb=" N MET b 224 " --> pdb=" O ARG b 220 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ASN b 225 " --> pdb=" O GLY b 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 220 through 225' Processing helix chain 'b' and resid 259 through 264 removed outlier: 5.951A pdb=" N ASP b 263 " --> pdb=" O ASN b 259 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N LYS b 264 " --> pdb=" O LYS b 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 259 through 264' Processing helix chain 'c' and resid 56 through 61 removed outlier: 5.853A pdb=" N THR c 61 " --> pdb=" O ALA c 57 " (cutoff:3.500A) Processing helix chain 'c' and resid 62 through 72 Processing helix chain 'c' and resid 98 through 103 removed outlier: 4.101A pdb=" N ALA c 102 " --> pdb=" O VAL c 98 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ASP c 103 " --> pdb=" O GLU c 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 98 through 103' Processing helix chain 'c' and resid 120 through 125 Processing helix chain 'c' and resid 39 through 44 Processing helix chain 'd' and resid 15 through 20 Processing helix chain 'd' and resid 24 through 40 removed outlier: 3.531A pdb=" N ARG d 40 " --> pdb=" O ALA d 36 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 116 removed outlier: 3.943A pdb=" N ARG d 114 " --> pdb=" O SER d 110 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 142 removed outlier: 3.823A pdb=" N LEU d 134 " --> pdb=" O LYS d 130 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 163 removed outlier: 3.664A pdb=" N ALA d 160 " --> pdb=" O ASN d 156 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG d 162 " --> pdb=" O PHE d 158 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ASN d 163 " --> pdb=" O LEU d 159 " (cutoff:3.500A) Processing helix chain 'd' and resid 176 through 183 Processing helix chain 'd' and resid 189 through 201 Processing helix chain 'e' and resid 1 through 20 removed outlier: 3.577A pdb=" N ASP e 9 " --> pdb=" O ASP e 5 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N VAL e 12 " --> pdb=" O LYS e 8 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU e 18 " --> pdb=" O LYS e 14 " (cutoff:3.500A) Processing helix chain 'e' and resid 45 through 60 removed outlier: 3.594A pdb=" N LEU e 49 " --> pdb=" O ASP e 45 " (cutoff:3.500A) Processing helix chain 'e' and resid 92 through 105 removed outlier: 4.828A pdb=" N TRP e 96 " --> pdb=" O GLY e 92 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE e 99 " --> pdb=" O MET e 95 " (cutoff:3.500A) Processing helix chain 'e' and resid 161 through 172 removed outlier: 3.944A pdb=" N PHE e 172 " --> pdb=" O LEU e 168 " (cutoff:3.500A) Processing helix chain 'f' and resid 1 through 7 removed outlier: 3.705A pdb=" N ALA f 6 " --> pdb=" O ARG f 2 " (cutoff:3.500A) Proline residue: f 7 - end of helix Processing helix chain 'f' and resid 59 through 80 Processing helix chain 'f' and resid 136 through 152 removed outlier: 3.867A pdb=" N ARG f 151 " --> pdb=" O LEU f 147 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 28 Processing helix chain 'g' and resid 29 through 34 Processing helix chain 'g' and resid 40 through 50 Processing helix chain 'g' and resid 53 through 73 removed outlier: 5.129A pdb=" N LYS g 57 " --> pdb=" O GLU g 53 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS g 71 " --> pdb=" O ALA g 67 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE g 72 " --> pdb=" O ARG g 68 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASN g 73 " --> pdb=" O ALA g 69 " (cutoff:3.500A) Processing helix chain 'g' and resid 95 through 107 removed outlier: 5.079A pdb=" N ILE g 99 " --> pdb=" O GLY g 95 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR g 104 " --> pdb=" O ALA g 100 " (cutoff:3.500A) Processing helix chain 'g' and resid 111 through 116 removed outlier: 4.142A pdb=" N VAL g 115 " --> pdb=" O ALA g 111 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ARG g 116 " --> pdb=" O LYS g 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 111 through 116' Processing helix chain 'j' and resid 24 through 38 Processing helix chain 'j' and resid 88 through 96 Processing helix chain 'j' and resid 97 through 110 removed outlier: 4.249A pdb=" N ILE j 101 " --> pdb=" O PRO j 97 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N MET j 108 " --> pdb=" O ALA j 104 " (cutoff:3.500A) Proline residue: j 110 - end of helix Processing helix chain 'j' and resid 112 through 122 removed outlier: 3.588A pdb=" N ARG j 120 " --> pdb=" O ARG j 116 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS j 121 " --> pdb=" O ALA j 117 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU j 122 " --> pdb=" O MET j 118 " (cutoff:3.500A) Processing helix chain 'k' and resid 109 through 119 removed outlier: 6.235A pdb=" N MET k 113 " --> pdb=" O SER k 109 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N LYS k 114 " --> pdb=" O GLU k 110 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ILE k 115 " --> pdb=" O LYS k 111 " (cutoff:3.500A) Processing helix chain 'l' and resid 56 through 62 Proline residue: l 62 - end of helix Processing helix chain 'l' and resid 68 through 75 removed outlier: 4.080A pdb=" N ALA l 72 " --> pdb=" O SER l 68 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE l 73 " --> pdb=" O ARG l 69 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR l 74 " --> pdb=" O LYS l 70 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ALA l 75 " --> pdb=" O ALA l 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 68 through 75' Processing helix chain 'l' and resid 78 through 85 removed outlier: 3.826A pdb=" N ALA l 83 " --> pdb=" O LEU l 79 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS l 84 " --> pdb=" O SER l 80 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL l 85 " --> pdb=" O ASP l 81 " (cutoff:3.500A) Processing helix chain 'l' and resid 91 through 99 removed outlier: 5.016A pdb=" N LEU l 95 " --> pdb=" O ASP l 91 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LYS l 96 " --> pdb=" O LEU l 92 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ALA l 97 " --> pdb=" O ASN l 93 " (cutoff:3.500A) Processing helix chain 'l' and resid 128 through 139 Processing helix chain 'm' and resid 42 through 58 removed outlier: 3.552A pdb=" N ALA m 56 " --> pdb=" O ALA m 52 " (cutoff:3.500A) Processing helix chain 'm' and resid 109 through 125 removed outlier: 4.036A pdb=" N LYS m 118 " --> pdb=" O ARG m 114 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS m 123 " --> pdb=" O LEU m 119 " (cutoff:3.500A) Proline residue: m 125 - end of helix Processing helix chain 'n' and resid 13 through 32 Processing helix chain 'n' and resid 38 through 58 removed outlier: 4.752A pdb=" N ARG n 46 " --> pdb=" O LYS n 42 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL n 47 " --> pdb=" O GLU n 43 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) Proline residue: n 50 - end of helix removed outlier: 4.403A pdb=" N THR n 57 " --> pdb=" O THR n 53 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ASP n 58 " --> pdb=" O LEU n 54 " (cutoff:3.500A) Processing helix chain 'n' and resid 59 through 71 removed outlier: 3.849A pdb=" N ARG n 63 " --> pdb=" O SER n 59 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N THR n 70 " --> pdb=" O ALA n 66 " (cutoff:3.500A) Processing helix chain 'n' and resid 72 through 82 removed outlier: 4.580A pdb=" N PHE n 80 " --> pdb=" O VAL n 76 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASN n 81 " --> pdb=" O ALA n 77 " (cutoff:3.500A) Processing helix chain 'n' and resid 83 through 88 Processing helix chain 'o' and resid 2 through 22 removed outlier: 5.155A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 63 removed outlier: 5.110A pdb=" N GLN o 61 " --> pdb=" O ALA o 57 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU o 62 " --> pdb=" O ILE o 58 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N LYS o 63 " --> pdb=" O ALA o 59 " (cutoff:3.500A) Processing helix chain 'o' and resid 67 through 86 removed outlier: 3.647A pdb=" N LEU o 83 " --> pdb=" O ALA o 79 " (cutoff:3.500A) Processing helix chain 'o' and resid 101 through 114 Processing helix chain 'p' and resid 1 through 12 removed outlier: 4.425A pdb=" N GLN p 11 " --> pdb=" O LEU p 7 " (cutoff:3.500A) Processing helix chain 'p' and resid 96 through 103 removed outlier: 4.742A pdb=" N ARG p 100 " --> pdb=" O LEU p 96 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLU p 101 " --> pdb=" O TYR p 97 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG p 102 " --> pdb=" O TYR p 98 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N THR p 103 " --> pdb=" O LEU p 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 96 through 103' Processing helix chain 'q' and resid 5 through 21 removed outlier: 6.303A pdb=" N ALA q 9 " --> pdb=" O ARG q 5 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLN q 19 " --> pdb=" O LYS q 15 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS q 21 " --> pdb=" O LEU q 17 " (cutoff:3.500A) Processing helix chain 'q' and resid 25 through 30 removed outlier: 4.047A pdb=" N ARG q 29 " --> pdb=" O GLY q 25 " (cutoff:3.500A) Processing helix chain 'q' and resid 38 through 60 removed outlier: 4.052A pdb=" N ARG q 50 " --> pdb=" O TYR q 46 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LYS q 53 " --> pdb=" O ARG q 49 " (cutoff:3.500A) Processing helix chain 'q' and resid 62 through 72 Processing helix chain 'q' and resid 74 through 86 Processing helix chain 'q' and resid 90 through 101 Processing helix chain 'q' and resid 102 through 117 Processing helix chain 's' and resid 13 through 25 removed outlier: 4.422A pdb=" N LEU s 23 " --> pdb=" O LEU s 19 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE s 24 " --> pdb=" O VAL s 20 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ARG s 25 " --> pdb=" O ALA s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 39 removed outlier: 4.038A pdb=" N TYR s 38 " --> pdb=" O ASP s 34 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 61 Processing helix chain 't' and resid 2 through 11 removed outlier: 3.750A pdb=" N LYS t 9 " --> pdb=" O GLU t 5 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU t 11 " --> pdb=" O LEU t 7 " (cutoff:3.500A) Processing helix chain 't' and resid 17 through 27 Processing helix chain 't' and resid 39 through 50 Processing helix chain 'u' and resid 65 through 70 removed outlier: 3.804A pdb=" N VAL u 69 " --> pdb=" O GLN u 65 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ALA u 70 " --> pdb=" O VAL u 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 65 through 70' Processing helix chain 'v' and resid 13 through 24 removed outlier: 3.690A pdb=" N ASN v 24 " --> pdb=" O LEU v 20 " (cutoff:3.500A) Processing helix chain 'v' and resid 43 through 54 removed outlier: 3.931A pdb=" N VAL v 47 " --> pdb=" O ASP v 43 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA v 52 " --> pdb=" O MET v 48 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS v 53 " --> pdb=" O ASN v 49 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ALA v 54 " --> pdb=" O MET v 50 " (cutoff:3.500A) Processing helix chain 'x' and resid 51 through 62 removed outlier: 4.633A pdb=" N GLY x 62 " --> pdb=" O ILE x 58 " (cutoff:3.500A) Processing helix chain 'x' and resid 63 through 74 Processing helix chain 'y' and resid 1 through 8 removed outlier: 4.162A pdb=" N LEU y 6 " --> pdb=" O LYS y 2 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG y 7 " --> pdb=" O ALA y 3 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLU y 8 " --> pdb=" O LYS y 4 " (cutoff:3.500A) Processing helix chain 'y' and resid 9 through 23 Processing helix chain 'y' and resid 25 through 35 removed outlier: 3.500A pdb=" N SER y 34 " --> pdb=" O MET y 30 " (cutoff:3.500A) Processing helix chain 'y' and resid 39 through 62 removed outlier: 5.233A pdb=" N LEU y 43 " --> pdb=" O GLN y 39 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLY y 62 " --> pdb=" O ASN y 58 " (cutoff:3.500A) Processing helix chain 'z' and resid 16 through 27 Processing helix chain 'z' and resid 40 through 51 Processing helix chain 'B' and resid 8 through 18 removed outlier: 4.942A pdb=" N HIS B 18 " --> pdb=" O MET B 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 Proline residue: C 30 - end of helix No H-bonds generated for 'chain 'C' and resid 25 through 30' Processing helix chain 'D' and resid 8 through 16 Processing helix chain 'D' and resid 17 through 25 removed outlier: 4.340A pdb=" N THR D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N LYS D 25 " --> pdb=" O ARG D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 38 Processing helix chain 'E' and resid 6 through 13 removed outlier: 3.541A pdb=" N LYS E 11 " --> pdb=" O ARG E 7 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG E 12 " --> pdb=" O GLY E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 45 Proline residue: E 45 - end of helix Processing helix chain 'E' and resid 50 through 62 removed outlier: 4.745A pdb=" N GLY E 55 " --> pdb=" O LYS E 51 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N LEU E 56 " --> pdb=" O GLY E 52 " (cutoff:3.500A) Proline residue: E 62 - end of helix Processing helix chain 'F' and resid 30 through 35 removed outlier: 3.823A pdb=" N LYS F 34 " --> pdb=" O GLU F 30 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLN F 35 " --> pdb=" O PRO F 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 30 through 35' Processing helix chain 'G' and resid 43 through 63 Proline residue: G 47 - end of helix removed outlier: 3.559A pdb=" N GLU G 51 " --> pdb=" O PRO G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 87 removed outlier: 4.973A pdb=" N GLU G 77 " --> pdb=" O ARG G 73 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N ALA G 78 " --> pdb=" O ALA G 74 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER G 85 " --> pdb=" O ASP G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 103 removed outlier: 5.284A pdb=" N TRP G 103 " --> pdb=" O MET G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 123 removed outlier: 4.433A pdb=" N GLN G 108 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN G 121 " --> pdb=" O GLU G 117 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASP G 122 " --> pdb=" O THR G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 129 removed outlier: 4.067A pdb=" N LEU G 128 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N THR G 129 " --> pdb=" O PHE G 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 124 through 129' Processing helix chain 'G' and resid 130 through 147 Processing helix chain 'G' and resid 164 through 169 Processing helix chain 'G' and resid 170 through 178 removed outlier: 3.675A pdb=" N ASN G 177 " --> pdb=" O LYS G 173 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N LEU G 178 " --> pdb=" O GLU G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 225 removed outlier: 4.226A pdb=" N VAL G 209 " --> pdb=" O ALA G 205 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY G 223 " --> pdb=" O THR G 219 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 153 removed outlier: 4.515A pdb=" N ASP G 152 " --> pdb=" O GLY G 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 11 removed outlier: 3.712A pdb=" N ARG H 10 " --> pdb=" O PRO H 6 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 47 removed outlier: 4.906A pdb=" N ALA H 29 " --> pdb=" O THR H 25 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ASP H 30 " --> pdb=" O LYS H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 77 Processing helix chain 'H' and resid 80 through 95 removed outlier: 4.647A pdb=" N ILE H 93 " --> pdb=" O VAL H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 112 removed outlier: 3.739A pdb=" N ASP H 111 " --> pdb=" O LYS H 107 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ALA H 112 " --> pdb=" O PRO H 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 107 through 112' Processing helix chain 'H' and resid 113 through 126 removed outlier: 3.582A pdb=" N ARG H 126 " --> pdb=" O GLN H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 144 removed outlier: 3.575A pdb=" N LEU H 143 " --> pdb=" O ASN H 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 15 removed outlier: 4.221A pdb=" N LEU I 10 " --> pdb=" O PRO I 6 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N SER I 11 " --> pdb=" O LYS I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 65 removed outlier: 3.757A pdb=" N TYR I 64 " --> pdb=" O VAL I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 82 removed outlier: 4.913A pdb=" N LYS I 82 " --> pdb=" O ALA I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 96 removed outlier: 4.656A pdb=" N ARG I 96 " --> pdb=" O LEU I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 105 Processing helix chain 'I' and resid 109 through 120 removed outlier: 3.691A pdb=" N HIS I 119 " --> pdb=" O GLN I 115 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LYS I 120 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 165 removed outlier: 5.881A pdb=" N LYS I 155 " --> pdb=" O GLN I 151 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA I 156 " --> pdb=" O SER I 152 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA I 161 " --> pdb=" O ALA I 157 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU I 162 " --> pdb=" O LEU I 158 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN I 163 " --> pdb=" O GLU I 159 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG I 164 " --> pdb=" O LEU I 160 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLU I 165 " --> pdb=" O ALA I 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 191 removed outlier: 5.938A pdb=" N SER I 191 " --> pdb=" O ARG I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 205 removed outlier: 4.518A pdb=" N ILE I 199 " --> pdb=" O ASN I 195 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS I 205 " --> pdb=" O GLU I 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 70 removed outlier: 3.892A pdb=" N GLU J 64 " --> pdb=" O GLN J 60 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS J 65 " --> pdb=" O LYS J 61 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N MET J 70 " --> pdb=" O ALA J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 118 removed outlier: 6.234A pdb=" N ALA J 112 " --> pdb=" O GLY J 108 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL J 113 " --> pdb=" O ALA J 109 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL J 116 " --> pdb=" O ALA J 112 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY J 118 " --> pdb=" O LEU J 114 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 147 removed outlier: 5.724A pdb=" N ASN J 147 " --> pdb=" O LEU J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 156 removed outlier: 3.757A pdb=" N ALA J 154 " --> pdb=" O GLU J 150 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS J 155 " --> pdb=" O MET J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 165 removed outlier: 3.660A pdb=" N LEU J 164 " --> pdb=" O VAL J 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 11 through 18 removed outlier: 3.656A pdb=" N GLN K 17 " --> pdb=" O ASP K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 33 Processing helix chain 'K' and resid 67 through 82 removed outlier: 3.568A pdb=" N PHE K 80 " --> pdb=" O THR K 76 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN K 81 " --> pdb=" O THR K 77 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ASP K 82 " --> pdb=" O PHE K 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 30 Processing helix chain 'L' and resid 36 through 53 Processing helix chain 'L' and resid 56 through 69 removed outlier: 3.635A pdb=" N ALA L 64 " --> pdb=" O ALA L 60 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ASN L 67 " --> pdb=" O VAL L 63 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL L 68 " --> pdb=" O ALA L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 111 removed outlier: 4.908A pdb=" N ALA L 97 " --> pdb=" O VAL L 93 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS L 109 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ARG L 110 " --> pdb=" O ALA L 106 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N GLY L 111 " --> pdb=" O ALA L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 129 Processing helix chain 'L' and resid 131 through 145 removed outlier: 4.071A pdb=" N GLU L 145 " --> pdb=" O HIS L 141 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 20 Processing helix chain 'M' and resid 29 through 43 Processing helix chain 'M' and resid 111 through 119 removed outlier: 3.626A pdb=" N GLN M 117 " --> pdb=" O ARG M 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 33 through 38 removed outlier: 4.477A pdb=" N PHE N 38 " --> pdb=" O LEU N 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 55 Proline residue: N 50 - end of helix removed outlier: 5.071A pdb=" N LEU N 53 " --> pdb=" O GLN N 49 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL N 54 " --> pdb=" O PRO N 50 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ASP N 55 " --> pdb=" O LEU N 51 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 61 removed outlier: 4.001A pdb=" N LEU N 60 " --> pdb=" O MET N 56 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASP N 61 " --> pdb=" O VAL N 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 56 through 61' Processing helix chain 'N' and resid 70 through 85 Processing helix chain 'N' and resid 90 through 101 removed outlier: 4.808A pdb=" N GLU N 96 " --> pdb=" O SER N 92 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY N 101 " --> pdb=" O LEU N 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 33 removed outlier: 4.292A pdb=" N GLN O 20 " --> pdb=" O ARG O 16 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA O 29 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N THR O 32 " --> pdb=" O THR O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 81 through 89 removed outlier: 4.542A pdb=" N ASP O 85 " --> pdb=" O GLU O 81 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ALA O 86 " --> pdb=" O LYS O 82 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ARG O 89 " --> pdb=" O ASP O 85 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 50 removed outlier: 4.234A pdb=" N GLY P 50 " --> pdb=" O ALA P 46 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 58 removed outlier: 3.544A pdb=" N SER P 57 " --> pdb=" O GLY P 53 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N THR P 58 " --> pdb=" O SER P 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 53 through 58' Processing helix chain 'P' and resid 59 through 77 removed outlier: 5.285A pdb=" N ALA P 72 " --> pdb=" O ARG P 68 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N VAL P 73 " --> pdb=" O CYS P 69 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LYS P 74 " --> pdb=" O ALA P 70 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N GLU P 75 " --> pdb=" O ASP P 71 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N TYR P 76 " --> pdb=" O ALA P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 103 removed outlier: 4.947A pdb=" N THR P 95 " --> pdb=" O GLY P 91 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE P 96 " --> pdb=" O ARG P 92 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG P 97 " --> pdb=" O GLU P 93 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 10 Proline residue: Q 10 - end of helix Processing helix chain 'Q' and resid 112 through 117 removed outlier: 4.925A pdb=" N TYR Q 116 " --> pdb=" O ALA Q 112 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLY Q 117 " --> pdb=" O ARG Q 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 112 through 117' Processing helix chain 'R' and resid 13 through 21 removed outlier: 3.632A pdb=" N SER R 20 " --> pdb=" O ILE R 16 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ILE R 21 " --> pdb=" O ALA R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 37 Processing helix chain 'R' and resid 43 through 48 removed outlier: 5.740A pdb=" N SER R 48 " --> pdb=" O ILE R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 63 removed outlier: 5.045A pdb=" N THR R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS R 61 " --> pdb=" O ASP R 57 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE R 62 " --> pdb=" O GLU R 58 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL R 63 " --> pdb=" O VAL R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 83 Processing helix chain 'R' and resid 84 through 93 Processing helix chain 'R' and resid 105 through 110 removed outlier: 3.701A pdb=" N GLY R 110 " --> pdb=" O ALA R 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 105 through 110' Processing helix chain 'S' and resid 2 through 19 removed outlier: 3.624A pdb=" N LYS S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N TYR S 19 " --> pdb=" O LEU S 15 " (cutoff:3.500A) Processing helix chain 'S' and resid 23 through 28 removed outlier: 3.752A pdb=" N LYS S 27 " --> pdb=" O ARG S 23 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 50 removed outlier: 4.176A pdb=" N TRP S 41 " --> pdb=" O ASP S 37 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN S 48 " --> pdb=" O VAL S 44 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR S 49 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU S 50 " --> pdb=" O LYS S 46 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 90 removed outlier: 3.574A pdb=" N ARG S 89 " --> pdb=" O GLU S 85 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 15 removed outlier: 4.100A pdb=" N SER T 12 " --> pdb=" O ALA T 8 " (cutoff:3.500A) Processing helix chain 'T' and resid 23 through 46 removed outlier: 4.424A pdb=" N GLY T 40 " --> pdb=" O ASN T 36 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N HIS T 41 " --> pdb=" O HIS T 37 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N HIS T 45 " --> pdb=" O HIS T 41 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LYS T 46 " --> pdb=" O PHE T 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 73 Processing helix chain 'T' and resid 74 through 85 Processing helix chain 'U' and resid 53 through 64 Processing helix chain 'U' and resid 68 through 79 Processing helix chain 'W' and resid 12 through 17 removed outlier: 3.609A pdb=" N VAL W 17 " --> pdb=" O THR W 13 " (cutoff:3.500A) Processing helix chain 'W' and resid 24 through 33 removed outlier: 4.044A pdb=" N TYR W 31 " --> pdb=" O THR W 27 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N THR W 33 " --> pdb=" O LYS W 29 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 45 Processing helix chain 'W' and resid 47 through 65 Processing helix chain 'X' and resid 11 through 25 Processing helix chain 'X' and resid 69 through 75 removed outlier: 4.851A pdb=" N PHE X 73 " --> pdb=" O LYS X 69 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA X 74 " --> pdb=" O LEU X 70 " (cutoff:3.500A) Proline residue: X 75 - end of helix No H-bonds generated for 'chain 'X' and resid 69 through 75' Processing helix chain 'Y' and resid 5 through 41 removed outlier: 3.581A pdb=" N ARG Y 9 " --> pdb=" O SER Y 5 " (cutoff:3.500A) Processing helix chain 'Y' and resid 42 through 64 Proline residue: Y 55 - end of helix Processing helix chain 'Y' and resid 67 through 86 removed outlier: 5.965A pdb=" N ALA Y 71 " --> pdb=" O HIS Y 67 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 23 removed outlier: 3.782A pdb=" N ARG Z 20 " --> pdb=" O ARG Z 16 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU Z 23 " --> pdb=" O LYS Z 19 " (cutoff:3.500A) Processing helix chain 'Z' and resid 26 through 33 removed outlier: 3.977A pdb=" N GLU Z 30 " --> pdb=" O GLY Z 26 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ARG Z 33 " --> pdb=" O ALA Z 29 " (cutoff:3.500A) Processing helix chain 'Z' and resid 38 through 61 removed outlier: 3.541A pdb=" N LYS Z 58 " --> pdb=" O ARG Z 54 " (cutoff:3.500A) Processing helix chain 'a' and resid 6 through 16 removed outlier: 3.613A pdb=" N LYS a 14 " --> pdb=" O VAL a 10 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ASP a 16 " --> pdb=" O ARG a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 22 through 34 removed outlier: 3.623A pdb=" N GLU a 32 " --> pdb=" O ALA a 28 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA a 34 " --> pdb=" O LEU a 30 " (cutoff:3.500A) Processing helix chain 'a' and resid 181 through 200 Processing sheet with id= 1, first strand: chain 'b' and resid 1 through 4 Processing sheet with id= 2, first strand: chain 'b' and resid 32 through 35 No H-bonds generated for sheet with id= 2 Processing sheet with id= 3, first strand: chain 'b' and resid 79 through 82 removed outlier: 6.892A pdb=" N LEU b 92 " --> pdb=" O GLU b 78 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ILE b 73 " --> pdb=" O SER b 117 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N SER b 117 " --> pdb=" O ILE b 73 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP b 113 " --> pdb=" O VAL b 77 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N GLY b 126 " --> pdb=" O GLN b 114 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLN b 116 " --> pdb=" O GLY b 126 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'b' and resid 137 through 141 removed outlier: 4.306A pdb=" N SER b 138 " --> pdb=" O ILE b 163 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N THR b 172 " --> pdb=" O VAL b 164 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU b 179 " --> pdb=" O LEU b 175 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'b' and resid 90 through 95 removed outlier: 3.920A pdb=" N GLU b 99 " --> pdb=" O TYR b 95 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'c' and resid 3 through 8 removed outlier: 4.695A pdb=" N SER c 199 " --> pdb=" O LYS c 8 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LYS c 105 " --> pdb=" O VAL c 177 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'c' and resid 11 through 16 removed outlier: 4.435A pdb=" N VAL c 20 " --> pdb=" O THR c 16 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'c' and resid 79 through 84 removed outlier: 6.023A pdb=" N ARG c 46 " --> pdb=" O LEU c 84 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLN c 49 " --> pdb=" O THR c 35 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N GLN c 94 " --> pdb=" O VAL c 34 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'd' and resid 1 through 5 removed outlier: 6.329A pdb=" N MET d 1 " --> pdb=" O THR d 13 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N THR d 13 " --> pdb=" O MET d 1 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N LEU d 3 " --> pdb=" O ALA d 11 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA d 11 " --> pdb=" O LEU d 3 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LEU d 5 " --> pdb=" O GLN d 9 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'd' and resid 117 through 120 removed outlier: 5.648A pdb=" N ARG d 117 " --> pdb=" O ASP d 184 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP d 168 " --> pdb=" O VAL d 146 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'e' and resid 64 through 68 removed outlier: 3.525A pdb=" N LYS e 32 " --> pdb=" O THR e 156 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY e 38 " --> pdb=" O GLY e 150 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N GLY e 150 " --> pdb=" O GLY e 38 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU e 151 " --> pdb=" O VAL e 131 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL e 131 " --> pdb=" O LEU e 151 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLY e 125 " --> pdb=" O THR e 157 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'f' and resid 15 through 18 Processing sheet with id= 13, first strand: chain 'f' and resid 40 through 44 Processing sheet with id= 14, first strand: chain 'f' and resid 81 through 88 removed outlier: 6.597A pdb=" N THR f 128 " --> pdb=" O LEU f 88 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'f' and resid 93 through 97 Processing sheet with id= 16, first strand: chain 'g' and resid 18 through 21 removed outlier: 3.557A pdb=" N VAL g 21 " --> pdb=" O MET g 1 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N GLN g 2 " --> pdb=" O ALA g 39 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'g' and resid 76 through 82 removed outlier: 5.894A pdb=" N GLU g 76 " --> pdb=" O LYS g 141 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE g 132 " --> pdb=" O ALA g 140 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'j' and resid 52 through 57 removed outlier: 4.714A pdb=" N ASP j 19 " --> pdb=" O LEU j 140 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'j' and resid 74 through 78 removed outlier: 7.284A pdb=" N GLY j 83 " --> pdb=" O THR j 78 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'k' and resid 18 through 21 removed outlier: 3.924A pdb=" N THR k 6 " --> pdb=" O CYS k 21 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ASN k 82 " --> pdb=" O MET k 7 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'l' and resid 120 through 123 removed outlier: 3.841A pdb=" N LYS l 141 " --> pdb=" O VAL l 120 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'm' and resid 62 through 65 removed outlier: 3.976A pdb=" N TYR m 103 " --> pdb=" O LEU m 33 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU m 33 " --> pdb=" O LEU m 102 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'm' and resid 30 through 36 removed outlier: 7.621A pdb=" N SER m 30 " --> pdb=" O LYS m 133 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LYS m 127 " --> pdb=" O VAL m 36 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'n' and resid 33 through 37 removed outlier: 6.940A pdb=" N MET n 110 " --> pdb=" O CYS n 100 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N TYR n 94 " --> pdb=" O VAL n 116 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'o' and resid 49 through 52 removed outlier: 3.612A pdb=" N VAL o 49 " --> pdb=" O VAL o 39 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL o 28 " --> pdb=" O ASP o 93 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'p' and resid 37 through 44 Processing sheet with id= 27, first strand: chain 'p' and resid 48 through 52 removed outlier: 4.326A pdb=" N ALA p 48 " --> pdb=" O THR p 59 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ARG p 52 " --> pdb=" O HIS p 55 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N SER p 56 " --> pdb=" O THR p 75 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'r' and resid 11 through 15 removed outlier: 3.859A pdb=" N PHE r 5 " --> pdb=" O HIS r 12 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'r' and resid 18 through 21 removed outlier: 4.680A pdb=" N GLN r 18 " --> pdb=" O ILE r 98 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASP r 95 " --> pdb=" O VAL r 64 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LYS r 60 " --> pdb=" O THR r 99 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLU r 31 " --> pdb=" O VAL r 63 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'r' and resid 65 through 68 Processing sheet with id= 31, first strand: chain 'r' and resid 71 through 78 removed outlier: 4.293A pdb=" N TYR r 83 " --> pdb=" O ARG r 78 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 's' and resid 2 through 8 removed outlier: 4.644A pdb=" N THR s 3 " --> pdb=" O VAL s 107 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N THR s 100 " --> pdb=" O GLY s 79 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 's' and resid 80 through 88 removed outlier: 3.734A pdb=" N ARG s 92 " --> pdb=" O ARG s 88 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 't' and resid 12 through 15 removed outlier: 5.431A pdb=" N VAL t 31 " --> pdb=" O HIS t 15 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASN t 28 " --> pdb=" O LEU t 87 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS t 81 " --> pdb=" O VAL t 34 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LYS t 66 " --> pdb=" O ARG t 77 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASP t 79 " --> pdb=" O LYS t 64 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LYS t 64 " --> pdb=" O ASP t 79 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LYS t 81 " --> pdb=" O VAL t 62 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL t 62 " --> pdb=" O LYS t 81 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA t 83 " --> pdb=" O THR t 60 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N THR t 60 " --> pdb=" O ALA t 83 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL t 85 " --> pdb=" O VAL t 58 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL t 58 " --> pdb=" O VAL t 85 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'u' and resid 39 through 44 No H-bonds generated for sheet with id= 35 Processing sheet with id= 36, first strand: chain 'u' and resid 83 through 86 Processing sheet with id= 37, first strand: chain 'v' and resid 69 through 72 removed outlier: 4.107A pdb=" N ILE v 4 " --> pdb=" O THR v 62 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE v 89 " --> pdb=" O PRO v 27 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'w' and resid 30 through 33 removed outlier: 4.549A pdb=" N SER w 31 " --> pdb=" O ALA w 57 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU w 55 " --> pdb=" O ILE w 33 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ASN w 46 " --> pdb=" O LYS w 58 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'w' and resid 41 through 44 Processing sheet with id= 40, first strand: chain 'x' and resid 11 through 18 removed outlier: 4.512A pdb=" N THR x 24 " --> pdb=" O ASN x 16 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER x 18 " --> pdb=" O ASN x 22 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASN x 22 " --> pdb=" O SER x 18 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'x' and resid 34 through 40 Processing sheet with id= 42, first strand: chain 'z' and resid 34 through 38 removed outlier: 7.919A pdb=" N MET z 53 " --> pdb=" O THR z 9 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'C' and resid 19 through 24 removed outlier: 7.111A pdb=" N ILE C 47 " --> pdb=" O SER C 13 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LEU C 33 " --> pdb=" O GLU C 50 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'E' and resid 21 through 24 removed outlier: 5.983A pdb=" N PHE E 21 " --> pdb=" O VAL E 49 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'F' and resid 13 through 19 removed outlier: 8.961A pdb=" N ASN F 13 " --> pdb=" O SER F 28 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER F 28 " --> pdb=" O ASN F 13 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'G' and resid 14 through 17 removed outlier: 4.639A pdb=" N HIS G 14 " --> pdb=" O ILE G 40 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY G 16 " --> pdb=" O HIS G 38 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N HIS G 38 " --> pdb=" O GLY G 16 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'G' and resid 88 through 92 removed outlier: 4.723A pdb=" N PHE G 197 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ALA G 184 " --> pdb=" O PHE G 197 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'H' and resid 53 through 58 removed outlier: 3.532A pdb=" N ARG H 53 " --> pdb=" O HIS H 68 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'H' and resid 163 through 170 removed outlier: 6.570A pdb=" N ASP H 180 " --> pdb=" O LYS H 203 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU H 205 " --> pdb=" O ARG H 178 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ARG H 178 " --> pdb=" O GLU H 205 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'I' and resid 140 through 143 removed outlier: 6.652A pdb=" N GLU I 178 " --> pdb=" O ASP I 173 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'J' and resid 10 through 15 removed outlier: 4.230A pdb=" N GLN J 11 " --> pdb=" O GLY J 39 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LEU J 35 " --> pdb=" O ILE J 15 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'J' and resid 82 through 85 removed outlier: 7.328A pdb=" N HIS J 82 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N TYR J 127 " --> pdb=" O ARG J 92 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'J' and resid 31 through 40 removed outlier: 4.637A pdb=" N GLY J 50 " --> pdb=" O ALA J 34 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ARG J 44 " --> pdb=" O ASP J 40 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'K' and resid 34 through 37 removed outlier: 3.597A pdb=" N LYS K 35 " --> pdb=" O GLU K 65 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU K 65 " --> pdb=" O LYS K 35 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ASN K 63 " --> pdb=" O HIS K 37 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE K 6 " --> pdb=" O MET K 62 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N HIS K 3 " --> pdb=" O THR K 92 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU K 5 " --> pdb=" O MET K 90 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N MET K 90 " --> pdb=" O GLU K 5 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'K' and resid 38 through 42 removed outlier: 4.012A pdb=" N ARG K 38 " --> pdb=" O ASN K 63 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ASN K 63 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU K 40 " --> pdb=" O LEU K 61 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TYR K 59 " --> pdb=" O TRP K 42 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'L' and resid 71 through 76 removed outlier: 5.958A pdb=" N THR L 71 " --> pdb=" O VAL L 90 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'M' and resid 22 through 27 removed outlier: 6.929A pdb=" N ALA M 22 " --> pdb=" O LEU M 62 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LYS M 55 " --> pdb=" O ASP M 53 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASP M 53 " --> pdb=" O LYS M 55 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU M 51 " --> pdb=" O GLU M 57 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'M' and resid 73 through 77 removed outlier: 3.774A pdb=" N SER M 73 " --> pdb=" O ALA M 129 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE M 125 " --> pdb=" O VAL M 77 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL M 102 " --> pdb=" O ILE M 125 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'N' and resid 4 through 10 removed outlier: 3.681A pdb=" N GLY N 9 " --> pdb=" O ALA N 16 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS N 67 " --> pdb=" O ALA N 15 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'O' and resid 6 through 12 Processing sheet with id= 61, first strand: chain 'O' and resid 39 through 42 removed outlier: 4.581A pdb=" N LEU O 42 " --> pdb=" O LEU O 71 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU O 71 " --> pdb=" O LEU O 42 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'P' and resid 29 through 34 removed outlier: 4.787A pdb=" N ASN P 108 " --> pdb=" O LEU P 81 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLY P 87 " --> pdb=" O VAL P 112 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'Q' and resid 28 through 32 removed outlier: 5.570A pdb=" N LEU Q 80 " --> pdb=" O VAL Q 97 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'Q' and resid 36 through 40 removed outlier: 5.207A pdb=" N LYS Q 50 " --> pdb=" O ILE Q 66 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N PHE Q 60 " --> pdb=" O LEU Q 56 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'U' and resid 4 through 10 removed outlier: 3.521A pdb=" N ALA U 7 " --> pdb=" O GLN U 18 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN U 18 " --> pdb=" O ALA U 7 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLY U 37 " --> pdb=" O VAL U 19 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'V' and resid 18 through 29 No H-bonds generated for sheet with id= 66 Processing sheet with id= 67, first strand: chain 'V' and resid 59 through 62 removed outlier: 6.909A pdb=" N GLU V 59 " --> pdb=" O VAL V 75 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'X' and resid 29 through 33 removed outlier: 3.925A pdb=" N LEU X 30 " --> pdb=" O THR X 47 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LEU X 46 " --> pdb=" O VAL X 61 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'a' and resid 60 through 65 removed outlier: 3.560A pdb=" N TYR a 163 " --> pdb=" O GLY a 61 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N GLY a 159 " --> pdb=" O LEU a 65 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'a' and resid 169 through 176 removed outlier: 5.894A pdb=" N GLY a 169 " --> pdb=" O LEU a 48 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE a 175 " --> pdb=" O VAL a 42 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL a 42 " --> pdb=" O ILE a 175 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LYS a 211 " --> pdb=" O ASN a 47 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N VAL a 212 " --> pdb=" O VAL a 224 " (cutoff:3.500A) 1776 hydrogen bonds defined for protein. 5250 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2986 hydrogen bonds 5020 hydrogen bond angles 0 basepair planarities 1213 basepair parallelities 2375 stacking parallelities Total time for adding SS restraints: 217.66 Time building geometry restraints manager: 66.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.07 - 1.22: 77 1.22 - 1.37: 38612 1.37 - 1.52: 79957 1.52 - 1.67: 38679 1.67 - 1.82: 258 Bond restraints: 157583 Sorted by residual: bond pdb=" C VAL a 59 " pdb=" O VAL a 59 " ideal model delta sigma weight residual 1.236 1.403 -0.168 1.09e-02 8.42e+03 2.36e+02 bond pdb=" C ARG I 61 " pdb=" O ARG I 61 " ideal model delta sigma weight residual 1.237 1.411 -0.175 1.19e-02 7.06e+03 2.15e+02 bond pdb=" C ILE o 58 " pdb=" O ILE o 58 " ideal model delta sigma weight residual 1.233 1.412 -0.179 1.22e-02 6.72e+03 2.14e+02 bond pdb=" C PHE W 12 " pdb=" O PHE W 12 " ideal model delta sigma weight residual 1.235 1.396 -0.161 1.14e-02 7.69e+03 2.00e+02 bond pdb=" C LYS c 157 " pdb=" O LYS c 157 " ideal model delta sigma weight residual 1.234 1.407 -0.173 1.27e-02 6.20e+03 1.86e+02 ... (remaining 157578 not shown) Histogram of bond angle deviations from ideal: 98.35 - 106.77: 28975 106.77 - 115.20: 104158 115.20 - 123.63: 78172 123.63 - 132.06: 23348 132.06 - 140.49: 1198 Bond angle restraints: 235851 Sorted by residual: angle pdb=" C GLY G 201 " pdb=" N ASN G 202 " pdb=" CA ASN G 202 " ideal model delta sigma weight residual 120.82 101.95 18.87 1.47e+00 4.63e-01 1.65e+02 angle pdb=" C HIS j 80 " pdb=" N ILE j 81 " pdb=" CA ILE j 81 " ideal model delta sigma weight residual 120.98 103.95 17.03 1.36e+00 5.41e-01 1.57e+02 angle pdb=" N ASN G 202 " pdb=" CA ASN G 202 " pdb=" C ASN G 202 " ideal model delta sigma weight residual 110.24 126.30 -16.06 1.30e+00 5.92e-01 1.53e+02 angle pdb=" N VAL g 9 " pdb=" CA VAL g 9 " pdb=" C VAL g 9 " ideal model delta sigma weight residual 108.12 124.42 -16.30 1.34e+00 5.57e-01 1.48e+02 angle pdb=" C ASP S 17 " pdb=" N LYS S 18 " pdb=" CA LYS S 18 " ideal model delta sigma weight residual 120.63 106.23 14.40 1.36e+00 5.41e-01 1.12e+02 ... (remaining 235846 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 89814 35.92 - 71.85: 10088 71.85 - 107.77: 1037 107.77 - 143.69: 12 143.69 - 179.61: 23 Dihedral angle restraints: 100974 sinusoidal: 84589 harmonic: 16385 Sorted by residual: dihedral pdb=" C4' G 11738 " pdb=" C3' G 11738 " pdb=" C2' G 11738 " pdb=" C1' G 11738 " ideal model delta sinusoidal sigma weight residual -35.00 34.30 -69.30 1 8.00e+00 1.56e-02 9.70e+01 dihedral pdb=" C5' G 11738 " pdb=" C4' G 11738 " pdb=" C3' G 11738 " pdb=" O3' G 11738 " ideal model delta sinusoidal sigma weight residual 147.00 79.73 67.27 1 8.00e+00 1.56e-02 9.21e+01 dihedral pdb=" C4' G 12286 " pdb=" C3' G 12286 " pdb=" C2' G 12286 " pdb=" C1' G 12286 " ideal model delta sinusoidal sigma weight residual -35.00 31.28 -66.28 1 8.00e+00 1.56e-02 8.97e+01 ... (remaining 100971 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 25243 0.114 - 0.229: 4498 0.229 - 0.343: 375 0.343 - 0.457: 37 0.457 - 0.571: 4 Chirality restraints: 30157 Sorted by residual: chirality pdb=" CA PRO Z 10 " pdb=" N PRO Z 10 " pdb=" C PRO Z 10 " pdb=" CB PRO Z 10 " both_signs ideal model delta sigma weight residual False 2.72 2.15 0.57 2.00e-01 2.50e+01 8.16e+00 chirality pdb=" CA VAL r 51 " pdb=" N VAL r 51 " pdb=" C VAL r 51 " pdb=" CB VAL r 51 " both_signs ideal model delta sigma weight residual False 2.44 2.96 -0.52 2.00e-01 2.50e+01 6.85e+00 chirality pdb=" C3' G 11738 " pdb=" C4' G 11738 " pdb=" O3' G 11738 " pdb=" C2' G 11738 " both_signs ideal model delta sigma weight residual False -2.74 -2.26 -0.48 2.00e-01 2.50e+01 5.84e+00 ... (remaining 30154 not shown) Planarity restraints: 12574 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 12061 " 0.270 2.00e-02 2.50e+03 1.11e-01 3.72e+02 pdb=" N9 G 12061 " -0.019 2.00e-02 2.50e+03 pdb=" C8 G 12061 " -0.123 2.00e-02 2.50e+03 pdb=" N7 G 12061 " -0.104 2.00e-02 2.50e+03 pdb=" C5 G 12061 " -0.048 2.00e-02 2.50e+03 pdb=" C6 G 12061 " 0.051 2.00e-02 2.50e+03 pdb=" O6 G 12061 " 0.166 2.00e-02 2.50e+03 pdb=" N1 G 12061 " 0.041 2.00e-02 2.50e+03 pdb=" C2 G 12061 " -0.028 2.00e-02 2.50e+03 pdb=" N2 G 12061 " -0.050 2.00e-02 2.50e+03 pdb=" N3 G 12061 " -0.077 2.00e-02 2.50e+03 pdb=" C4 G 12061 " -0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 11328 " -0.214 2.00e-02 2.50e+03 9.21e-02 2.33e+02 pdb=" N9 A 11328 " 0.016 2.00e-02 2.50e+03 pdb=" C8 A 11328 " 0.084 2.00e-02 2.50e+03 pdb=" N7 A 11328 " 0.070 2.00e-02 2.50e+03 pdb=" C5 A 11328 " 0.039 2.00e-02 2.50e+03 pdb=" C6 A 11328 " -0.033 2.00e-02 2.50e+03 pdb=" N6 A 11328 " -0.137 2.00e-02 2.50e+03 pdb=" N1 A 11328 " -0.019 2.00e-02 2.50e+03 pdb=" C2 A 11328 " 0.040 2.00e-02 2.50e+03 pdb=" N3 A 11328 " 0.083 2.00e-02 2.50e+03 pdb=" C4 A 11328 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 12319 " 0.205 2.00e-02 2.50e+03 8.52e-02 2.18e+02 pdb=" N9 G 12319 " -0.014 2.00e-02 2.50e+03 pdb=" C8 G 12319 " -0.094 2.00e-02 2.50e+03 pdb=" N7 G 12319 " -0.083 2.00e-02 2.50e+03 pdb=" C5 G 12319 " -0.037 2.00e-02 2.50e+03 pdb=" C6 G 12319 " 0.039 2.00e-02 2.50e+03 pdb=" O6 G 12319 " 0.129 2.00e-02 2.50e+03 pdb=" N1 G 12319 " 0.032 2.00e-02 2.50e+03 pdb=" C2 G 12319 " -0.021 2.00e-02 2.50e+03 pdb=" N2 G 12319 " -0.042 2.00e-02 2.50e+03 pdb=" N3 G 12319 " -0.055 2.00e-02 2.50e+03 pdb=" C4 G 12319 " -0.058 2.00e-02 2.50e+03 ... (remaining 12571 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 4477 2.66 - 3.22: 124811 3.22 - 3.78: 285363 3.78 - 4.34: 383925 4.34 - 4.90: 510290 Nonbonded interactions: 1308866 Sorted by model distance: nonbonded pdb=" O HIS G 14 " pdb=" O PHE G 15 " model vdw 2.098 3.040 nonbonded pdb=" N6 A 12590 " pdb=" O4 U 12604 " model vdw 2.266 2.520 nonbonded pdb=" O2' G 11738 " pdb=" OP2 A 11739 " model vdw 2.296 2.440 nonbonded pdb=" O GLU H 160 " pdb=" O2' A 31055 " model vdw 2.322 2.440 nonbonded pdb=" O ASN l 93 " pdb=" OG1 THR l 94 " model vdw 2.339 2.440 ... (remaining 1308861 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: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 12.350 Check model and map are aligned: 1.530 Set scattering table: 0.960 Process input model: 506.180 Find NCS groups from input model: 2.850 Set up NCS constraints: 0.380 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:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 528.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 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 : 0.008 0.179 157583 Z= 0.528 Angle : 1.067 18.869 235851 Z= 0.720 Chirality : 0.088 0.571 30157 Planarity : 0.013 0.111 12574 Dihedral : 22.450 179.614 90402 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.60 % Allowed : 9.29 % Favored : 90.11 % Rotamer: Outliers : 0.43 % Allowed : 4.17 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.73 (0.09), residues: 5652 helix: -3.69 (0.07), residues: 1687 sheet: -2.69 (0.14), residues: 1031 loop : -2.96 (0.10), residues: 2934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.006 TRP S 41 HIS 0.002 0.000 HIS m 13 PHE 0.022 0.003 PHE o 117 TYR 0.037 0.005 TYR s 38 ARG 0.005 0.000 ARG U 8 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11304 Ramachandran restraints generated. 5652 Oldfield, 0 Emsley, 5652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11304 Ramachandran restraints generated. 5652 Oldfield, 0 Emsley, 5652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1205 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 1185 time to evaluate : 6.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 63 ILE cc_start: 0.9341 (mt) cc_final: 0.9096 (tp) REVERT: b 114 GLN cc_start: 0.9126 (tt0) cc_final: 0.8902 (tp-100) REVERT: b 115 ILE cc_start: 0.9128 (pt) cc_final: 0.8854 (pt) REVERT: b 180 MET cc_start: 0.8434 (mmm) cc_final: 0.7263 (mmm) REVERT: d 101 TYR cc_start: 0.8986 (t80) cc_final: 0.8711 (t80) REVERT: f 25 ILE cc_start: 0.7710 (mt) cc_final: 0.7369 (mm) REVERT: f 28 LYS cc_start: 0.8988 (ttpp) cc_final: 0.8671 (mmtm) REVERT: f 68 ARG cc_start: 0.8048 (ttp80) cc_final: 0.7651 (ttp80) REVERT: g 33 GLN cc_start: 0.9106 (mm-40) cc_final: 0.8762 (mp10) REVERT: g 40 THR cc_start: 0.8893 (p) cc_final: 0.8618 (p) REVERT: g 60 GLU cc_start: 0.9555 (tp30) cc_final: 0.9352 (mt-10) REVERT: k 20 MET cc_start: 0.7896 (ttp) cc_final: 0.7324 (ttp) REVERT: k 104 THR cc_start: 0.8828 (p) cc_final: 0.8219 (p) REVERT: m 112 LEU cc_start: 0.9548 (tp) cc_final: 0.9270 (tp) REVERT: n 78 LYS cc_start: 0.9261 (tttt) cc_final: 0.8896 (tttt) REVERT: p 12 MET cc_start: 0.7059 (mtp) cc_final: 0.6611 (mtp) REVERT: q 48 ASP cc_start: 0.7299 (m-30) cc_final: 0.7097 (m-30) REVERT: r 26 ASP cc_start: 0.7700 (p0) cc_final: 0.7466 (p0) REVERT: r 41 ILE cc_start: 0.9045 (mt) cc_final: 0.8753 (tp) REVERT: r 101 ILE cc_start: 0.9337 (mm) cc_final: 0.9124 (mm) REVERT: t 2 ILE cc_start: 0.8154 (mm) cc_final: 0.7794 (mm) REVERT: t 87 LEU cc_start: 0.9225 (mt) cc_final: 0.9006 (mp) REVERT: v 90 ASP cc_start: 0.7955 (m-30) cc_final: 0.7751 (m-30) REVERT: x 45 PHE cc_start: 0.8758 (m-80) cc_final: 0.8542 (m-10) REVERT: y 39 GLN cc_start: 0.8174 (mt0) cc_final: 0.7800 (mt0) REVERT: B 47 TYR cc_start: 0.8448 (m-80) cc_final: 0.7830 (m-80) REVERT: C 4 ILE cc_start: 0.8964 (mm) cc_final: 0.8013 (mm) REVERT: D 14 ARG cc_start: 0.8449 (mmt90) cc_final: 0.7955 (mmt90) REVERT: F 1 MET cc_start: 0.5376 (tpt) cc_final: 0.3944 (ptt) REVERT: F 24 ARG cc_start: 0.8804 (ttm170) cc_final: 0.8303 (mtt-85) REVERT: F 35 GLN cc_start: 0.8679 (pt0) cc_final: 0.8386 (mt0) REVERT: G 161 PHE cc_start: 0.8770 (t80) cc_final: 0.8549 (t80) REVERT: H 28 PHE cc_start: 0.9121 (t80) cc_final: 0.8444 (t80) REVERT: H 68 HIS cc_start: 0.8189 (m90) cc_final: 0.7986 (m-70) REVERT: H 71 ARG cc_start: 0.9028 (mtt180) cc_final: 0.8735 (tpm170) REVERT: H 111 ASP cc_start: 0.8537 (m-30) cc_final: 0.8024 (m-30) REVERT: H 129 PHE cc_start: 0.7939 (p90) cc_final: 0.7603 (p90) REVERT: H 167 TYR cc_start: 0.8695 (t80) cc_final: 0.8246 (t80) REVERT: H 183 TYR cc_start: 0.8635 (t80) cc_final: 0.7785 (t80) REVERT: I 75 TYR cc_start: 0.9156 (t80) cc_final: 0.8889 (t80) REVERT: I 134 TYR cc_start: 0.8625 (t80) cc_final: 0.8424 (t80) REVERT: I 135 GLN cc_start: 0.8734 (mm110) cc_final: 0.8308 (pp30) REVERT: J 13 LYS cc_start: 0.9101 (tptp) cc_final: 0.8787 (tttm) REVERT: J 28 ARG cc_start: 0.8482 (mtm180) cc_final: 0.8144 (ptp-110) REVERT: J 65 LYS cc_start: 0.9559 (mttm) cc_final: 0.9353 (mmtp) REVERT: J 96 GLN cc_start: 0.8681 (mt0) cc_final: 0.7798 (mm-40) REVERT: J 115 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8814 (mt-10) REVERT: J 146 MET cc_start: 0.8405 (ttp) cc_final: 0.7979 (tmm) REVERT: K 11 HIS cc_start: 0.8664 (t-90) cc_final: 0.8372 (t70) REVERT: K 21 MET cc_start: 0.9463 (mtp) cc_final: 0.9192 (mmm) REVERT: K 33 GLU cc_start: 0.9067 (tt0) cc_final: 0.8855 (tm-30) REVERT: K 56 LYS cc_start: 0.9529 (mttt) cc_final: 0.8989 (mmtp) REVERT: K 62 MET cc_start: 0.9474 (mmm) cc_final: 0.9124 (mmm) REVERT: K 89 VAL cc_start: 0.7127 (OUTLIER) cc_final: 0.6689 (m) REVERT: M 26 MET cc_start: 0.7317 (ptp) cc_final: 0.5670 (mtt) REVERT: M 110 MET cc_start: 0.6766 (ptp) cc_final: 0.5957 (ptp) REVERT: M 127 TYR cc_start: 0.8820 (m-80) cc_final: 0.8549 (m-80) REVERT: N 36 GLN cc_start: 0.8790 (tp-100) cc_final: 0.8431 (tm-30) REVERT: O 49 PHE cc_start: 0.8620 (m-80) cc_final: 0.8307 (m-80) REVERT: O 66 GLU cc_start: 0.8994 (pt0) cc_final: 0.8676 (pm20) REVERT: P 17 ASP cc_start: 0.8654 (m-30) cc_final: 0.8362 (t70) REVERT: P 37 GLN cc_start: 0.9039 (mm-40) cc_final: 0.8317 (tm-30) REVERT: P 79 LYS cc_start: 0.9606 (tptt) cc_final: 0.9370 (tmmt) REVERT: P 93 GLU cc_start: 0.9212 (tt0) cc_final: 0.8941 (tm-30) REVERT: Q 74 GLN cc_start: 0.7561 (mt0) cc_final: 0.7183 (mm110) REVERT: Q 76 HIS cc_start: 0.7801 (m-70) cc_final: 0.7436 (m-70) REVERT: Q 95 HIS cc_start: 0.8943 (m90) cc_final: 0.8277 (m-70) REVERT: S 19 TYR cc_start: 0.7147 (p90) cc_final: 0.6908 (p90) REVERT: S 76 PHE cc_start: 0.8639 (m-80) cc_final: 0.8310 (m-80) REVERT: T 3 SER cc_start: 0.7032 (t) cc_final: 0.6604 (t) REVERT: T 13 GLU cc_start: 0.9642 (tt0) cc_final: 0.9386 (tm-30) REVERT: T 44 GLU cc_start: 0.8673 (pt0) cc_final: 0.8349 (pt0) REVERT: U 12 LYS cc_start: 0.8834 (ttpt) cc_final: 0.7763 (pttt) REVERT: U 31 ARG cc_start: 0.8307 (ttp-170) cc_final: 0.7869 (ttp80) REVERT: U 32 PHE cc_start: 0.8818 (p90) cc_final: 0.8518 (p90) REVERT: U 69 ASP cc_start: 0.9116 (p0) cc_final: 0.8866 (p0) REVERT: X 65 MET cc_start: 0.7398 (ptm) cc_final: 0.7095 (ppp) REVERT: Y 26 MET cc_start: 0.9516 (ttp) cc_final: 0.9206 (tmm) REVERT: Y 27 MET cc_start: 0.9058 (mmm) cc_final: 0.7911 (mmm) REVERT: Y 31 ILE cc_start: 0.9647 (mt) cc_final: 0.8555 (tp) REVERT: Y 47 GLN cc_start: 0.9160 (mt0) cc_final: 0.8597 (mp10) REVERT: Y 54 GLN cc_start: 0.8865 (tt0) cc_final: 0.8641 (tt0) REVERT: a 8 MET cc_start: -0.5187 (mpp) cc_final: -0.5452 (mpp) REVERT: a 218 MET cc_start: 0.0425 (mmm) cc_final: 0.0052 (mmm) outliers start: 20 outliers final: 7 residues processed: 1200 average time/residue: 1.3282 time to fit residues: 2706.0573 Evaluate side-chains 750 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 742 time to evaluate : 5.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 151 THR Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain G residue 119 GLN Chi-restraints excluded: chain I residue 151 GLN Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain V residue 37 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 858 optimal weight: 40.0000 chunk 770 optimal weight: 20.0000 chunk 427 optimal weight: 20.0000 chunk 263 optimal weight: 5.9990 chunk 519 optimal weight: 40.0000 chunk 411 optimal weight: 6.9990 chunk 797 optimal weight: 10.0000 chunk 308 optimal weight: 6.9990 chunk 484 optimal weight: 9.9990 chunk 593 optimal weight: 50.0000 chunk 923 optimal weight: 50.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 44 ASN b 45 ASN b 59 GLN b 89 ASN ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 133 ASN b 196 ASN b 199 HIS b 259 ASN c 36 GLN c 42 ASN c 130 GLN c 164 GLN c 167 ASN d 9 GLN d 24 ASN d 94 GLN d 136 GLN d 163 ASN ** d 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 20 ASN ** e 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 138 GLN f 142 GLN g 11 ASN g 20 ASN g 73 ASN j 40 HIS j 58 ASN j 80 HIS j 136 GLN j 138 GLN l 35 HIS l 54 GLN n 62 ASN o 104 GLN p 6 GLN p 11 GLN p 65 ASN q 43 GLN q 55 GLN q 65 ASN ** r 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 40 ASN t 59 ASN u 53 GLN u 68 ASN u 98 ASN v 49 ASN v 78 GLN x 16 ASN x 22 ASN y 20 ASN z 19 HIS ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 ASN D 29 GLN E 42 HIS ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 ASN G 41 ASN G 57 ASN G 88 GLN G 121 GLN G 176 ASN ** G 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 2 GLN H 138 GLN H 139 ASN ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 130 ASN I 195 ASN J 69 ASN ** J 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 52 ASN ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 ASN L 96 ASN L 121 ASN ** M 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 125 GLN ** O 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 7 ASN R 51 GLN ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 42 ASN S 48 GLN S 59 GLN T 27 GLN U 26 ASN ** U 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 79 ASN W 30 ASN W 73 HIS ** X 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 68 HIS Y 19 HIS Y 69 ASN Y 83 ASN a 67 HIS a 160 GLN ** a 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 188 ASN Total number of N/Q/H flips: 87 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.160 157583 Z= 0.291 Angle : 0.686 12.274 235851 Z= 0.356 Chirality : 0.038 0.354 30157 Planarity : 0.006 0.066 12574 Dihedral : 23.486 178.039 79097 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.16 % Favored : 91.74 % Rotamer: Outliers : 2.32 % Allowed : 11.91 % Favored : 85.77 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.10), residues: 5652 helix: -1.44 (0.11), residues: 1803 sheet: -2.28 (0.15), residues: 969 loop : -2.53 (0.11), residues: 2880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP H 200 HIS 0.012 0.002 HIS Y 67 PHE 0.026 0.002 PHE M 44 TYR 0.018 0.002 TYR T 68 ARG 0.011 0.001 ARG f 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11304 Ramachandran restraints generated. 5652 Oldfield, 0 Emsley, 5652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11304 Ramachandran restraints generated. 5652 Oldfield, 0 Emsley, 5652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 980 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 871 time to evaluate : 5.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 63 ILE cc_start: 0.9315 (mt) cc_final: 0.9037 (tp) REVERT: b 66 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.8099 (p90) REVERT: b 160 TYR cc_start: 0.8232 (p90) cc_final: 0.7915 (p90) REVERT: b 269 ARG cc_start: 0.7854 (tpt90) cc_final: 0.7603 (tpt90) REVERT: d 101 TYR cc_start: 0.9058 (t80) cc_final: 0.8710 (t80) REVERT: f 25 ILE cc_start: 0.7927 (mt) cc_final: 0.7577 (mm) REVERT: f 68 ARG cc_start: 0.7668 (ttp80) cc_final: 0.7234 (ttp80) REVERT: f 148 ARG cc_start: 0.8171 (tpt170) cc_final: 0.7950 (ttp-110) REVERT: f 150 TYR cc_start: 0.8288 (m-80) cc_final: 0.7965 (m-80) REVERT: f 176 LYS cc_start: 0.6344 (tmtt) cc_final: 0.5934 (ptmm) REVERT: g 29 PHE cc_start: 0.8389 (t80) cc_final: 0.8123 (t80) REVERT: g 33 GLN cc_start: 0.9099 (mm-40) cc_final: 0.8893 (mp10) REVERT: j 103 ILE cc_start: 0.9175 (mm) cc_final: 0.8868 (mm) REVERT: k 51 LYS cc_start: 0.9218 (mtmt) cc_final: 0.9008 (pttm) REVERT: k 104 THR cc_start: 0.8910 (p) cc_final: 0.8390 (p) REVERT: k 106 GLU cc_start: 0.7775 (mp0) cc_final: 0.7568 (mp0) REVERT: m 112 LEU cc_start: 0.9534 (tp) cc_final: 0.9045 (tt) REVERT: p 114 ASN cc_start: 0.8871 (OUTLIER) cc_final: 0.8619 (p0) REVERT: q 51 GLN cc_start: 0.8292 (mt0) cc_final: 0.8061 (mt0) REVERT: t 1 MET cc_start: 0.4474 (tpt) cc_final: 0.4156 (tpt) REVERT: t 5 GLU cc_start: 0.8273 (mp0) cc_final: 0.6860 (mp0) REVERT: w 64 LYS cc_start: 0.8945 (tppt) cc_final: 0.8333 (tppt) REVERT: x 65 THR cc_start: 0.9230 (p) cc_final: 0.8872 (p) REVERT: z 31 ILE cc_start: 0.9242 (OUTLIER) cc_final: 0.9022 (mm) REVERT: B 47 TYR cc_start: 0.8537 (m-80) cc_final: 0.7928 (m-80) REVERT: C 34 GLU cc_start: 0.6564 (tp30) cc_final: 0.6044 (mm-30) REVERT: E 29 ARG cc_start: 0.8267 (mmm-85) cc_final: 0.8024 (mmm-85) REVERT: F 1 MET cc_start: 0.5551 (tpt) cc_final: 0.3873 (ptt) REVERT: G 41 ASN cc_start: 0.7867 (OUTLIER) cc_final: 0.7605 (p0) REVERT: G 48 MET cc_start: 0.9401 (ttp) cc_final: 0.8996 (ttp) REVERT: H 28 PHE cc_start: 0.9074 (t80) cc_final: 0.8646 (t80) REVERT: H 68 HIS cc_start: 0.8394 (m90) cc_final: 0.8083 (m-70) REVERT: H 71 ARG cc_start: 0.8998 (mtt180) cc_final: 0.8660 (tpm170) REVERT: H 111 ASP cc_start: 0.8426 (m-30) cc_final: 0.8174 (m-30) REVERT: H 128 MET cc_start: 0.8103 (mmt) cc_final: 0.7810 (tpp) REVERT: H 167 TYR cc_start: 0.8747 (t80) cc_final: 0.8195 (t80) REVERT: H 183 TYR cc_start: 0.8743 (t80) cc_final: 0.8517 (t80) REVERT: I 73 ASN cc_start: 0.9361 (m-40) cc_final: 0.9061 (m-40) REVERT: I 74 TYR cc_start: 0.9505 (m-10) cc_final: 0.9223 (m-80) REVERT: I 75 TYR cc_start: 0.8913 (t80) cc_final: 0.8701 (t80) REVERT: I 102 TYR cc_start: 0.8355 (t80) cc_final: 0.8125 (t80) REVERT: I 134 TYR cc_start: 0.8720 (t80) cc_final: 0.8303 (t80) REVERT: I 135 GLN cc_start: 0.8796 (mm110) cc_final: 0.8294 (pp30) REVERT: J 13 LYS cc_start: 0.9168 (tptp) cc_final: 0.8842 (tttm) REVERT: J 25 LYS cc_start: 0.9622 (tmmt) cc_final: 0.9221 (tppt) REVERT: J 28 ARG cc_start: 0.8443 (mtm180) cc_final: 0.8117 (ptp-110) REVERT: J 35 LEU cc_start: 0.9265 (tp) cc_final: 0.9052 (tp) REVERT: J 53 ARG cc_start: 0.8432 (tpp80) cc_final: 0.7737 (mpt-90) REVERT: J 61 LYS cc_start: 0.9466 (mtpp) cc_final: 0.9158 (mtmm) REVERT: J 63 MET cc_start: 0.9309 (mmm) cc_final: 0.9096 (mmm) REVERT: J 115 GLU cc_start: 0.9174 (mt-10) cc_final: 0.8795 (mt-10) REVERT: J 141 ASP cc_start: 0.9297 (t0) cc_final: 0.8982 (t0) REVERT: K 9 MET cc_start: 0.9148 (OUTLIER) cc_final: 0.8871 (mmt) REVERT: K 11 HIS cc_start: 0.8586 (t-90) cc_final: 0.8329 (t70) REVERT: K 13 ASP cc_start: 0.9125 (m-30) cc_final: 0.8834 (p0) REVERT: K 21 MET cc_start: 0.9516 (mtp) cc_final: 0.9142 (mtm) REVERT: K 22 ILE cc_start: 0.9146 (mt) cc_final: 0.8885 (mt) REVERT: K 25 TYR cc_start: 0.8630 (m-80) cc_final: 0.8034 (m-80) REVERT: K 59 TYR cc_start: 0.7366 (m-10) cc_final: 0.6578 (m-10) REVERT: K 62 MET cc_start: 0.9463 (mmm) cc_final: 0.9134 (mmm) REVERT: L 30 MET cc_start: 0.8251 (tmm) cc_final: 0.7372 (tmm) REVERT: L 100 MET cc_start: 0.9218 (ttm) cc_final: 0.8828 (ttm) REVERT: L 141 HIS cc_start: 0.7387 (m-70) cc_final: 0.6762 (m-70) REVERT: M 2 MET cc_start: 0.7939 (tpt) cc_final: 0.7685 (tpt) REVERT: M 26 MET cc_start: 0.6115 (ptp) cc_final: 0.5152 (mtt) REVERT: M 60 LEU cc_start: 0.8863 (mt) cc_final: 0.8375 (mt) REVERT: M 110 MET cc_start: 0.6276 (ptp) cc_final: 0.5750 (ptp) REVERT: N 36 GLN cc_start: 0.8604 (tp-100) cc_final: 0.8177 (tm-30) REVERT: O 49 PHE cc_start: 0.8541 (m-80) cc_final: 0.8322 (m-80) REVERT: O 66 GLU cc_start: 0.9408 (pt0) cc_final: 0.9030 (pm20) REVERT: P 17 ASP cc_start: 0.8597 (m-30) cc_final: 0.8175 (t70) REVERT: P 37 GLN cc_start: 0.9174 (mm-40) cc_final: 0.8452 (tm-30) REVERT: P 51 PHE cc_start: 0.6759 (m-80) cc_final: 0.6525 (m-10) REVERT: P 79 LYS cc_start: 0.9647 (tptt) cc_final: 0.9443 (tmmt) REVERT: P 93 GLU cc_start: 0.9094 (tt0) cc_final: 0.8785 (tm-30) REVERT: Q 95 HIS cc_start: 0.8921 (m90) cc_final: 0.8437 (m-70) REVERT: R 65 GLU cc_start: 0.9039 (tt0) cc_final: 0.8664 (mp0) REVERT: S 5 MET cc_start: 0.5322 (mmt) cc_final: 0.5106 (mmt) REVERT: S 76 PHE cc_start: 0.8756 (m-80) cc_final: 0.8406 (m-80) REVERT: T 13 GLU cc_start: 0.9631 (tt0) cc_final: 0.9309 (pt0) REVERT: T 44 GLU cc_start: 0.8796 (pt0) cc_final: 0.8465 (pt0) REVERT: U 12 LYS cc_start: 0.9183 (ttpt) cc_final: 0.8299 (pttt) REVERT: U 31 ARG cc_start: 0.8613 (ttp-170) cc_final: 0.7862 (ttp80) REVERT: U 32 PHE cc_start: 0.8808 (p90) cc_final: 0.8574 (p90) REVERT: U 56 ARG cc_start: 0.9044 (mmm160) cc_final: 0.8652 (tpt90) REVERT: V 76 ARG cc_start: 0.8969 (ptt-90) cc_final: 0.8653 (ptt-90) REVERT: X 46 LEU cc_start: 0.7938 (mm) cc_final: 0.7559 (mp) REVERT: X 65 MET cc_start: 0.7398 (ptm) cc_final: 0.6980 (ppp) REVERT: Y 11 ILE cc_start: 0.8874 (mp) cc_final: 0.8655 (mp) REVERT: Y 24 ARG cc_start: 0.9316 (mtm-85) cc_final: 0.8962 (mtm180) REVERT: Y 26 MET cc_start: 0.9472 (ttp) cc_final: 0.9149 (ptp) REVERT: Y 31 ILE cc_start: 0.9697 (mt) cc_final: 0.9289 (mt) REVERT: Y 35 TYR cc_start: 0.8966 (m-80) cc_final: 0.8754 (m-80) REVERT: Y 47 GLN cc_start: 0.9167 (mt0) cc_final: 0.8694 (mp10) REVERT: Z 23 GLU cc_start: 0.3335 (OUTLIER) cc_final: 0.2642 (pp20) REVERT: Z 44 ARG cc_start: 0.7741 (ppt170) cc_final: 0.7114 (tmm160) REVERT: a 218 MET cc_start: 0.0186 (mmm) cc_final: -0.0053 (mmt) outliers start: 109 outliers final: 57 residues processed: 925 average time/residue: 1.3159 time to fit residues: 2096.9481 Evaluate side-chains 768 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 705 time to evaluate : 6.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 66 PHE Chi-restraints excluded: chain b residue 124 LYS Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain c residue 167 ASN Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 199 MET Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 82 TYR Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain f residue 23 ILE Chi-restraints excluded: chain g residue 115 VAL Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 37 ASP Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 9 PHE Chi-restraints excluded: chain m residue 102 LEU Chi-restraints excluded: chain p residue 114 ASN Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain v residue 35 GLU Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain w residue 28 LEU Chi-restraints excluded: chain x residue 39 VAL Chi-restraints excluded: chain x residue 63 ILE Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain x residue 76 LYS Chi-restraints excluded: chain z residue 11 SER Chi-restraints excluded: chain z residue 31 ILE Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 119 GLN Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 197 PHE Chi-restraints excluded: chain H residue 24 ASN Chi-restraints excluded: chain H residue 151 GLU Chi-restraints excluded: chain H residue 192 TYR Chi-restraints excluded: chain I residue 140 ASP Chi-restraints excluded: chain I residue 151 GLN Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain K residue 9 MET Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 150 PHE Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 13 PHE Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain Z residue 23 GLU Chi-restraints excluded: chain Z residue 42 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 513 optimal weight: 0.4980 chunk 286 optimal weight: 10.0000 chunk 768 optimal weight: 20.0000 chunk 628 optimal weight: 40.0000 chunk 254 optimal weight: 10.0000 chunk 925 optimal weight: 30.0000 chunk 999 optimal weight: 30.0000 chunk 823 optimal weight: 40.0000 chunk 917 optimal weight: 50.0000 chunk 315 optimal weight: 8.9990 chunk 742 optimal weight: 50.0000 overall best weight: 9.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 134 HIS ** c 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 165 HIS e 20 ASN ** e 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 76 HIS ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 93 ASN ** y 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 GLN ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 GLN ** G 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 ASN G 119 GLN ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 73 ASN ** I 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 GLN J 76 ASN J 81 GLN K 14 GLN K 52 ASN ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 GLN ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 27 ASN ** P 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 7 ASN ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 42 ASN ** T 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 58 ASN a 188 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 157583 Z= 0.328 Angle : 0.663 11.930 235851 Z= 0.343 Chirality : 0.037 0.283 30157 Planarity : 0.005 0.065 12574 Dihedral : 23.870 178.390 79092 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 22.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.68 % Favored : 90.27 % Rotamer: Outliers : 3.28 % Allowed : 13.43 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.10), residues: 5652 helix: -0.49 (0.11), residues: 1805 sheet: -2.11 (0.15), residues: 995 loop : -2.24 (0.11), residues: 2852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 200 HIS 0.012 0.002 HIS Y 67 PHE 0.024 0.002 PHE I 71 TYR 0.019 0.002 TYR C 48 ARG 0.018 0.001 ARG V 10 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11304 Ramachandran restraints generated. 5652 Oldfield, 0 Emsley, 5652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11304 Ramachandran restraints generated. 5652 Oldfield, 0 Emsley, 5652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 927 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 773 time to evaluate : 6.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 63 ILE cc_start: 0.9362 (mt) cc_final: 0.9030 (tp) REVERT: b 66 PHE cc_start: 0.8639 (OUTLIER) cc_final: 0.8263 (p90) REVERT: e 16 MET cc_start: 0.8302 (mmp) cc_final: 0.8045 (mmp) REVERT: e 34 THR cc_start: 0.8505 (OUTLIER) cc_final: 0.8276 (t) REVERT: e 95 MET cc_start: 0.8916 (ptm) cc_final: 0.8624 (ptm) REVERT: e 137 PHE cc_start: 0.7606 (m-80) cc_final: 0.7213 (m-10) REVERT: e 168 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.9057 (mt) REVERT: f 68 ARG cc_start: 0.7447 (ttp80) cc_final: 0.7189 (ttp80) REVERT: f 150 TYR cc_start: 0.8486 (m-80) cc_final: 0.8196 (m-80) REVERT: g 20 ASN cc_start: 0.9286 (p0) cc_final: 0.9074 (m-40) REVERT: g 33 GLN cc_start: 0.9077 (mm-40) cc_final: 0.8794 (mp10) REVERT: g 60 GLU cc_start: 0.9590 (tp30) cc_final: 0.9181 (mt-10) REVERT: l 55 MET cc_start: 0.8510 (mmm) cc_final: 0.8193 (tpt) REVERT: l 135 ILE cc_start: 0.9234 (mm) cc_final: 0.8999 (mm) REVERT: m 124 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8726 (mm) REVERT: o 80 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8675 (pt0) REVERT: p 47 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8596 (mm) REVERT: p 114 ASN cc_start: 0.8945 (OUTLIER) cc_final: 0.8576 (p0) REVERT: q 17 LEU cc_start: 0.9397 (mm) cc_final: 0.9155 (mm) REVERT: q 19 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8329 (mt0) REVERT: q 51 GLN cc_start: 0.8280 (mt0) cc_final: 0.8030 (mt0) REVERT: s 65 ASP cc_start: 0.8030 (t0) cc_final: 0.5470 (t0) REVERT: t 5 GLU cc_start: 0.8138 (mp0) cc_final: 0.7914 (mp0) REVERT: v 24 ASN cc_start: 0.8420 (t0) cc_final: 0.8015 (t0) REVERT: x 48 LEU cc_start: 0.9204 (mm) cc_final: 0.8995 (mm) REVERT: x 65 THR cc_start: 0.9307 (p) cc_final: 0.8931 (p) REVERT: z 18 LYS cc_start: 0.8642 (mmmt) cc_final: 0.8325 (tptt) REVERT: B 47 TYR cc_start: 0.8517 (m-80) cc_final: 0.8079 (m-80) REVERT: F 1 MET cc_start: 0.5436 (OUTLIER) cc_final: 0.4309 (ptt) REVERT: H 18 ASN cc_start: 0.8694 (m-40) cc_final: 0.7887 (p0) REVERT: H 28 PHE cc_start: 0.9084 (t80) cc_final: 0.8761 (t80) REVERT: H 68 HIS cc_start: 0.8224 (m90) cc_final: 0.7872 (m-70) REVERT: H 71 ARG cc_start: 0.9135 (mtt180) cc_final: 0.8711 (tpm170) REVERT: H 111 ASP cc_start: 0.8643 (m-30) cc_final: 0.8272 (m-30) REVERT: H 167 TYR cc_start: 0.8931 (t80) cc_final: 0.8441 (t80) REVERT: I 74 TYR cc_start: 0.9501 (m-10) cc_final: 0.9146 (m-80) REVERT: I 134 TYR cc_start: 0.8830 (t80) cc_final: 0.8297 (t80) REVERT: I 135 GLN cc_start: 0.8756 (mm110) cc_final: 0.8147 (pp30) REVERT: I 163 GLN cc_start: 0.8709 (pt0) cc_final: 0.8434 (pm20) REVERT: J 35 LEU cc_start: 0.9331 (tp) cc_final: 0.9125 (tp) REVERT: J 53 ARG cc_start: 0.8588 (tpp80) cc_final: 0.8028 (mtt90) REVERT: J 63 MET cc_start: 0.9255 (mmm) cc_final: 0.9017 (mmm) REVERT: J 65 LYS cc_start: 0.9550 (mttm) cc_final: 0.9103 (mtmm) REVERT: J 141 ASP cc_start: 0.9206 (t0) cc_final: 0.8840 (t0) REVERT: K 9 MET cc_start: 0.8778 (mmp) cc_final: 0.8225 (mmp) REVERT: K 11 HIS cc_start: 0.8646 (t-90) cc_final: 0.8316 (t70) REVERT: K 21 MET cc_start: 0.9485 (mtp) cc_final: 0.8997 (mmm) REVERT: K 25 TYR cc_start: 0.8748 (m-10) cc_final: 0.8006 (m-80) REVERT: K 62 MET cc_start: 0.9341 (mmm) cc_final: 0.9091 (mmm) REVERT: K 76 THR cc_start: 0.9509 (p) cc_final: 0.9235 (p) REVERT: L 30 MET cc_start: 0.8210 (tmm) cc_final: 0.7362 (tmm) REVERT: L 100 MET cc_start: 0.9212 (ttm) cc_final: 0.8789 (ttt) REVERT: L 141 HIS cc_start: 0.7149 (m-70) cc_final: 0.6570 (m-70) REVERT: M 2 MET cc_start: 0.8008 (tpt) cc_final: 0.7669 (tpt) REVERT: M 26 MET cc_start: 0.6445 (ptp) cc_final: 0.5240 (mtm) REVERT: M 51 GLU cc_start: 0.9054 (mp0) cc_final: 0.8496 (mp0) REVERT: M 110 MET cc_start: 0.6263 (ptp) cc_final: 0.5787 (ptp) REVERT: N 111 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7658 (mp0) REVERT: O 49 PHE cc_start: 0.8546 (m-80) cc_final: 0.8189 (m-80) REVERT: O 66 GLU cc_start: 0.9344 (pt0) cc_final: 0.8976 (pm20) REVERT: P 17 ASP cc_start: 0.8445 (m-30) cc_final: 0.8132 (t70) REVERT: P 37 GLN cc_start: 0.9081 (mm-40) cc_final: 0.8440 (tm-30) REVERT: P 93 GLU cc_start: 0.9220 (tt0) cc_final: 0.8742 (tm-30) REVERT: Q 95 HIS cc_start: 0.8891 (m90) cc_final: 0.8326 (m-70) REVERT: Q 116 TYR cc_start: 0.8247 (m-80) cc_final: 0.8044 (m-80) REVERT: R 65 GLU cc_start: 0.9189 (tt0) cc_final: 0.8794 (mp0) REVERT: S 76 PHE cc_start: 0.8858 (m-80) cc_final: 0.8449 (m-80) REVERT: S 92 ILE cc_start: 0.8875 (mt) cc_final: 0.8626 (mp) REVERT: T 88 ARG cc_start: 0.8863 (mmp80) cc_final: 0.8587 (mmp80) REVERT: U 12 LYS cc_start: 0.9258 (ttpt) cc_final: 0.8327 (pttt) REVERT: U 31 ARG cc_start: 0.8700 (ttp-170) cc_final: 0.8015 (ppt170) REVERT: U 32 PHE cc_start: 0.8711 (p90) cc_final: 0.8504 (p90) REVERT: V 16 MET cc_start: 0.5787 (mpp) cc_final: 0.5578 (mpp) REVERT: V 76 ARG cc_start: 0.8954 (ptt-90) cc_final: 0.8652 (ptt-90) REVERT: X 46 LEU cc_start: 0.8151 (mm) cc_final: 0.7761 (mt) REVERT: X 65 MET cc_start: 0.7547 (ptm) cc_final: 0.6940 (ppp) REVERT: Y 20 ASN cc_start: 0.9293 (t0) cc_final: 0.8197 (t0) REVERT: Y 24 ARG cc_start: 0.9273 (mtm-85) cc_final: 0.8727 (mtm180) REVERT: Y 26 MET cc_start: 0.9529 (ttp) cc_final: 0.9181 (ptp) REVERT: Y 31 ILE cc_start: 0.9737 (mt) cc_final: 0.8461 (tp) REVERT: Y 35 TYR cc_start: 0.9025 (m-80) cc_final: 0.8601 (m-80) REVERT: Y 47 GLN cc_start: 0.9136 (mt0) cc_final: 0.8643 (mp10) REVERT: Z 23 GLU cc_start: 0.3034 (OUTLIER) cc_final: 0.2409 (pp20) REVERT: Z 44 ARG cc_start: 0.7782 (ppt170) cc_final: 0.7163 (tmm160) REVERT: a 218 MET cc_start: -0.0045 (mmm) cc_final: -0.0352 (mmt) outliers start: 154 outliers final: 90 residues processed: 863 average time/residue: 1.2436 time to fit residues: 1864.7927 Evaluate side-chains 771 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 672 time to evaluate : 6.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 66 PHE Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 124 LYS Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain c residue 183 GLU Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 199 MET Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 15 LEU Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 41 LYS Chi-restraints excluded: chain g residue 115 VAL Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain g residue 144 VAL Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain k residue 37 ASP Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain n residue 48 VAL Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 115 LEU Chi-restraints excluded: chain p residue 2 ASN Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain p residue 114 ASN Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 19 GLN Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 101 ASP Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 19 LEU Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain v residue 35 GLU Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain w residue 28 LEU Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain w residue 76 ILE Chi-restraints excluded: chain x residue 13 THR Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain x residue 76 LYS Chi-restraints excluded: chain z residue 39 ASP Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 89 PHE Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 197 PHE Chi-restraints excluded: chain H residue 24 ASN Chi-restraints excluded: chain H residue 192 TYR Chi-restraints excluded: chain I residue 140 ASP Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 94 PHE Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain L residue 51 GLN Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 150 PHE Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 13 PHE Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain R residue 7 ASN Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 3 SER Chi-restraints excluded: chain T residue 48 ASP Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain W residue 34 GLU Chi-restraints excluded: chain Z residue 23 GLU Chi-restraints excluded: chain a residue 202 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 914 optimal weight: 10.0000 chunk 695 optimal weight: 20.0000 chunk 480 optimal weight: 20.0000 chunk 102 optimal weight: 0.6980 chunk 441 optimal weight: 5.9990 chunk 621 optimal weight: 30.0000 chunk 928 optimal weight: 20.0000 chunk 983 optimal weight: 10.0000 chunk 485 optimal weight: 50.0000 chunk 880 optimal weight: 20.0000 chunk 264 optimal weight: 8.9990 overall best weight: 7.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 62 GLN ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 36 ASN e 51 ASN ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 87 GLN u 98 ASN ** y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 GLN ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 ASN G 102 ASN H 5 HIS ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 GLN ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 45 HIS ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 44 HIS X 55 GLN ** Y 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 20 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 157583 Z= 0.244 Angle : 0.599 11.648 235851 Z= 0.310 Chirality : 0.035 0.282 30157 Planarity : 0.005 0.065 12574 Dihedral : 23.906 179.117 79086 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 20.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.56 % Favored : 91.38 % Rotamer: Outliers : 3.11 % Allowed : 15.51 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.11), residues: 5652 helix: -0.13 (0.12), residues: 1820 sheet: -1.99 (0.15), residues: 1011 loop : -2.05 (0.11), residues: 2821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 166 HIS 0.009 0.001 HIS Y 67 PHE 0.027 0.002 PHE P 60 TYR 0.030 0.002 TYR I 75 ARG 0.010 0.001 ARG u 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11304 Ramachandran restraints generated. 5652 Oldfield, 0 Emsley, 5652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11304 Ramachandran restraints generated. 5652 Oldfield, 0 Emsley, 5652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 754 time to evaluate : 6.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 63 ILE cc_start: 0.9383 (mt) cc_final: 0.9044 (tp) REVERT: c 11 MET cc_start: 0.8049 (ttm) cc_final: 0.7724 (ttm) REVERT: d 153 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8610 (mm) REVERT: e 16 MET cc_start: 0.8287 (mmp) cc_final: 0.7983 (mmp) REVERT: e 95 MET cc_start: 0.8876 (ptm) cc_final: 0.8373 (ptm) REVERT: e 137 PHE cc_start: 0.7890 (m-80) cc_final: 0.7649 (m-10) REVERT: e 168 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.9004 (mt) REVERT: f 148 ARG cc_start: 0.8267 (tpt170) cc_final: 0.7994 (ttp-170) REVERT: f 150 TYR cc_start: 0.8510 (m-80) cc_final: 0.8272 (m-80) REVERT: g 33 GLN cc_start: 0.9063 (mm-40) cc_final: 0.8854 (mp10) REVERT: g 60 GLU cc_start: 0.9607 (tp30) cc_final: 0.9216 (mt-10) REVERT: j 92 MET cc_start: 0.8443 (mmm) cc_final: 0.7727 (tpp) REVERT: l 55 MET cc_start: 0.8415 (mmm) cc_final: 0.8171 (tpt) REVERT: m 124 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8624 (mm) REVERT: n 43 GLU cc_start: 0.7893 (mp0) cc_final: 0.7671 (mp0) REVERT: o 3 LYS cc_start: 0.8850 (mmtt) cc_final: 0.8637 (tptt) REVERT: p 47 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8769 (mm) REVERT: q 17 LEU cc_start: 0.9389 (mm) cc_final: 0.9160 (mm) REVERT: q 43 GLN cc_start: 0.8685 (mt0) cc_final: 0.8210 (mt0) REVERT: q 51 GLN cc_start: 0.8223 (mt0) cc_final: 0.8015 (mt0) REVERT: r 13 ARG cc_start: 0.8804 (ttp80) cc_final: 0.8466 (ttp80) REVERT: r 22 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.8815 (pp) REVERT: r 34 GLU cc_start: 0.8309 (mm-30) cc_final: 0.8054 (mm-30) REVERT: r 40 MET cc_start: 0.8527 (tmm) cc_final: 0.7631 (tmm) REVERT: s 65 ASP cc_start: 0.7830 (t0) cc_final: 0.7618 (t0) REVERT: s 68 ASP cc_start: 0.7881 (p0) cc_final: 0.7494 (p0) REVERT: t 1 MET cc_start: 0.5544 (tpt) cc_final: 0.3096 (tpt) REVERT: t 5 GLU cc_start: 0.8102 (mp0) cc_final: 0.7859 (mp0) REVERT: t 56 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7377 (tm-30) REVERT: v 24 ASN cc_start: 0.8472 (t0) cc_final: 0.8043 (t0) REVERT: x 48 LEU cc_start: 0.9235 (mm) cc_final: 0.8999 (mm) REVERT: x 65 THR cc_start: 0.9311 (p) cc_final: 0.8980 (p) REVERT: B 47 TYR cc_start: 0.8463 (m-80) cc_final: 0.7996 (m-80) REVERT: F 1 MET cc_start: 0.5463 (OUTLIER) cc_final: 0.3747 (mtt) REVERT: F 18 LYS cc_start: 0.7494 (mtmt) cc_final: 0.7228 (mttt) REVERT: G 48 MET cc_start: 0.9338 (OUTLIER) cc_final: 0.9130 (ptp) REVERT: H 18 ASN cc_start: 0.8584 (m-40) cc_final: 0.7872 (p0) REVERT: H 28 PHE cc_start: 0.9122 (t80) cc_final: 0.8711 (t80) REVERT: H 68 HIS cc_start: 0.8195 (m90) cc_final: 0.7756 (m90) REVERT: H 71 ARG cc_start: 0.9144 (mtt180) cc_final: 0.8552 (tpm170) REVERT: H 111 ASP cc_start: 0.8596 (m-30) cc_final: 0.8144 (m-30) REVERT: H 129 PHE cc_start: 0.8115 (p90) cc_final: 0.7846 (p90) REVERT: H 167 TYR cc_start: 0.8870 (t80) cc_final: 0.8308 (t80) REVERT: I 70 GLN cc_start: 0.9438 (pm20) cc_final: 0.9181 (pm20) REVERT: I 74 TYR cc_start: 0.9525 (m-10) cc_final: 0.9211 (m-80) REVERT: I 134 TYR cc_start: 0.8837 (t80) cc_final: 0.8384 (t80) REVERT: I 135 GLN cc_start: 0.8680 (mm110) cc_final: 0.8067 (pp30) REVERT: I 163 GLN cc_start: 0.8683 (pt0) cc_final: 0.8399 (pm20) REVERT: J 28 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8017 (mtt90) REVERT: J 53 ARG cc_start: 0.8524 (tpp80) cc_final: 0.8107 (mtt90) REVERT: J 63 MET cc_start: 0.9253 (mmm) cc_final: 0.9015 (mmm) REVERT: J 65 LYS cc_start: 0.9550 (mttm) cc_final: 0.9140 (mtmm) REVERT: J 141 ASP cc_start: 0.9287 (t0) cc_final: 0.8862 (t0) REVERT: K 9 MET cc_start: 0.8623 (mmp) cc_final: 0.8313 (mmp) REVERT: K 11 HIS cc_start: 0.8549 (t-90) cc_final: 0.8242 (t70) REVERT: K 17 GLN cc_start: 0.8371 (tm-30) cc_final: 0.8122 (tm-30) REVERT: K 21 MET cc_start: 0.9505 (mtp) cc_final: 0.9207 (mmm) REVERT: K 25 TYR cc_start: 0.8300 (m-10) cc_final: 0.8016 (m-80) REVERT: L 30 MET cc_start: 0.8302 (tmm) cc_final: 0.7459 (tmm) REVERT: L 100 MET cc_start: 0.9221 (ttm) cc_final: 0.8799 (ttt) REVERT: L 141 HIS cc_start: 0.6996 (m-70) cc_final: 0.6471 (m-70) REVERT: M 2 MET cc_start: 0.7996 (tpt) cc_final: 0.7691 (tpt) REVERT: M 20 ASN cc_start: 0.9224 (m-40) cc_final: 0.8925 (m-40) REVERT: M 26 MET cc_start: 0.6872 (ptp) cc_final: 0.5755 (mtm) REVERT: M 51 GLU cc_start: 0.8793 (mp0) cc_final: 0.8070 (mp0) REVERT: M 59 GLU cc_start: 0.8276 (mp0) cc_final: 0.7813 (mp0) REVERT: N 111 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7661 (mp0) REVERT: O 49 PHE cc_start: 0.8546 (m-80) cc_final: 0.8144 (m-80) REVERT: O 66 GLU cc_start: 0.9296 (pt0) cc_final: 0.9003 (pm20) REVERT: P 17 ASP cc_start: 0.8555 (m-30) cc_final: 0.7816 (t70) REVERT: P 37 GLN cc_start: 0.9176 (mm-40) cc_final: 0.8477 (tm-30) REVERT: P 86 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8337 (ptmt) REVERT: P 93 GLU cc_start: 0.9143 (tt0) cc_final: 0.8754 (tm-30) REVERT: Q 19 ASN cc_start: 0.9196 (p0) cc_final: 0.8859 (t0) REVERT: Q 95 HIS cc_start: 0.8742 (m90) cc_final: 0.8165 (m-70) REVERT: R 65 GLU cc_start: 0.9088 (tt0) cc_final: 0.8691 (mp0) REVERT: R 67 ASP cc_start: 0.9149 (t70) cc_final: 0.8657 (p0) REVERT: S 76 PHE cc_start: 0.8856 (m-80) cc_final: 0.8493 (m-80) REVERT: S 92 ILE cc_start: 0.8851 (mt) cc_final: 0.8453 (pt) REVERT: U 1 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.7506 (tpt) REVERT: U 12 LYS cc_start: 0.9307 (ttpt) cc_final: 0.8300 (pttt) REVERT: U 31 ARG cc_start: 0.8648 (ttp-170) cc_final: 0.7970 (ppt170) REVERT: U 32 PHE cc_start: 0.8651 (p90) cc_final: 0.8449 (p90) REVERT: V 16 MET cc_start: 0.5854 (mpp) cc_final: 0.5507 (mpp) REVERT: V 76 ARG cc_start: 0.8999 (ptt-90) cc_final: 0.8691 (ptt-90) REVERT: X 46 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7923 (mp) REVERT: X 65 MET cc_start: 0.7553 (ptm) cc_final: 0.6942 (ppp) REVERT: Y 26 MET cc_start: 0.9473 (ttp) cc_final: 0.9122 (mtp) REVERT: Y 31 ILE cc_start: 0.9706 (mt) cc_final: 0.8450 (tp) REVERT: Y 35 TYR cc_start: 0.9005 (m-80) cc_final: 0.8529 (m-80) REVERT: Y 47 GLN cc_start: 0.9129 (mt0) cc_final: 0.8622 (mp10) REVERT: Z 23 GLU cc_start: 0.2801 (OUTLIER) cc_final: 0.2353 (pp20) REVERT: Z 44 ARG cc_start: 0.7701 (ppt170) cc_final: 0.7071 (tmm160) outliers start: 146 outliers final: 88 residues processed: 842 average time/residue: 1.2556 time to fit residues: 1838.7923 Evaluate side-chains 771 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 671 time to evaluate : 6.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 66 PHE Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 124 LYS Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 153 LEU Chi-restraints excluded: chain d residue 199 MET Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 170 THR Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 41 LYS Chi-restraints excluded: chain g residue 115 VAL Chi-restraints excluded: chain g residue 144 VAL Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain k residue 37 ASP Chi-restraints excluded: chain k residue 53 LYS Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain m residue 5 LYS Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 9 PHE Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 115 LEU Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 101 ASP Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 98 ILE Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 19 LEU Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 29 SER Chi-restraints excluded: chain v residue 35 GLU Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain w residue 28 LEU Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain x residue 76 LYS Chi-restraints excluded: chain y residue 45 GLN Chi-restraints excluded: chain z residue 39 ASP Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 197 PHE Chi-restraints excluded: chain H residue 24 ASN Chi-restraints excluded: chain H residue 192 TYR Chi-restraints excluded: chain J residue 13 LYS Chi-restraints excluded: chain J residue 28 ARG Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 94 PHE Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain L residue 150 PHE Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 13 PHE Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 48 ASP Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 53 ASP Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain X residue 46 LEU Chi-restraints excluded: chain Z residue 23 GLU Chi-restraints excluded: chain a residue 202 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 818 optimal weight: 20.0000 chunk 558 optimal weight: 40.0000 chunk 14 optimal weight: 0.8980 chunk 731 optimal weight: 10.0000 chunk 405 optimal weight: 50.0000 chunk 838 optimal weight: 10.0000 chunk 679 optimal weight: 50.0000 chunk 1 optimal weight: 6.9990 chunk 501 optimal weight: 0.0970 chunk 882 optimal weight: 20.0000 chunk 248 optimal weight: 0.6980 overall best weight: 3.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 51 ASN ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 21 GLN ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 GLN ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 189 HIS ** I 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 115 GLN ** I 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 23 HIS ** P 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 4 ASN R 7 ASN R 104 ASN ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 157583 Z= 0.162 Angle : 0.550 12.010 235851 Z= 0.284 Chirality : 0.032 0.260 30157 Planarity : 0.004 0.067 12574 Dihedral : 23.815 178.232 79086 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.51 % Favored : 91.44 % Rotamer: Outliers : 2.72 % Allowed : 17.00 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.11), residues: 5652 helix: 0.16 (0.12), residues: 1830 sheet: -1.74 (0.15), residues: 1014 loop : -1.91 (0.11), residues: 2808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 166 HIS 0.011 0.001 HIS Y 67 PHE 0.021 0.001 PHE I 106 TYR 0.031 0.001 TYR K 59 ARG 0.007 0.001 ARG K 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11304 Ramachandran restraints generated. 5652 Oldfield, 0 Emsley, 5652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11304 Ramachandran restraints generated. 5652 Oldfield, 0 Emsley, 5652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 893 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 765 time to evaluate : 6.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 63 ILE cc_start: 0.9369 (mt) cc_final: 0.9038 (tp) REVERT: e 16 MET cc_start: 0.8159 (mmp) cc_final: 0.7796 (mmp) REVERT: e 95 MET cc_start: 0.8919 (ptm) cc_final: 0.8379 (ptm) REVERT: e 137 PHE cc_start: 0.7957 (m-80) cc_final: 0.7737 (m-10) REVERT: e 168 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8979 (mt) REVERT: f 148 ARG cc_start: 0.8156 (tpt170) cc_final: 0.7752 (tmm160) REVERT: f 150 TYR cc_start: 0.8563 (m-80) cc_final: 0.8295 (m-80) REVERT: g 29 PHE cc_start: 0.8491 (t80) cc_final: 0.8175 (t80) REVERT: g 33 GLN cc_start: 0.9083 (mm-40) cc_final: 0.8791 (mp10) REVERT: g 60 GLU cc_start: 0.9631 (tp30) cc_final: 0.9216 (mt-10) REVERT: j 92 MET cc_start: 0.8369 (mmm) cc_final: 0.7639 (tpp) REVERT: k 7 MET cc_start: 0.8193 (mmm) cc_final: 0.7721 (mmm) REVERT: m 105 MET cc_start: 0.8745 (tpp) cc_final: 0.8108 (mmm) REVERT: m 124 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8585 (mm) REVERT: o 3 LYS cc_start: 0.8832 (mmtt) cc_final: 0.8464 (tptt) REVERT: p 47 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8777 (mm) REVERT: q 17 LEU cc_start: 0.9391 (mm) cc_final: 0.9155 (mm) REVERT: r 13 ARG cc_start: 0.8837 (ttp80) cc_final: 0.8496 (ttp80) REVERT: r 22 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8559 (pp) REVERT: r 34 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7999 (mm-30) REVERT: r 84 ARG cc_start: 0.8013 (ttp80) cc_final: 0.7804 (ttp-170) REVERT: s 68 ASP cc_start: 0.7683 (p0) cc_final: 0.7239 (p0) REVERT: t 1 MET cc_start: 0.5553 (tpt) cc_final: 0.3309 (tpt) REVERT: t 56 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7193 (tm-30) REVERT: v 24 ASN cc_start: 0.8503 (t0) cc_final: 0.8113 (t0) REVERT: x 65 THR cc_start: 0.9296 (p) cc_final: 0.8555 (p) REVERT: z 38 GLU cc_start: 0.8114 (pm20) cc_final: 0.7885 (pm20) REVERT: B 47 TYR cc_start: 0.8519 (m-80) cc_final: 0.7984 (m-80) REVERT: D 12 ARG cc_start: 0.7665 (ttm-80) cc_final: 0.7430 (ttm-80) REVERT: F 1 MET cc_start: 0.5704 (tpt) cc_final: 0.3316 (mtt) REVERT: G 48 MET cc_start: 0.9358 (mtm) cc_final: 0.9137 (ptp) REVERT: H 18 ASN cc_start: 0.8598 (m-40) cc_final: 0.8031 (t0) REVERT: H 28 PHE cc_start: 0.9109 (t80) cc_final: 0.8707 (t80) REVERT: H 68 HIS cc_start: 0.8182 (m90) cc_final: 0.7739 (m90) REVERT: H 71 ARG cc_start: 0.9146 (mtt180) cc_final: 0.8432 (tpm170) REVERT: H 111 ASP cc_start: 0.8495 (m-30) cc_final: 0.8087 (m-30) REVERT: H 167 TYR cc_start: 0.8935 (t80) cc_final: 0.8389 (t80) REVERT: I 70 GLN cc_start: 0.9472 (pm20) cc_final: 0.9256 (pm20) REVERT: I 74 TYR cc_start: 0.9475 (m-10) cc_final: 0.9081 (m-80) REVERT: I 102 TYR cc_start: 0.8760 (t80) cc_final: 0.8407 (t80) REVERT: I 134 TYR cc_start: 0.8949 (t80) cc_final: 0.8495 (t80) REVERT: I 135 GLN cc_start: 0.8626 (mm110) cc_final: 0.8049 (pp30) REVERT: I 163 GLN cc_start: 0.8656 (pt0) cc_final: 0.8323 (pm20) REVERT: J 53 ARG cc_start: 0.8484 (tpp80) cc_final: 0.8161 (mtt180) REVERT: J 61 LYS cc_start: 0.9270 (mtmm) cc_final: 0.8735 (mtmm) REVERT: J 63 MET cc_start: 0.9237 (mmm) cc_final: 0.8984 (mmm) REVERT: J 64 GLU cc_start: 0.8959 (mp0) cc_final: 0.8516 (pm20) REVERT: J 65 LYS cc_start: 0.9566 (mttm) cc_final: 0.9338 (mtmm) REVERT: J 141 ASP cc_start: 0.9369 (t0) cc_final: 0.9053 (t0) REVERT: K 11 HIS cc_start: 0.8536 (t-90) cc_final: 0.8334 (t70) REVERT: K 17 GLN cc_start: 0.9019 (tm-30) cc_final: 0.8660 (tm-30) REVERT: K 25 TYR cc_start: 0.8330 (m-10) cc_final: 0.7785 (m-80) REVERT: L 30 MET cc_start: 0.8140 (tmm) cc_final: 0.7272 (tmm) REVERT: L 141 HIS cc_start: 0.7041 (m-70) cc_final: 0.6701 (m-70) REVERT: M 2 MET cc_start: 0.7867 (tpt) cc_final: 0.7535 (tpt) REVERT: M 20 ASN cc_start: 0.9267 (m-40) cc_final: 0.9003 (m-40) REVERT: M 26 MET cc_start: 0.6467 (ptp) cc_final: 0.5832 (mtm) REVERT: M 42 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8584 (tp30) REVERT: M 110 MET cc_start: 0.6479 (ptp) cc_final: 0.5771 (ptt) REVERT: N 89 TYR cc_start: 0.7646 (m-10) cc_final: 0.7340 (m-80) REVERT: N 102 PHE cc_start: 0.8210 (m-10) cc_final: 0.7918 (m-10) REVERT: N 111 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7955 (mp0) REVERT: O 49 PHE cc_start: 0.8595 (m-80) cc_final: 0.8335 (m-80) REVERT: O 66 GLU cc_start: 0.9293 (pt0) cc_final: 0.8562 (tm-30) REVERT: O 67 ILE cc_start: 0.7812 (OUTLIER) cc_final: 0.7408 (mt) REVERT: P 37 GLN cc_start: 0.9169 (mm-40) cc_final: 0.8477 (tm-30) REVERT: P 86 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8479 (ptmt) REVERT: P 93 GLU cc_start: 0.9073 (tt0) cc_final: 0.8698 (tm-30) REVERT: Q 4 ASN cc_start: 0.8650 (OUTLIER) cc_final: 0.8254 (t0) REVERT: Q 19 ASN cc_start: 0.9127 (p0) cc_final: 0.8831 (t0) REVERT: Q 95 HIS cc_start: 0.8583 (m90) cc_final: 0.8042 (m-70) REVERT: R 7 ASN cc_start: 0.6072 (OUTLIER) cc_final: 0.5378 (m110) REVERT: R 67 ASP cc_start: 0.9215 (t70) cc_final: 0.8625 (p0) REVERT: S 76 PHE cc_start: 0.8839 (m-80) cc_final: 0.8324 (m-80) REVERT: U 1 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8427 (mpp) REVERT: U 12 LYS cc_start: 0.9196 (ttpt) cc_final: 0.8195 (pttt) REVERT: U 26 ASN cc_start: 0.7465 (OUTLIER) cc_final: 0.6739 (m-40) REVERT: U 31 ARG cc_start: 0.8690 (ttp-170) cc_final: 0.8145 (ppt170) REVERT: U 32 PHE cc_start: 0.8623 (p90) cc_final: 0.8404 (p90) REVERT: U 76 LYS cc_start: 0.8177 (ptmt) cc_final: 0.7783 (pttp) REVERT: V 16 MET cc_start: 0.6263 (mpp) cc_final: 0.6016 (mpp) REVERT: X 46 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7984 (mp) REVERT: X 65 MET cc_start: 0.7821 (ptm) cc_final: 0.7184 (ppp) REVERT: Y 26 MET cc_start: 0.9441 (ttp) cc_final: 0.9081 (mtp) REVERT: Y 31 ILE cc_start: 0.9693 (mt) cc_final: 0.8458 (tp) REVERT: Y 35 TYR cc_start: 0.9002 (m-80) cc_final: 0.8419 (m-80) REVERT: Y 47 GLN cc_start: 0.9149 (mt0) cc_final: 0.8653 (mp10) REVERT: Z 44 ARG cc_start: 0.7716 (ppt170) cc_final: 0.6428 (tmm160) outliers start: 128 outliers final: 72 residues processed: 846 average time/residue: 1.2562 time to fit residues: 1843.4854 Evaluate side-chains 759 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 676 time to evaluate : 5.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 66 PHE Chi-restraints excluded: chain b residue 124 LYS Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 41 LYS Chi-restraints excluded: chain g residue 144 VAL Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain k residue 37 ASP Chi-restraints excluded: chain k residue 53 LYS Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 9 PHE Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain n residue 18 GLN Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 115 LEU Chi-restraints excluded: chain p residue 2 ASN Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain q residue 116 LEU Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 98 ILE Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 19 LEU Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain v residue 35 GLU Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain w residue 28 LEU Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain z residue 39 ASP Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 197 PHE Chi-restraints excluded: chain H residue 24 ASN Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 192 TYR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain O residue 13 PHE Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain Q residue 4 ASN Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 7 ASN Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 3 SER Chi-restraints excluded: chain T residue 13 GLU Chi-restraints excluded: chain T residue 61 GLN Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 26 ASN Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain X residue 46 LEU Chi-restraints excluded: chain a residue 202 THR Chi-restraints excluded: chain a residue 212 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 330 optimal weight: 5.9990 chunk 885 optimal weight: 20.0000 chunk 194 optimal weight: 10.0000 chunk 577 optimal weight: 30.0000 chunk 242 optimal weight: 0.6980 chunk 983 optimal weight: 20.0000 chunk 816 optimal weight: 50.0000 chunk 455 optimal weight: 0.0870 chunk 81 optimal weight: 0.1980 chunk 325 optimal weight: 40.0000 chunk 516 optimal weight: 30.0000 overall best weight: 3.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 167 ASN ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 9 GLN p 14 GLN q 43 GLN ** y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 GLN ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 ASN ** J 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 118 ASN Q 4 ASN Q 5 GLN ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 60 GLN ** Y 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 157583 Z= 0.155 Angle : 0.544 13.059 235851 Z= 0.280 Chirality : 0.032 0.258 30157 Planarity : 0.004 0.062 12574 Dihedral : 23.774 179.703 79086 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.93 % Favored : 92.02 % Rotamer: Outliers : 2.79 % Allowed : 18.70 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.11), residues: 5652 helix: 0.21 (0.12), residues: 1850 sheet: -1.58 (0.16), residues: 1008 loop : -1.79 (0.12), residues: 2794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP H 200 HIS 0.013 0.001 HIS Y 67 PHE 0.017 0.001 PHE H 129 TYR 0.039 0.001 TYR I 75 ARG 0.011 0.000 ARG U 14 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11304 Ramachandran restraints generated. 5652 Oldfield, 0 Emsley, 5652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11304 Ramachandran restraints generated. 5652 Oldfield, 0 Emsley, 5652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 860 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 729 time to evaluate : 6.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 63 ILE cc_start: 0.9377 (mt) cc_final: 0.9056 (tp) REVERT: d 153 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8582 (mm) REVERT: e 16 MET cc_start: 0.8102 (mmp) cc_final: 0.7809 (mmp) REVERT: e 95 MET cc_start: 0.8959 (ptm) cc_final: 0.8384 (ptm) REVERT: e 168 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8973 (mt) REVERT: f 148 ARG cc_start: 0.8142 (tpt170) cc_final: 0.7702 (tmm160) REVERT: f 150 TYR cc_start: 0.8562 (m-80) cc_final: 0.8254 (m-80) REVERT: f 162 ARG cc_start: 0.8382 (ptm160) cc_final: 0.8177 (ptm-80) REVERT: g 29 PHE cc_start: 0.8542 (t80) cc_final: 0.8323 (t80) REVERT: g 33 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8857 (mp10) REVERT: g 60 GLU cc_start: 0.9628 (tp30) cc_final: 0.9217 (mt-10) REVERT: j 92 MET cc_start: 0.8430 (mmm) cc_final: 0.7746 (tpp) REVERT: l 77 ILE cc_start: 0.9453 (mp) cc_final: 0.9217 (mm) REVERT: n 43 GLU cc_start: 0.7833 (mp0) cc_final: 0.7602 (mp0) REVERT: p 47 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8730 (mm) REVERT: q 17 LEU cc_start: 0.9387 (mm) cc_final: 0.9148 (mm) REVERT: r 13 ARG cc_start: 0.8872 (ttp80) cc_final: 0.8520 (ttp80) REVERT: r 22 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8528 (pp) REVERT: r 34 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7930 (mm-30) REVERT: s 38 TYR cc_start: 0.8421 (m-80) cc_final: 0.8096 (m-80) REVERT: s 65 ASP cc_start: 0.7706 (t0) cc_final: 0.7501 (t0) REVERT: s 68 ASP cc_start: 0.7865 (p0) cc_final: 0.7329 (p0) REVERT: t 1 MET cc_start: 0.5466 (tpt) cc_final: 0.3487 (tpt) REVERT: t 56 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7230 (tm-30) REVERT: v 24 ASN cc_start: 0.8623 (t0) cc_final: 0.8207 (t0) REVERT: x 65 THR cc_start: 0.9320 (p) cc_final: 0.9094 (p) REVERT: z 46 MET cc_start: 0.8242 (mtt) cc_final: 0.7927 (mtt) REVERT: B 47 TYR cc_start: 0.8423 (m-80) cc_final: 0.7840 (m-80) REVERT: F 1 MET cc_start: 0.5605 (tpt) cc_final: 0.3320 (mtt) REVERT: F 36 ARG cc_start: 0.7638 (ttp-170) cc_final: 0.7275 (ttm-80) REVERT: G 48 MET cc_start: 0.9376 (mtm) cc_final: 0.9158 (ptp) REVERT: G 153 MET cc_start: 0.8500 (mmm) cc_final: 0.8250 (mmm) REVERT: H 5 HIS cc_start: 0.7317 (t70) cc_final: 0.7117 (t-90) REVERT: H 18 ASN cc_start: 0.8676 (m-40) cc_final: 0.8159 (p0) REVERT: H 28 PHE cc_start: 0.9120 (t80) cc_final: 0.8691 (t80) REVERT: H 68 HIS cc_start: 0.8438 (m90) cc_final: 0.8095 (m90) REVERT: H 71 ARG cc_start: 0.9158 (mtt180) cc_final: 0.8424 (tpm170) REVERT: H 111 ASP cc_start: 0.8458 (m-30) cc_final: 0.8051 (m-30) REVERT: H 167 TYR cc_start: 0.8913 (t80) cc_final: 0.8348 (t80) REVERT: I 102 TYR cc_start: 0.8743 (t80) cc_final: 0.8412 (t80) REVERT: I 134 TYR cc_start: 0.8947 (t80) cc_final: 0.8618 (t80) REVERT: I 135 GLN cc_start: 0.8633 (mm110) cc_final: 0.7967 (pp30) REVERT: J 53 ARG cc_start: 0.8441 (tpp80) cc_final: 0.8040 (mtt180) REVERT: J 61 LYS cc_start: 0.9282 (mtmm) cc_final: 0.8650 (mtmm) REVERT: J 63 MET cc_start: 0.9238 (mmm) cc_final: 0.9000 (mmm) REVERT: J 64 GLU cc_start: 0.8896 (mp0) cc_final: 0.8501 (pm20) REVERT: J 65 LYS cc_start: 0.9562 (mttm) cc_final: 0.9342 (mtmm) REVERT: J 141 ASP cc_start: 0.9391 (t0) cc_final: 0.9060 (t0) REVERT: K 11 HIS cc_start: 0.8584 (t-90) cc_final: 0.8362 (t70) REVERT: K 21 MET cc_start: 0.9152 (mmm) cc_final: 0.8919 (mpp) REVERT: K 25 TYR cc_start: 0.8465 (m-10) cc_final: 0.8081 (m-80) REVERT: K 72 ASP cc_start: 0.9769 (t0) cc_final: 0.9361 (m-30) REVERT: L 30 MET cc_start: 0.8142 (tmm) cc_final: 0.7218 (tmm) REVERT: L 141 HIS cc_start: 0.7206 (m-70) cc_final: 0.6907 (m-70) REVERT: M 2 MET cc_start: 0.7956 (tpt) cc_final: 0.7584 (tpt) REVERT: M 42 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8607 (tp30) REVERT: M 44 PHE cc_start: 0.7871 (m-80) cc_final: 0.7572 (m-80) REVERT: M 51 GLU cc_start: 0.8754 (mp0) cc_final: 0.8186 (mp0) REVERT: N 63 TYR cc_start: 0.6866 (t80) cc_final: 0.6572 (t80) REVERT: N 89 TYR cc_start: 0.7634 (m-80) cc_final: 0.7308 (m-80) REVERT: N 111 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7798 (mp0) REVERT: O 49 PHE cc_start: 0.8543 (m-80) cc_final: 0.8300 (m-80) REVERT: O 66 GLU cc_start: 0.9265 (pt0) cc_final: 0.8564 (tm-30) REVERT: P 37 GLN cc_start: 0.9160 (mm-40) cc_final: 0.8485 (tm-30) REVERT: P 86 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8491 (ptmt) REVERT: P 93 GLU cc_start: 0.9022 (tt0) cc_final: 0.8687 (tm-30) REVERT: Q 19 ASN cc_start: 0.9139 (p0) cc_final: 0.8876 (t0) REVERT: Q 95 HIS cc_start: 0.8540 (m90) cc_final: 0.8008 (m-70) REVERT: R 7 ASN cc_start: 0.6674 (m-40) cc_final: 0.5731 (m110) REVERT: S 76 PHE cc_start: 0.8825 (m-80) cc_final: 0.8343 (m-80) REVERT: T 13 GLU cc_start: 0.9470 (OUTLIER) cc_final: 0.9017 (pt0) REVERT: U 1 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.7559 (tpt) REVERT: U 12 LYS cc_start: 0.9305 (ttpt) cc_final: 0.8131 (pttt) REVERT: U 26 ASN cc_start: 0.7334 (OUTLIER) cc_final: 0.6659 (m-40) REVERT: U 31 ARG cc_start: 0.8702 (ttp-170) cc_final: 0.8218 (ppt170) REVERT: U 32 PHE cc_start: 0.8630 (p90) cc_final: 0.8411 (p90) REVERT: U 76 LYS cc_start: 0.8163 (ptmt) cc_final: 0.7761 (pttp) REVERT: X 46 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8055 (mp) REVERT: X 65 MET cc_start: 0.7751 (ptm) cc_final: 0.7178 (ppp) REVERT: Y 17 ARG cc_start: 0.9399 (ttp80) cc_final: 0.9110 (ttp80) REVERT: Y 26 MET cc_start: 0.9507 (ttp) cc_final: 0.9071 (mtp) REVERT: Y 31 ILE cc_start: 0.9662 (mt) cc_final: 0.8399 (tp) REVERT: Y 35 TYR cc_start: 0.8899 (m-80) cc_final: 0.8552 (m-80) REVERT: Y 47 GLN cc_start: 0.9119 (mt0) cc_final: 0.8678 (mp10) REVERT: Z 44 ARG cc_start: 0.7694 (ppt170) cc_final: 0.6347 (tmm160) outliers start: 131 outliers final: 87 residues processed: 813 average time/residue: 1.2560 time to fit residues: 1782.3397 Evaluate side-chains 781 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 685 time to evaluate : 6.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 66 PHE Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 124 LYS Chi-restraints excluded: chain b residue 263 ASP Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain c residue 167 ASN Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 153 LEU Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 7 TYR Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 170 THR Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 41 LYS Chi-restraints excluded: chain g residue 144 VAL Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain k residue 37 ASP Chi-restraints excluded: chain k residue 53 LYS Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 2 LEU Chi-restraints excluded: chain m residue 9 PHE Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 115 LEU Chi-restraints excluded: chain p residue 2 ASN Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain p residue 47 ILE Chi-restraints excluded: chain q residue 101 ASP Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 98 ILE Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 19 LEU Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain s residue 103 ILE Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain v residue 35 GLU Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain w residue 28 LEU Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain y residue 45 GLN Chi-restraints excluded: chain z residue 39 ASP Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 197 PHE Chi-restraints excluded: chain H residue 24 ASN Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 192 TYR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain L residue 150 PHE Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain O residue 13 PHE Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 13 GLU Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 26 ASN Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain X residue 46 LEU Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain a residue 202 THR Chi-restraints excluded: chain a residue 212 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 948 optimal weight: 20.0000 chunk 110 optimal weight: 40.0000 chunk 560 optimal weight: 50.0000 chunk 718 optimal weight: 10.0000 chunk 556 optimal weight: 40.0000 chunk 828 optimal weight: 10.0000 chunk 549 optimal weight: 6.9990 chunk 980 optimal weight: 30.0000 chunk 613 optimal weight: 40.0000 chunk 597 optimal weight: 50.0000 chunk 452 optimal weight: 50.0000 overall best weight: 15.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 85 ASN c 130 GLN ** c 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 20 ASN ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 29 ASN ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 104 GLN n 13 ASN o 29 HIS q 43 GLN ** s 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 73 ASN ** y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 8 GLN ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 GLN ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 138 GLN ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 37 GLN ** Q 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 7 ASN ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 18 GLN ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.5010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.155 157583 Z= 0.477 Angle : 0.790 13.619 235851 Z= 0.396 Chirality : 0.041 0.294 30157 Planarity : 0.006 0.063 12574 Dihedral : 24.251 178.396 79086 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 32.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.18 % Favored : 88.75 % Rotamer: Outliers : 3.74 % Allowed : 18.51 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.11), residues: 5652 helix: -0.16 (0.12), residues: 1839 sheet: -1.75 (0.15), residues: 1049 loop : -1.98 (0.11), residues: 2764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 200 HIS 0.012 0.002 HIS Y 67 PHE 0.022 0.003 PHE x 37 TYR 0.042 0.003 TYR K 59 ARG 0.018 0.001 ARG V 76 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11304 Ramachandran restraints generated. 5652 Oldfield, 0 Emsley, 5652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11304 Ramachandran restraints generated. 5652 Oldfield, 0 Emsley, 5652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 848 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 672 time to evaluate : 8.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 63 ILE cc_start: 0.9464 (mt) cc_final: 0.9090 (tp) REVERT: d 153 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8682 (mm) REVERT: e 95 MET cc_start: 0.9030 (ptm) cc_final: 0.8390 (ptm) REVERT: e 168 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.9051 (mt) REVERT: f 148 ARG cc_start: 0.8345 (tpt170) cc_final: 0.7959 (ttp-170) REVERT: f 150 TYR cc_start: 0.8679 (m-80) cc_final: 0.8317 (m-80) REVERT: g 33 GLN cc_start: 0.9176 (mm-40) cc_final: 0.8889 (mp10) REVERT: g 60 GLU cc_start: 0.9617 (tp30) cc_final: 0.9229 (mt-10) REVERT: g 127 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7522 (tp30) REVERT: j 92 MET cc_start: 0.8619 (mmm) cc_final: 0.8047 (tpp) REVERT: k 37 ASP cc_start: 0.6708 (OUTLIER) cc_final: 0.6362 (m-30) REVERT: k 110 GLU cc_start: 0.8601 (pp20) cc_final: 0.8321 (pp20) REVERT: l 135 ILE cc_start: 0.9248 (mm) cc_final: 0.9004 (mm) REVERT: m 124 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.9010 (mm) REVERT: q 17 LEU cc_start: 0.9453 (mm) cc_final: 0.9247 (mm) REVERT: r 34 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7926 (mm-30) REVERT: r 95 ASP cc_start: 0.8072 (p0) cc_final: 0.7740 (p0) REVERT: t 1 MET cc_start: 0.5826 (tpt) cc_final: 0.3567 (tpt) REVERT: t 56 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7647 (tm-30) REVERT: u 73 ASN cc_start: 0.9062 (OUTLIER) cc_final: 0.8600 (t0) REVERT: v 24 ASN cc_start: 0.8674 (t0) cc_final: 0.8302 (t0) REVERT: y 30 MET cc_start: 0.8814 (tmm) cc_final: 0.8598 (tmm) REVERT: z 18 LYS cc_start: 0.8611 (mmmt) cc_final: 0.8266 (tptt) REVERT: B 47 TYR cc_start: 0.8617 (m-80) cc_final: 0.8089 (m-80) REVERT: C 32 LYS cc_start: 0.8916 (tmtt) cc_final: 0.8706 (tmtt) REVERT: D 1 MET cc_start: 0.7617 (tmm) cc_final: 0.7077 (tmm) REVERT: F 1 MET cc_start: 0.5538 (tpt) cc_final: 0.4531 (mtt) REVERT: F 35 GLN cc_start: 0.7376 (mm-40) cc_final: 0.6951 (mm-40) REVERT: G 48 MET cc_start: 0.9289 (mtm) cc_final: 0.9007 (ptp) REVERT: H 5 HIS cc_start: 0.7366 (t70) cc_final: 0.7051 (t70) REVERT: H 18 ASN cc_start: 0.8604 (m-40) cc_final: 0.8024 (p0) REVERT: H 28 PHE cc_start: 0.9065 (t80) cc_final: 0.8695 (t80) REVERT: H 68 HIS cc_start: 0.8052 (m90) cc_final: 0.7676 (m90) REVERT: H 71 ARG cc_start: 0.9180 (mtt180) cc_final: 0.8455 (tpm170) REVERT: H 111 ASP cc_start: 0.8263 (m-30) cc_final: 0.7872 (m-30) REVERT: H 167 TYR cc_start: 0.8987 (t80) cc_final: 0.8322 (t80) REVERT: I 74 TYR cc_start: 0.9507 (m-10) cc_final: 0.9238 (m-80) REVERT: I 134 TYR cc_start: 0.8954 (t80) cc_final: 0.8297 (t80) REVERT: I 135 GLN cc_start: 0.8793 (mm110) cc_final: 0.8042 (pp30) REVERT: I 163 GLN cc_start: 0.8563 (pt0) cc_final: 0.8245 (pm20) REVERT: J 53 ARG cc_start: 0.8533 (tpp80) cc_final: 0.8129 (mtt180) REVERT: J 63 MET cc_start: 0.9318 (mmm) cc_final: 0.8983 (mmm) REVERT: J 141 ASP cc_start: 0.9386 (t0) cc_final: 0.9073 (t0) REVERT: K 25 TYR cc_start: 0.8427 (m-10) cc_final: 0.7980 (m-10) REVERT: K 90 MET cc_start: 0.8588 (ttp) cc_final: 0.8127 (ttp) REVERT: L 30 MET cc_start: 0.8254 (tmm) cc_final: 0.7384 (tmm) REVERT: L 141 HIS cc_start: 0.7060 (m-70) cc_final: 0.6759 (m-70) REVERT: M 2 MET cc_start: 0.7696 (tpt) cc_final: 0.7323 (tpt) REVERT: M 123 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8460 (mt-10) REVERT: N 102 PHE cc_start: 0.8283 (m-10) cc_final: 0.8039 (m-10) REVERT: O 49 PHE cc_start: 0.8566 (m-80) cc_final: 0.8277 (m-80) REVERT: O 66 GLU cc_start: 0.9005 (pt0) cc_final: 0.8419 (tm-30) REVERT: P 37 GLN cc_start: 0.9209 (mm110) cc_final: 0.8405 (tm-30) REVERT: P 60 PHE cc_start: 0.9176 (t80) cc_final: 0.8900 (t80) REVERT: P 86 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.7892 (pttm) REVERT: P 93 GLU cc_start: 0.9295 (tt0) cc_final: 0.8967 (tm-30) REVERT: Q 95 HIS cc_start: 0.8841 (m90) cc_final: 0.8352 (m-70) REVERT: R 7 ASN cc_start: 0.6185 (OUTLIER) cc_final: 0.5276 (m110) REVERT: R 67 ASP cc_start: 0.9003 (t0) cc_final: 0.8454 (p0) REVERT: S 76 PHE cc_start: 0.8841 (m-80) cc_final: 0.8466 (m-80) REVERT: U 1 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.7507 (mmt) REVERT: U 12 LYS cc_start: 0.9379 (ttpt) cc_final: 0.9087 (ttmm) REVERT: U 31 ARG cc_start: 0.8870 (ttp-170) cc_final: 0.8230 (ppt170) REVERT: U 32 PHE cc_start: 0.8687 (p90) cc_final: 0.8473 (p90) REVERT: U 51 ARG cc_start: 0.8272 (ttp-170) cc_final: 0.7999 (ttp-170) REVERT: U 76 LYS cc_start: 0.8186 (ptmt) cc_final: 0.7798 (pttp) REVERT: X 65 MET cc_start: 0.7713 (ptm) cc_final: 0.7046 (ppp) REVERT: Y 26 MET cc_start: 0.9503 (ttp) cc_final: 0.9192 (mtp) REVERT: Y 31 ILE cc_start: 0.9714 (mt) cc_final: 0.8581 (tp) REVERT: Y 35 TYR cc_start: 0.9080 (m-80) cc_final: 0.8721 (m-80) REVERT: Y 47 GLN cc_start: 0.9130 (mt0) cc_final: 0.8750 (mp10) outliers start: 176 outliers final: 122 residues processed: 786 average time/residue: 1.2598 time to fit residues: 1736.3757 Evaluate side-chains 755 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 625 time to evaluate : 6.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 66 PHE Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 124 LYS Chi-restraints excluded: chain b residue 263 ASP Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 153 LEU Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 7 TYR Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 41 LYS Chi-restraints excluded: chain g residue 115 VAL Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain g residue 144 VAL Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain k residue 37 ASP Chi-restraints excluded: chain k residue 53 LYS Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 113 MET Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 2 LEU Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 20 LEU Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain n residue 18 GLN Chi-restraints excluded: chain n residue 34 ILE Chi-restraints excluded: chain n residue 113 ILE Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 78 VAL Chi-restraints excluded: chain o residue 83 LEU Chi-restraints excluded: chain o residue 115 LEU Chi-restraints excluded: chain p residue 2 ASN Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain p residue 91 VAL Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain q residue 16 ILE Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain q residue 101 ASP Chi-restraints excluded: chain q residue 116 LEU Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 59 ILE Chi-restraints excluded: chain r residue 98 ILE Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 19 LEU Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain u residue 13 LEU Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain u residue 73 ASN Chi-restraints excluded: chain v residue 30 ILE Chi-restraints excluded: chain v residue 35 GLU Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain w residue 28 LEU Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain x residue 13 THR Chi-restraints excluded: chain x residue 63 ILE Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain z residue 39 ASP Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 5 MET Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 197 PHE Chi-restraints excluded: chain H residue 24 ASN Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 192 TYR Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain L residue 150 PHE Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 13 PHE Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain R residue 7 ASN Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 61 LYS Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 13 GLU Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 26 ASN Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 33 TYR Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain a residue 202 THR Chi-restraints excluded: chain a residue 212 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 606 optimal weight: 40.0000 chunk 391 optimal weight: 50.0000 chunk 585 optimal weight: 30.0000 chunk 295 optimal weight: 8.9990 chunk 192 optimal weight: 6.9990 chunk 189 optimal weight: 9.9990 chunk 623 optimal weight: 30.0000 chunk 667 optimal weight: 50.0000 chunk 484 optimal weight: 0.9980 chunk 91 optimal weight: 30.0000 chunk 770 optimal weight: 20.0000 overall best weight: 9.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 164 GLN ** c 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 13 ASN n 31 HIS r 82 HIS ** y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 5 GLN R 7 ASN ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.4955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 157583 Z= 0.305 Angle : 0.650 12.643 235851 Z= 0.332 Chirality : 0.037 0.324 30157 Planarity : 0.005 0.060 12574 Dihedral : 24.206 179.488 79086 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 25.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.18 % Favored : 90.75 % Rotamer: Outliers : 3.21 % Allowed : 19.64 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.11), residues: 5652 helix: -0.02 (0.12), residues: 1843 sheet: -1.63 (0.16), residues: 1012 loop : -1.89 (0.12), residues: 2797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 200 HIS 0.016 0.001 HIS Y 67 PHE 0.018 0.002 PHE H 129 TYR 0.040 0.002 TYR I 75 ARG 0.012 0.001 ARG U 14 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11304 Ramachandran restraints generated. 5652 Oldfield, 0 Emsley, 5652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11304 Ramachandran restraints generated. 5652 Oldfield, 0 Emsley, 5652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 664 time to evaluate : 6.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 63 ILE cc_start: 0.9395 (mt) cc_final: 0.9040 (tp) REVERT: d 153 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8642 (mm) REVERT: e 16 MET cc_start: 0.8398 (mmp) cc_final: 0.8188 (mmp) REVERT: e 95 MET cc_start: 0.9008 (ptm) cc_final: 0.8432 (ptm) REVERT: e 168 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.9030 (mt) REVERT: f 61 TRP cc_start: 0.8426 (m100) cc_final: 0.8037 (t-100) REVERT: f 148 ARG cc_start: 0.8294 (tpt170) cc_final: 0.7836 (ttp-170) REVERT: f 150 TYR cc_start: 0.8712 (m-80) cc_final: 0.8387 (m-80) REVERT: g 33 GLN cc_start: 0.9188 (mm-40) cc_final: 0.8921 (mp10) REVERT: g 60 GLU cc_start: 0.9614 (tp30) cc_final: 0.9232 (mt-10) REVERT: g 127 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7534 (tp30) REVERT: j 92 MET cc_start: 0.8551 (mmm) cc_final: 0.7955 (tpp) REVERT: k 110 GLU cc_start: 0.8355 (pp20) cc_final: 0.8109 (pp20) REVERT: m 105 MET cc_start: 0.8274 (mmm) cc_final: 0.8017 (mmm) REVERT: m 124 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8766 (mm) REVERT: o 3 LYS cc_start: 0.8773 (mmtt) cc_final: 0.8512 (tptt) REVERT: q 17 LEU cc_start: 0.9424 (mm) cc_final: 0.9201 (mm) REVERT: r 22 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.8912 (pp) REVERT: r 34 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7875 (mm-30) REVERT: r 73 LYS cc_start: 0.7981 (tptp) cc_final: 0.7569 (tptt) REVERT: s 65 ASP cc_start: 0.7973 (t0) cc_final: 0.7690 (t0) REVERT: s 68 ASP cc_start: 0.7966 (p0) cc_final: 0.7480 (p0) REVERT: t 1 MET cc_start: 0.5583 (tpt) cc_final: 0.3845 (tpt) REVERT: t 56 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7617 (tm-30) REVERT: v 24 ASN cc_start: 0.8663 (t0) cc_final: 0.8144 (t0) REVERT: x 70 LEU cc_start: 0.9468 (tp) cc_final: 0.8296 (tt) REVERT: z 48 ASN cc_start: 0.8797 (p0) cc_final: 0.8596 (p0) REVERT: B 47 TYR cc_start: 0.8508 (m-80) cc_final: 0.8052 (m-80) REVERT: C 9 LYS cc_start: 0.9074 (tttt) cc_final: 0.8727 (tttp) REVERT: D 1 MET cc_start: 0.7470 (tmm) cc_final: 0.7183 (tmm) REVERT: F 1 MET cc_start: 0.5084 (OUTLIER) cc_final: 0.4169 (mtt) REVERT: G 48 MET cc_start: 0.9293 (mtm) cc_final: 0.8914 (ptp) REVERT: H 5 HIS cc_start: 0.7337 (t70) cc_final: 0.7136 (t70) REVERT: H 18 ASN cc_start: 0.8664 (m-40) cc_final: 0.8181 (t0) REVERT: H 28 PHE cc_start: 0.9131 (t80) cc_final: 0.8679 (t80) REVERT: H 68 HIS cc_start: 0.8032 (m90) cc_final: 0.7655 (m90) REVERT: H 71 ARG cc_start: 0.9179 (mtt180) cc_final: 0.8446 (tpm170) REVERT: H 111 ASP cc_start: 0.8407 (m-30) cc_final: 0.8046 (m-30) REVERT: H 166 TRP cc_start: 0.8478 (p-90) cc_final: 0.8245 (p-90) REVERT: H 167 TYR cc_start: 0.8988 (t80) cc_final: 0.8338 (t80) REVERT: I 70 GLN cc_start: 0.9432 (pm20) cc_final: 0.9225 (pm20) REVERT: I 74 TYR cc_start: 0.9478 (m-10) cc_final: 0.9128 (m-80) REVERT: I 134 TYR cc_start: 0.8925 (t80) cc_final: 0.8415 (t80) REVERT: I 135 GLN cc_start: 0.8891 (mm110) cc_final: 0.8119 (pp30) REVERT: J 61 LYS cc_start: 0.9292 (mtmm) cc_final: 0.8594 (mtmm) REVERT: J 63 MET cc_start: 0.9195 (mmm) cc_final: 0.8989 (mmm) REVERT: J 64 GLU cc_start: 0.8955 (mp0) cc_final: 0.8556 (pm20) REVERT: J 65 LYS cc_start: 0.9561 (mttm) cc_final: 0.9262 (mtmm) REVERT: J 141 ASP cc_start: 0.9401 (t0) cc_final: 0.9091 (t0) REVERT: K 1 MET cc_start: 0.7359 (tpp) cc_final: 0.6962 (tpt) REVERT: K 17 GLN cc_start: 0.8410 (tm-30) cc_final: 0.8023 (tm-30) REVERT: K 25 TYR cc_start: 0.8453 (m-10) cc_final: 0.7899 (m-80) REVERT: L 25 PHE cc_start: 0.9489 (t80) cc_final: 0.9277 (t80) REVERT: L 30 MET cc_start: 0.8252 (tmm) cc_final: 0.7479 (tmm) REVERT: L 141 HIS cc_start: 0.7268 (m-70) cc_final: 0.6811 (m-70) REVERT: M 2 MET cc_start: 0.7718 (tpt) cc_final: 0.7493 (tpt) REVERT: M 44 PHE cc_start: 0.8126 (m-80) cc_final: 0.7792 (m-80) REVERT: N 102 PHE cc_start: 0.8230 (m-10) cc_final: 0.8001 (m-10) REVERT: O 49 PHE cc_start: 0.8555 (m-80) cc_final: 0.8257 (m-80) REVERT: P 37 GLN cc_start: 0.9195 (mm110) cc_final: 0.8388 (tm-30) REVERT: P 86 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8457 (ptmt) REVERT: P 93 GLU cc_start: 0.9251 (tt0) cc_final: 0.8966 (tm-30) REVERT: Q 95 HIS cc_start: 0.8805 (m90) cc_final: 0.8267 (m-70) REVERT: R 7 ASN cc_start: 0.5818 (OUTLIER) cc_final: 0.5495 (m-40) REVERT: S 76 PHE cc_start: 0.8836 (m-80) cc_final: 0.8390 (m-80) REVERT: U 12 LYS cc_start: 0.9320 (ttpt) cc_final: 0.8533 (ptpp) REVERT: U 31 ARG cc_start: 0.8727 (ttp-170) cc_final: 0.8083 (ppt170) REVERT: U 32 PHE cc_start: 0.8544 (p90) cc_final: 0.8294 (p90) REVERT: U 51 ARG cc_start: 0.8102 (ttp-170) cc_final: 0.7786 (ttp-170) REVERT: U 76 LYS cc_start: 0.8180 (ptmt) cc_final: 0.7790 (pttp) REVERT: X 46 LEU cc_start: 0.7848 (mm) cc_final: 0.7609 (mp) REVERT: X 65 MET cc_start: 0.7764 (ptm) cc_final: 0.7159 (ppp) REVERT: Y 26 MET cc_start: 0.9467 (ttp) cc_final: 0.9156 (mtp) REVERT: Y 31 ILE cc_start: 0.9706 (mt) cc_final: 0.8590 (tp) REVERT: Y 35 TYR cc_start: 0.9033 (m-80) cc_final: 0.8674 (m-80) REVERT: Y 65 LEU cc_start: 0.8353 (pp) cc_final: 0.8090 (mm) outliers start: 151 outliers final: 110 residues processed: 763 average time/residue: 1.3028 time to fit residues: 1750.7840 Evaluate side-chains 747 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 630 time to evaluate : 6.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 66 PHE Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 124 LYS Chi-restraints excluded: chain b residue 263 ASP Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 153 LEU Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain g residue 4 ILE Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 41 LYS Chi-restraints excluded: chain g residue 115 VAL Chi-restraints excluded: chain g residue 144 VAL Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain k residue 37 ASP Chi-restraints excluded: chain k residue 53 LYS Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 2 LEU Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 20 LEU Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 115 LEU Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain p residue 91 VAL Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 59 ILE Chi-restraints excluded: chain r residue 98 ILE Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 19 LEU Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain t residue 79 ASP Chi-restraints excluded: chain u residue 5 ARG Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain v residue 35 GLU Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain w residue 28 LEU Chi-restraints excluded: chain x residue 13 THR Chi-restraints excluded: chain x residue 63 ILE Chi-restraints excluded: chain x residue 64 ASP Chi-restraints excluded: chain y residue 45 GLN Chi-restraints excluded: chain z residue 39 ASP Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 197 PHE Chi-restraints excluded: chain H residue 24 ASN Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 192 TYR Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain L residue 150 PHE Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 51 GLU Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 80 HIS Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 13 PHE Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain R residue 7 ASN Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 61 LYS Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 13 GLU Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 26 ASN Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain Z residue 31 VAL Chi-restraints excluded: chain Z residue 45 LYS Chi-restraints excluded: chain a residue 202 THR Chi-restraints excluded: chain a residue 212 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 891 optimal weight: 20.0000 chunk 939 optimal weight: 20.0000 chunk 856 optimal weight: 60.0000 chunk 913 optimal weight: 10.0000 chunk 938 optimal weight: 10.0000 chunk 549 optimal weight: 9.9990 chunk 397 optimal weight: 50.0000 chunk 717 optimal weight: 20.0000 chunk 280 optimal weight: 8.9990 chunk 825 optimal weight: 10.0000 chunk 863 optimal weight: 20.0000 overall best weight: 9.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 13 ASN ** y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 ASN J 81 GLN ** J 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 7 ASN ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.5094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 157583 Z= 0.321 Angle : 0.668 16.905 235851 Z= 0.339 Chirality : 0.037 0.283 30157 Planarity : 0.005 0.060 12574 Dihedral : 24.229 179.029 79086 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 26.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.67 % Favored : 89.28 % Rotamer: Outliers : 3.11 % Allowed : 20.00 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.85 (0.11), residues: 5652 helix: -0.03 (0.12), residues: 1832 sheet: -1.66 (0.16), residues: 1023 loop : -1.87 (0.12), residues: 2797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP H 200 HIS 0.018 0.001 HIS Y 67 PHE 0.017 0.002 PHE u 72 TYR 0.031 0.002 TYR I 75 ARG 0.011 0.001 ARG U 14 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11304 Ramachandran restraints generated. 5652 Oldfield, 0 Emsley, 5652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11304 Ramachandran restraints generated. 5652 Oldfield, 0 Emsley, 5652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 645 time to evaluate : 6.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 153 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8642 (mm) REVERT: e 16 MET cc_start: 0.8343 (mmp) cc_final: 0.8013 (mmm) REVERT: e 95 MET cc_start: 0.9004 (ptm) cc_final: 0.8689 (ptm) REVERT: e 168 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.9021 (mt) REVERT: f 61 TRP cc_start: 0.8387 (m100) cc_final: 0.7981 (t-100) REVERT: f 148 ARG cc_start: 0.8286 (tpt170) cc_final: 0.7787 (ttp-170) REVERT: f 150 TYR cc_start: 0.8647 (m-80) cc_final: 0.8330 (m-80) REVERT: g 33 GLN cc_start: 0.9202 (mm-40) cc_final: 0.8909 (mp10) REVERT: g 60 GLU cc_start: 0.9612 (tp30) cc_final: 0.9233 (mt-10) REVERT: g 127 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7548 (tp30) REVERT: j 92 MET cc_start: 0.8573 (mmm) cc_final: 0.7967 (tpp) REVERT: l 135 ILE cc_start: 0.9241 (mm) cc_final: 0.8987 (mm) REVERT: m 105 MET cc_start: 0.8244 (mmm) cc_final: 0.7951 (mmm) REVERT: m 124 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8678 (mm) REVERT: o 3 LYS cc_start: 0.8785 (mmtt) cc_final: 0.8531 (tptt) REVERT: q 17 LEU cc_start: 0.9433 (mm) cc_final: 0.9212 (mm) REVERT: q 43 GLN cc_start: 0.8711 (mt0) cc_final: 0.8288 (mt0) REVERT: r 13 ARG cc_start: 0.8903 (tmm-80) cc_final: 0.8656 (ttp80) REVERT: r 34 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7873 (mm-30) REVERT: s 65 ASP cc_start: 0.7938 (t0) cc_final: 0.7634 (t0) REVERT: s 68 ASP cc_start: 0.7999 (p0) cc_final: 0.7427 (p0) REVERT: s 78 GLU cc_start: 0.7770 (pm20) cc_final: 0.7516 (pm20) REVERT: t 1 MET cc_start: 0.5509 (tpt) cc_final: 0.4052 (tpt) REVERT: t 56 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7670 (tm-30) REVERT: v 24 ASN cc_start: 0.8553 (t0) cc_final: 0.8185 (t0) REVERT: x 76 LYS cc_start: 0.8785 (mmmt) cc_final: 0.8581 (mmmt) REVERT: z 46 MET cc_start: 0.8349 (mtt) cc_final: 0.8099 (mtt) REVERT: B 47 TYR cc_start: 0.8493 (m-80) cc_final: 0.7934 (m-80) REVERT: D 1 MET cc_start: 0.7512 (tmm) cc_final: 0.7230 (tmm) REVERT: E 48 MET cc_start: 0.7631 (tpp) cc_final: 0.7366 (tpt) REVERT: F 1 MET cc_start: 0.5218 (tpt) cc_final: 0.4179 (mtt) REVERT: G 48 MET cc_start: 0.9290 (OUTLIER) cc_final: 0.8920 (ptp) REVERT: H 5 HIS cc_start: 0.7177 (t70) cc_final: 0.6953 (t70) REVERT: H 18 ASN cc_start: 0.8661 (m-40) cc_final: 0.8174 (t0) REVERT: H 28 PHE cc_start: 0.9138 (t80) cc_final: 0.8694 (t80) REVERT: H 68 HIS cc_start: 0.8033 (m90) cc_final: 0.7655 (m90) REVERT: H 71 ARG cc_start: 0.9184 (mtt180) cc_final: 0.8452 (tpm170) REVERT: H 111 ASP cc_start: 0.8216 (m-30) cc_final: 0.7816 (m-30) REVERT: H 166 TRP cc_start: 0.8506 (p-90) cc_final: 0.8232 (p-90) REVERT: H 167 TYR cc_start: 0.8992 (t80) cc_final: 0.8369 (t80) REVERT: I 74 TYR cc_start: 0.9485 (m-10) cc_final: 0.9207 (m-80) REVERT: I 134 TYR cc_start: 0.8919 (t80) cc_final: 0.8400 (t80) REVERT: I 135 GLN cc_start: 0.8885 (mm110) cc_final: 0.8113 (pp30) REVERT: J 61 LYS cc_start: 0.9344 (mtmm) cc_final: 0.8730 (mtmm) REVERT: J 63 MET cc_start: 0.9200 (mmm) cc_final: 0.8990 (mmm) REVERT: J 64 GLU cc_start: 0.8959 (mp0) cc_final: 0.8562 (pm20) REVERT: J 110 MET cc_start: 0.8174 (ttp) cc_final: 0.7954 (ttp) REVERT: J 141 ASP cc_start: 0.9399 (t0) cc_final: 0.9075 (t0) REVERT: K 1 MET cc_start: 0.6986 (tpp) cc_final: 0.6711 (tpt) REVERT: K 17 GLN cc_start: 0.8637 (tm-30) cc_final: 0.8432 (tm-30) REVERT: K 25 TYR cc_start: 0.8430 (m-10) cc_final: 0.7954 (m-10) REVERT: L 25 PHE cc_start: 0.9488 (t80) cc_final: 0.9273 (t80) REVERT: L 30 MET cc_start: 0.8259 (tmm) cc_final: 0.7795 (tmm) REVERT: L 141 HIS cc_start: 0.7117 (m-70) cc_final: 0.6645 (m-70) REVERT: M 2 MET cc_start: 0.7660 (tpt) cc_final: 0.7395 (tpt) REVERT: M 44 PHE cc_start: 0.8276 (m-80) cc_final: 0.7946 (m-80) REVERT: M 95 MET cc_start: 0.8618 (ptp) cc_final: 0.8122 (pmm) REVERT: N 102 PHE cc_start: 0.8233 (m-10) cc_final: 0.7996 (m-10) REVERT: O 49 PHE cc_start: 0.8504 (m-80) cc_final: 0.8213 (m-80) REVERT: P 37 GLN cc_start: 0.9172 (mm110) cc_final: 0.8398 (tm-30) REVERT: P 86 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8467 (ptmt) REVERT: P 93 GLU cc_start: 0.9246 (tt0) cc_final: 0.8995 (tm-30) REVERT: Q 75 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7627 (tp30) REVERT: Q 95 HIS cc_start: 0.8800 (m90) cc_final: 0.8265 (m-70) REVERT: R 7 ASN cc_start: 0.5995 (OUTLIER) cc_final: 0.5262 (m110) REVERT: S 76 PHE cc_start: 0.8813 (m-80) cc_final: 0.8435 (m-80) REVERT: U 1 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.7438 (mmt) REVERT: U 12 LYS cc_start: 0.9364 (ttpt) cc_final: 0.9051 (ttmm) REVERT: U 31 ARG cc_start: 0.8707 (ttp-170) cc_final: 0.8095 (ppt170) REVERT: U 32 PHE cc_start: 0.8564 (p90) cc_final: 0.7886 (p90) REVERT: U 51 ARG cc_start: 0.8082 (ttp-170) cc_final: 0.7760 (ttp-170) REVERT: U 76 LYS cc_start: 0.8168 (ptmt) cc_final: 0.7762 (pttp) REVERT: V 16 MET cc_start: 0.6931 (mpp) cc_final: 0.6454 (mpp) REVERT: X 46 LEU cc_start: 0.7886 (mm) cc_final: 0.7670 (mp) REVERT: X 65 MET cc_start: 0.7761 (ptm) cc_final: 0.7156 (ppp) REVERT: Y 26 MET cc_start: 0.9464 (ttp) cc_final: 0.9155 (mtp) REVERT: Y 31 ILE cc_start: 0.9718 (mt) cc_final: 0.8592 (tp) REVERT: Y 35 TYR cc_start: 0.8995 (m-80) cc_final: 0.8632 (m-80) outliers start: 146 outliers final: 125 residues processed: 740 average time/residue: 1.2298 time to fit residues: 1595.2510 Evaluate side-chains 760 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 628 time to evaluate : 6.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 66 PHE Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 124 LYS Chi-restraints excluded: chain b residue 263 ASP Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 153 LEU Chi-restraints excluded: chain d residue 167 VAL Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 170 THR Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 41 LYS Chi-restraints excluded: chain g residue 115 VAL Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain g residue 144 VAL Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain k residue 32 TYR Chi-restraints excluded: chain k residue 37 ASP Chi-restraints excluded: chain k residue 53 LYS Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 113 MET Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 2 LEU Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 20 LEU Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain n residue 113 ILE Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 115 LEU Chi-restraints excluded: chain p residue 2 ASN Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain p residue 91 VAL Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 59 ILE Chi-restraints excluded: chain r residue 98 ILE Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 19 LEU Chi-restraints excluded: chain s residue 36 LEU Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain t residue 79 ASP Chi-restraints excluded: chain u residue 5 ARG Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain v residue 35 GLU Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain w residue 28 LEU Chi-restraints excluded: chain x residue 13 THR Chi-restraints excluded: chain x residue 63 ILE Chi-restraints excluded: chain y residue 9 LYS Chi-restraints excluded: chain y residue 45 GLN Chi-restraints excluded: chain z residue 39 ASP Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 197 PHE Chi-restraints excluded: chain H residue 24 ASN Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 192 TYR Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 206 ILE Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 94 PHE Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain L residue 150 PHE Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 51 GLU Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 80 HIS Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 13 PHE Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain R residue 7 ASN Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 54 THR Chi-restraints excluded: chain R residue 61 LYS Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 13 GLU Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 26 ASN Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 33 TYR Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain Z residue 45 LYS Chi-restraints excluded: chain a residue 202 THR Chi-restraints excluded: chain a residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 910 optimal weight: 10.0000 chunk 599 optimal weight: 50.0000 chunk 965 optimal weight: 10.0000 chunk 589 optimal weight: 30.0000 chunk 458 optimal weight: 6.9990 chunk 671 optimal weight: 50.0000 chunk 1013 optimal weight: 50.0000 chunk 932 optimal weight: 10.0000 chunk 806 optimal weight: 10.0000 chunk 83 optimal weight: 30.0000 chunk 623 optimal weight: 40.0000 overall best weight: 9.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 57 HIS ** b 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 7 ASN ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.5255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.133 157583 Z= 0.309 Angle : 0.661 14.902 235851 Z= 0.336 Chirality : 0.037 0.287 30157 Planarity : 0.005 0.058 12574 Dihedral : 24.258 178.994 79086 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 26.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.70 % Favored : 90.25 % Rotamer: Outliers : 2.98 % Allowed : 20.19 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.84 (0.11), residues: 5652 helix: -0.07 (0.12), residues: 1840 sheet: -1.61 (0.16), residues: 995 loop : -1.84 (0.12), residues: 2817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP H 200 HIS 0.021 0.001 HIS Y 67 PHE 0.023 0.002 PHE H 129 TYR 0.023 0.002 TYR K 59 ARG 0.011 0.001 ARG P 92 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11304 Ramachandran restraints generated. 5652 Oldfield, 0 Emsley, 5652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11304 Ramachandran restraints generated. 5652 Oldfield, 0 Emsley, 5652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 645 time to evaluate : 6.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 153 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8635 (mm) REVERT: e 16 MET cc_start: 0.8366 (mmp) cc_final: 0.8023 (mmm) REVERT: e 95 MET cc_start: 0.8922 (ptm) cc_final: 0.8575 (ptm) REVERT: e 168 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.9016 (mt) REVERT: f 61 TRP cc_start: 0.8434 (m100) cc_final: 0.8073 (t-100) REVERT: f 148 ARG cc_start: 0.8279 (tpt170) cc_final: 0.7761 (ttp-170) REVERT: f 150 TYR cc_start: 0.8685 (m-80) cc_final: 0.8326 (m-80) REVERT: f 162 ARG cc_start: 0.8082 (ptm160) cc_final: 0.7821 (ptm-80) REVERT: g 33 GLN cc_start: 0.9196 (mm-40) cc_final: 0.8918 (mp10) REVERT: g 60 GLU cc_start: 0.9611 (tp30) cc_final: 0.9238 (mt-10) REVERT: j 92 MET cc_start: 0.8567 (mmm) cc_final: 0.7975 (tpp) REVERT: k 37 ASP cc_start: 0.6463 (OUTLIER) cc_final: 0.6126 (m-30) REVERT: l 135 ILE cc_start: 0.9232 (mm) cc_final: 0.8971 (mm) REVERT: m 105 MET cc_start: 0.8174 (mmm) cc_final: 0.7810 (mmm) REVERT: m 124 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8713 (mm) REVERT: q 17 LEU cc_start: 0.9430 (mm) cc_final: 0.9203 (mm) REVERT: q 43 GLN cc_start: 0.8687 (mt0) cc_final: 0.8253 (mt0) REVERT: r 22 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8918 (pp) REVERT: r 34 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7941 (mm-30) REVERT: r 73 LYS cc_start: 0.8323 (tptt) cc_final: 0.7612 (tptt) REVERT: r 86 GLN cc_start: 0.8602 (mm-40) cc_final: 0.8372 (tp40) REVERT: s 78 GLU cc_start: 0.7580 (pm20) cc_final: 0.7248 (pm20) REVERT: t 56 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7621 (tm-30) REVERT: v 24 ASN cc_start: 0.8671 (t0) cc_final: 0.8354 (t0) REVERT: x 76 LYS cc_start: 0.8375 (mmmt) cc_final: 0.7846 (mmmt) REVERT: y 1 MET cc_start: 0.7988 (mmm) cc_final: 0.7243 (tpp) REVERT: z 46 MET cc_start: 0.8348 (mtt) cc_final: 0.8074 (mtt) REVERT: B 11 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8710 (mmtm) REVERT: B 47 TYR cc_start: 0.8487 (m-80) cc_final: 0.8034 (m-80) REVERT: C 9 LYS cc_start: 0.9019 (tttt) cc_final: 0.8667 (tttp) REVERT: C 32 LYS cc_start: 0.8937 (tmtt) cc_final: 0.8610 (tmtt) REVERT: D 1 MET cc_start: 0.7455 (tmm) cc_final: 0.7173 (tmm) REVERT: G 48 MET cc_start: 0.9277 (OUTLIER) cc_final: 0.8738 (ptm) REVERT: G 212 TYR cc_start: 0.8915 (m-80) cc_final: 0.8606 (m-80) REVERT: H 5 HIS cc_start: 0.7176 (t70) cc_final: 0.6639 (t-90) REVERT: H 18 ASN cc_start: 0.8664 (m-40) cc_final: 0.8162 (t0) REVERT: H 28 PHE cc_start: 0.9142 (t80) cc_final: 0.8704 (t80) REVERT: H 68 HIS cc_start: 0.8006 (m90) cc_final: 0.7626 (m90) REVERT: H 71 ARG cc_start: 0.9188 (mtt180) cc_final: 0.8457 (tpm170) REVERT: H 111 ASP cc_start: 0.8191 (m-30) cc_final: 0.7792 (m-30) REVERT: H 166 TRP cc_start: 0.8525 (p-90) cc_final: 0.8155 (p-90) REVERT: H 167 TYR cc_start: 0.9015 (t80) cc_final: 0.8429 (t80) REVERT: I 70 GLN cc_start: 0.9385 (pm20) cc_final: 0.9126 (pm20) REVERT: I 74 TYR cc_start: 0.9530 (m-10) cc_final: 0.9072 (m-80) REVERT: I 134 TYR cc_start: 0.8910 (t80) cc_final: 0.8396 (t80) REVERT: I 135 GLN cc_start: 0.8864 (mm110) cc_final: 0.8114 (pp30) REVERT: J 53 ARG cc_start: 0.8484 (tpp80) cc_final: 0.7938 (mtt180) REVERT: J 61 LYS cc_start: 0.9355 (mtmm) cc_final: 0.8703 (mtmm) REVERT: J 64 GLU cc_start: 0.9000 (mp0) cc_final: 0.8551 (pm20) REVERT: J 110 MET cc_start: 0.8166 (ttp) cc_final: 0.7904 (ttp) REVERT: J 141 ASP cc_start: 0.9412 (t0) cc_final: 0.9109 (t0) REVERT: K 9 MET cc_start: 0.9251 (mmm) cc_final: 0.9007 (mmm) REVERT: K 17 GLN cc_start: 0.8662 (tm-30) cc_final: 0.8331 (tm-30) REVERT: K 25 TYR cc_start: 0.8427 (m-10) cc_final: 0.7959 (m-10) REVERT: L 25 PHE cc_start: 0.9495 (t80) cc_final: 0.9282 (t80) REVERT: L 30 MET cc_start: 0.8308 (tmm) cc_final: 0.7802 (tmm) REVERT: L 141 HIS cc_start: 0.7154 (m-70) cc_final: 0.6699 (m-70) REVERT: M 2 MET cc_start: 0.7591 (tpt) cc_final: 0.7254 (tpt) REVERT: M 42 GLU cc_start: 0.9185 (mm-30) cc_final: 0.8565 (tp30) REVERT: N 102 PHE cc_start: 0.8302 (m-10) cc_final: 0.8046 (m-10) REVERT: O 49 PHE cc_start: 0.8555 (m-80) cc_final: 0.8310 (m-80) REVERT: P 37 GLN cc_start: 0.9164 (mm110) cc_final: 0.8367 (tm-30) REVERT: P 86 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8472 (ptmt) REVERT: Q 75 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7669 (tp30) REVERT: Q 95 HIS cc_start: 0.8801 (m90) cc_final: 0.8310 (m-70) REVERT: R 7 ASN cc_start: 0.5769 (OUTLIER) cc_final: 0.5364 (m-40) REVERT: S 76 PHE cc_start: 0.8817 (m-80) cc_final: 0.8445 (m-80) REVERT: S 88 MET cc_start: 0.8710 (mmm) cc_final: 0.8347 (tpt) REVERT: U 1 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.7460 (mmt) REVERT: U 31 ARG cc_start: 0.8715 (ttp-170) cc_final: 0.8066 (ppt170) REVERT: U 32 PHE cc_start: 0.8538 (p90) cc_final: 0.7855 (p90) REVERT: U 51 ARG cc_start: 0.8034 (ttp-170) cc_final: 0.7724 (ttp-170) REVERT: U 76 LYS cc_start: 0.8159 (ptmt) cc_final: 0.7755 (pttp) REVERT: V 16 MET cc_start: 0.7062 (mpp) cc_final: 0.6601 (mpp) REVERT: X 46 LEU cc_start: 0.7778 (mm) cc_final: 0.7560 (mp) REVERT: X 65 MET cc_start: 0.7762 (ptm) cc_final: 0.7169 (ppp) REVERT: Y 26 MET cc_start: 0.9458 (ttp) cc_final: 0.9154 (mtp) REVERT: Y 31 ILE cc_start: 0.9710 (mt) cc_final: 0.8560 (tp) REVERT: Y 35 TYR cc_start: 0.9034 (m-80) cc_final: 0.8718 (m-80) outliers start: 140 outliers final: 121 residues processed: 736 average time/residue: 1.2436 time to fit residues: 1607.2632 Evaluate side-chains 755 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 624 time to evaluate : 6.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain b residue 66 PHE Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 124 LYS Chi-restraints excluded: chain b residue 263 ASP Chi-restraints excluded: chain c residue 2 ILE Chi-restraints excluded: chain c residue 18 ASP Chi-restraints excluded: chain c residue 103 ASP Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 149 ILE Chi-restraints excluded: chain d residue 153 LEU Chi-restraints excluded: chain d residue 167 VAL Chi-restraints excluded: chain e residue 6 TYR Chi-restraints excluded: chain e residue 107 VAL Chi-restraints excluded: chain e residue 168 LEU Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 170 THR Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 41 LYS Chi-restraints excluded: chain g residue 115 VAL Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain g residue 144 VAL Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain k residue 32 TYR Chi-restraints excluded: chain k residue 37 ASP Chi-restraints excluded: chain k residue 53 LYS Chi-restraints excluded: chain k residue 56 ASP Chi-restraints excluded: chain k residue 113 MET Chi-restraints excluded: chain l residue 67 THR Chi-restraints excluded: chain l residue 81 ASP Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 2 LEU Chi-restraints excluded: chain m residue 7 THR Chi-restraints excluded: chain m residue 20 LEU Chi-restraints excluded: chain m residue 124 LEU Chi-restraints excluded: chain o residue 28 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 115 LEU Chi-restraints excluded: chain p residue 2 ASN Chi-restraints excluded: chain p residue 15 ASP Chi-restraints excluded: chain p residue 91 VAL Chi-restraints excluded: chain p residue 96 LEU Chi-restraints excluded: chain p residue 103 THR Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain r residue 14 VAL Chi-restraints excluded: chain r residue 22 LEU Chi-restraints excluded: chain r residue 38 VAL Chi-restraints excluded: chain r residue 59 ILE Chi-restraints excluded: chain r residue 98 ILE Chi-restraints excluded: chain s residue 4 ILE Chi-restraints excluded: chain s residue 19 LEU Chi-restraints excluded: chain s residue 36 LEU Chi-restraints excluded: chain s residue 66 ILE Chi-restraints excluded: chain s residue 74 ILE Chi-restraints excluded: chain t residue 79 ASP Chi-restraints excluded: chain u residue 5 ARG Chi-restraints excluded: chain u residue 27 VAL Chi-restraints excluded: chain v residue 35 GLU Chi-restraints excluded: chain v residue 47 VAL Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain w residue 28 LEU Chi-restraints excluded: chain x residue 13 THR Chi-restraints excluded: chain x residue 63 ILE Chi-restraints excluded: chain y residue 9 LYS Chi-restraints excluded: chain y residue 45 GLN Chi-restraints excluded: chain z residue 39 ASP Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 56 VAL Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 197 PHE Chi-restraints excluded: chain H residue 24 ASN Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 192 TYR Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 94 PHE Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain L residue 150 PHE Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 41 GLU Chi-restraints excluded: chain M residue 51 GLU Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 80 HIS Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 13 PHE Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain R residue 7 ASN Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 54 THR Chi-restraints excluded: chain R residue 61 LYS Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 13 GLU Chi-restraints excluded: chain T residue 74 VAL Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 20 VAL Chi-restraints excluded: chain U residue 26 ASN Chi-restraints excluded: chain U residue 29 ASN Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 33 TYR Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain Z residue 31 VAL Chi-restraints excluded: chain Z residue 45 LYS Chi-restraints excluded: chain a residue 202 THR Chi-restraints excluded: chain a residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 494 optimal weight: 20.0000 chunk 640 optimal weight: 30.0000 chunk 859 optimal weight: 60.0000 chunk 247 optimal weight: 20.0000 chunk 743 optimal weight: 20.0000 chunk 119 optimal weight: 5.9990 chunk 224 optimal weight: 6.9990 chunk 808 optimal weight: 10.0000 chunk 338 optimal weight: 50.0000 chunk 829 optimal weight: 20.0000 chunk 102 optimal weight: 0.0370 overall best weight: 8.6070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 119 ASN ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 13 ASN ** r 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 2 GLN ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 7 ASN ** T 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.059903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.037661 restraints weight = 1106328.732| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.00 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.5340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 157583 Z= 0.288 Angle : 0.651 16.558 235851 Z= 0.331 Chirality : 0.036 0.287 30157 Planarity : 0.005 0.063 12574 Dihedral : 24.255 178.653 79086 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 25.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.23 % Favored : 89.72 % Rotamer: Outliers : 2.85 % Allowed : 20.62 % Favored : 76.53 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.79 (0.11), residues: 5652 helix: -0.02 (0.12), residues: 1845 sheet: -1.61 (0.16), residues: 1010 loop : -1.82 (0.12), residues: 2797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP H 200 HIS 0.020 0.001 HIS Y 67 PHE 0.025 0.002 PHE N 126 TYR 0.023 0.002 TYR e 127 ARG 0.012 0.001 ARG Y 9 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30919.61 seconds wall clock time: 546 minutes 30.70 seconds (32790.70 seconds total)